Mercurial > repos > proteore > proteore_maps_visualization
changeset 0:9845dc9c7323 draft
planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
| author | proteore |
|---|---|
| date | Tue, 18 Dec 2018 10:02:54 -0500 |
| parents | |
| children | 6f389729a30b |
| files | README.rst kegg_maps_visualization.R kegg_maps_visualization.xml kegg_pathways_list_index.loc.sample test-data/Lacombe_et_al_2017_OK.txt test-data/hsa00010.pathview.png test-data/hsa04514.pathview.png test-data/hsa05167.pathview.png tool-data/hsa_pathways.loc tool-data/hsa_pathways.loc.sample tool-data/mmu_pathways.loc tool-data/mmu_pathways.loc.sample tool-data/rno_pathways.loc tool-data/rno_pathways.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 15 files changed, 2947 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,94 @@ +Wrapper for Pathview tool +============================= + +**Authors** + +David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + +============================= + +This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. + +You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat. + +If your input have another type of IDs, please use the ID_Converter tool. + +**Input:** + + +- KEGG Pathways IDs to be used for mapping can be set by: + - chosing from the KEGG pathways name list + - giving a list (copy/paste) + - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column) +- Genes/proteins ids to map can be either a list of Entrez genes IDs / Uniprot accession number or a file (tabular, tsv, txt) containing at least one column of Entrez genes IDs / Uniprot accession number. +- fold change values (up to three columns) from a dataset (same dataset as for Genes/proteins ids to map) + +You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values. + +.. csv-table:: Simulated data + :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3" + + "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759" + "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064" + "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729" + "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788" + +| + + + +.. class:: warningmark + +If there's more than one id per line in the defined column, it will be split to have only one id per line. For example this table: + +.. csv-table:: Simulated data + :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" + + "ENSG00000136881","Q14032","BAAT_HUMAN" + "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000244731","P0C0L4","CO4A_HUMAN" + +| + +will become: + +.. csv-table:: Simulated data + :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" + + "ENSG00000136881","Q14032","BAAT_HUMAN" + "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000244731","P0C0L4","CO4A_HUMAN" + +| + +**Output:** + +- a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway. +- a **summary text file** (.tsv) of the mapping(s) with the following columns + - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids + - **pathway name**: name(s) of KEGG pathway(s) used for mapping + - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs + - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping + - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway + - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway + - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs + - **Entrez gene ID mapped**: list of mapped Entrez gene IDs + - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs + +----- + +.. class:: infomark + +**Database:** + +KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/ + +User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_maps_visualization.R Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,354 @@ +#!/usr/bin/Rscript +#Rscript made for mapping genesID on KEGG pathway with Pathview package +#input : csv file containing ids (uniprot or geneID) to map, plus parameters +#output : KEGG pathway : jpeg or pdf file. + +options(warn=-1) #TURN OFF WARNINGS !!!!!! +suppressMessages(library("pathview")) +suppressMessages(library(KEGGREST)) + +read_file <- function(path,header){ + file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F, comment.char = "#"),silent=TRUE) + if (inherits(file,"try-error")){ + stop("File not found !") + }else{ + return(file) + } +} + +##### fuction to clean and concatenate pathway name (allow more flexibility for user input) +concat_string <- function(x){ + x <- gsub(" - .*","",x) + x <- gsub(" ","",x) + x <- gsub("-","",x) + x <- gsub("_","",x) + x <- gsub(",","",x) + x <- gsub("\\'","",x) + x <- gsub("\\(.*)","",x) + x <- gsub("\\/","",x) + x <- tolower(x) + return(x) +} + +#return output suffix (pathway name) from id kegg (ex : hsa:00010) +get_suffix <- function(pathways_list,species,id){ + suffix = gsub("/","or",pathways_list[pathways_list[,1]==paste(species,id,sep=""),2]) + suffix = gsub(" ","_",suffix) + if (nchar(suffix) > 50){ + suffix = substr(suffix,1,50) + } + return(suffix) +} + +str2bool <- function(x){ + if (any(is.element(c("t","true"),tolower(x)))){ + return (TRUE) + }else if (any(is.element(c("f","false"),tolower(x)))){ + return (FALSE) + }else{ + return(NULL) + } +} + +is.letter <- function(x) grepl("[[:alpha:]]", x) + +#### hsa00010 -> 00010 +remove_kegg_prefix <- function(x){ + x = gsub(":","",x) + if (substr(x,1,4) == 'path'){ + x=substr(x,5,nchar(x)) + } + if (is.letter(substr(x,1,3))){ + x <- substr(x,4,nchar(x)) + } + return(x) +} + +kegg_to_geneID <- function(vector){ + vector <- sapply(vector, function(x) unlist(strsplit(x,":"))[2],USE.NAMES = F) + return (vector) +} + +clean_bad_character <- function(string) { + string <- gsub("X","",string) + return(string) +} + +get_list_from_cp <-function(list){ + list = strsplit(list, "[ \t\n]+")[[1]] + list = list[list != ""] #remove empty entry + list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2") + return(list) +} + +get_ref_pathways <- function(species){ + ##all available pathways for the species + pathways <-keggLink("pathway", species) + tot_path<-unique(pathways) + + ##formating the dat into a list object + ##key= pathway ID, value = genes of the pathway in the kegg format + pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway))) + return (pathways_list) +} + +mapping_summary <- function(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID){ + ref_pathways = get_ref_pathways(species) + names(ref_pathways) <- sapply(names(ref_pathways), function(x) gsub("path:[a-z]{3}","",x),USE.NAMES = F) + + #genes present in pathway + genes = ref_pathways[id][[1]] + nb_genes = length(genes) + + #genes mapped on pathway genes + mapped <- unlist(sapply(pv.out$plot.data.gene$all.mapped, function(x) strsplit(x,",")),use.names = F) + mapped = unique(mapped[mapped!=""]) + nb_mapped <- length(mapped) + + #compue ratio of mapping + ratio = round((nb_mapped/nb_genes)*100, 2) + if (is.nan(ratio)) { ratio = ""} + pathway_id = paste(species,id,sep="") + pathway_name = as.character(pathways_list[pathways_list[,1]==pathway_id,][2]) + + if (id_type=="geneid" || id_type=="keggid") { + row <- c(pathway_id,pathway_name,length(unique(geneID)),nb_mapped,nb_genes,ratio,paste(mapped,collapse=";")) + names(row) <- c("KEGG pathway ID","pathway name","nb of Entrez gene ID used","nb of Entrez gene ID mapped", + "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped") + } else if (id_type=="uniprotid") { + row <- c(pathway_id,pathway_name,length(unique(uniprotID)),length(unique(geneID)),nb_mapped,nb_genes,ratio,paste(mapped,collapse=";"),paste(mapped2geneID[which(mapped2geneID[,2] %in% mapped)],collapse=";")) + names(row) <- c("KEGG pathway ID","pathway name","nb of Uniprot_AC used","nb of Entrez gene ID used","nb of Entrez gene ID mapped", + "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped","uniprot_AC mapped") + } + return(row) +} + +#take data frame, return data frame +split_ids_per_line <- function(line,ncol){ + + #print (line) + header = colnames(line) + line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol]) + + if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) { + if (length(line)==1 ) { + lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F) + } else { + if (ncol==1) { #first column + lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)])) + } else if (ncol==length(line)) { #last column + lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";")))) + } else { + lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)])) + } + } + colnames(lines)=header + return(lines) + } else { + return(line) + } +} + +#create new lines if there's more than one id per cell in the columns in order to have only one id per line +one_id_one_line <-function(tab,ncol){ + + if (ncol(tab)>1){ + + tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x)) + header=colnames(tab) + res=as.data.frame(matrix(ncol=ncol(tab),nrow=0)) + for (i in 1:nrow(tab) ) { + lines = split_ids_per_line(tab[i,],ncol) + res = rbind(res,lines) + } + }else { + res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F) + res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F) + colnames(res)=colnames(tab) + } + return(res) +} + +get_limit <- function(mat) { + min = min(apply(mat,2,min)) + max = max(apply(mat,2,max)) + return(c(min,max)) +} + +get_args <- function(){ + + ## Collect arguments + args <- commandArgs(TRUE) + + ## Default setting when no arguments passed + if(length(args) < 1) { + args <- c("--help") + } + + ## Help section + if("--help" %in% args) { + cat("Pathview R script + Arguments: + --help Print this test + --input path of the input file (must contains a colum of uniprot and/or geneID accession number) + --id_list list of ids to use, ',' separated + --pathways_id Id(s) of pathway(s) to use, if several, semicolon separated list : hsa00010;hsa05412 + --id_type Type of accession number ('uniprotID' or 'geneID') + --id_column Column containing accesion number of interest (ex : 'c1') + --header Boolean, TRUE if header FALSE if not + --output Output filename + --fold_change_col Column(s) containing fold change values (comma separated) + --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph + --species KEGG species (hsa, mmu, ...) + --pathways_input Tab with pathways in a column, output format of find_pathways + --pathway_col Column of pathways to use + --header2 Boolean, TRUE if header FALSE if not + --pathways_list path of file containg the species pathways list (hsa_pathways.loc, mmu_pathways.loc, ...) + + Example: + ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n") + + q(save="no") + } + + parseArgs <- function(x) strsplit(sub("^--", "", x), "=") + argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) + args <- as.list(as.character(argsDF$V2)) + names(args) <- argsDF$V1 + + return(args) +} + +main <- function(){ + + args <- get_args() + + #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_maps_visualization/args.Rda") + #load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_maps_visualization/args.Rda") + + ###setting variables + if (!is.null(args$pathways_id)) { + ids <- get_list_from_cp(clean_bad_character(args$pathways_id)) + ids <- sapply(ids, function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) + }else if (!is.null(args$pathways_input)){ + header2 <- str2bool(args$header2) + pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col)) + pathways_file = read_file(args$pathways_input,header2) + ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) + } + pathways_list <- read_file(args$pathways_list,F) + if (!is.null(args$id_list)) { + id_list <- get_list_from_cp(args$id_list) + } + id_type <- tolower(args$id_type) + ncol <- as.numeric(gsub("c", "" ,args$id_column)) + header <- str2bool(args$header) + native_kegg <- str2bool(args$native_kegg) + species=args$species + fold_change_data = str2bool(args$fold_change_data) + + #org list used in mapped2geneID + org <- c('Hs','Mm','Rn') + names(org) <- c('hsa','mmu','rno') + + #read input file or list + if (!is.null(args$input)){ + tab <- read_file(args$input,header) + tab <- data.frame(tab[which(tab[ncol]!=""),],stringsAsFactors = F) + tab = one_id_one_line(tab,ncol) + } else { + id_list = gsub("[[:blank:]]|\u00A0|NA","",id_list) + id_list = unique(id_list[id_list!=""]) + tab <- data.frame(id_list,stringsAsFactors = F) + ncol=1 + } + + + ##### map uniprotID to entrez geneID and kegg to geneID + uniprotID="" + mapped2geneID="" + if (id_type == "uniprotid") { + uniprotID=tab[,ncol] + mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL) + geneID = mapped2geneID[,2] + tab = cbind(tab,geneID) + ncol=ncol(tab) + }else if (id_type == "keggid"){ + keggID = tab[,ncol] + geneID = kegg_to_geneID(keggID) + tab = cbind(tab,geneID) + ncol=ncol(tab) + }else if (id_type == "geneid"){ + colnames(tab)[ncol] <- "geneID" + } + + ##### build matrix to map on KEGG pathway (kgml : KEGG xml) + geneID_indices = which(!is.na(tab$geneID)) + if (fold_change_data) { + fold_change <- as.integer(unlist(strsplit(gsub("c","",args$fold_change_col),","))) + if (length(fold_change) > 3) { fold_change= fold_change[1:3] } + if (length(fold_change)==1){ + tab[,fold_change] <- as.double(gsub(",",".",as.character(tab[,fold_change]) )) + } else { + tab[,fold_change] <- apply(tab[,fold_change],2,function(x) as.double(gsub(",",".",as.character(x)))) + } + mat = tab[geneID_indices,c(ncol,fold_change)] + mat = mat[(!duplicated(mat$geneID)),] + geneID=mat$geneID + mat = as.data.frame(mat[,-1]) + row.names(mat)=geneID + limit = get_limit(mat) + } else { + mat = unique(as.character(tab$geneID[!is.na(tab$geneID[tab$geneID!=""])])) + geneID=mat + limit=1 + } + + #####mapping geneID (with or without expression values) on KEGG pathway + plot.col.key= TRUE + low_color = "green" + mid_color = "#F3F781" #yellow + high_color = "red" + if (!fold_change_data) { + plot.col.key= FALSE #if there's no exrepession data, we don't show the color key + high_color = "#81BEF7" #blue + } + + #create graph(s) and text output + for (id in ids) { + suffix= get_suffix(pathways_list,species,id) + pv.out <- suppressMessages(pathview(gene.data = mat, + gene.idtype = "entrez", + pathway.id = id, + species = species, + kegg.dir = ".", + out.suffix=suffix, + kegg.native = native_kegg, + low = list(gene = low_color, cpd = "blue"), + mid = list(gene = mid_color, cpd = "transparent"), + high = list(gene = high_color, cpd = "yellow"), + na.col="#D8D8D8", #gray + cpd.data=NULL, + plot.col.key = plot.col.key, + pdf.size=c(9,9), + limit=list(gene=limit, cpd=limit))) + + if (is.list(pv.out)){ + + #creating text file + if (!exists("DF")) { + DF <- data.frame(t(mapping_summary(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID)),stringsAsFactors = F,check.names = F) + } else { + #print (mapping_summary(pv.out,species,id)) + DF <- rbind(DF,data.frame(t(mapping_summary(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID)),stringsAsFactors = F,check.names = F)) + } + } + } + + DF <- as.data.frame(apply(DF, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA + + #text file output + write.table(DF,file=args$output,quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE) +} + +main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_maps_visualization.xml Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,347 @@ +<tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.18"> + <description>of (differentially expressed) genes/proteins</description> + <requirements> + <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> + <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/kegg_maps_visualization.R + #if $input.ids == "text" + --id_list="$input.txt" + #else + --input="$input.file" + --id_column="$input.ncol" + --header="$input.header" + #end if + #if $species.pathways.pathways_id != "pathways_file" + --pathways_id="$species.pathways.pids" + #else + --pathways_input="$species.pathways.file" + --header2="$species.pathways.header2" + --pathway_col="$species.pathways.ncol2" + #end if + --id_type="$id_type" + --native_kegg="$native" + + + #if $input.ids=="file" and $input.foldchange.fc=="true" + --fold_change_data="$input.foldchange.fc" + --fold_change_col="$input.foldchange.fc_col" + #else + --fold_change_data="false" + #end if + + --species=${species.ref_file} + --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] } + --output="$text_output" + + ]]></command> + <inputs> + <!--section name="pathways_section" title="Pathways" expanded="True"--> + <conditional name="species"> + <param name="ref_file" type="select" label="Species" > + <option value="hsa">Human (Homo sapiens)</option> + <option value="mmu">Mouse (Mus musculus)</option> + <option value="rno">Rat (Rattus norvegicus)</option> + </param> + <when value="hsa"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="Enter your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> + <option value="pathways_names">KEGG pathway name(s)</option> + <option value="pathways_ids">KEGG pathway IDs</option> + <option value="pathways_file">KEGG pathway IDs from file</option> + </param> + <when value="pathways_names"> + <param name="pids" type="select" label="Select pathway(s) (by clicking in the box)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> + <options from_data_table="hsa_pathways"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="pathways_ids"> + <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + <when value="pathways_file"> + <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> + <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> + <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> + </conditional> + </when> + <when value="mmu"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="Enter your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> + <option value="pathways_names">KEGG pathway name(s)</option> + <option value="pathways_ids">KEGG pathway IDs</option> + <option value="pathways_file">KEGG pathway IDs from file</option> + </param> + <when value="pathways_names"> + <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> + <options from_data_table="mmu_pathways"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="pathways_ids"> + <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "mmu00053 mmu00340"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + <when value="pathways_file"> + <param name="file" type="data" format="txt,tabular" label="Enter your file" help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" /> + <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> + <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> + </conditional> + </when> + <when value="rno"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="Enter your pathway(s) name/id" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> + <option value="pathways_names">KEGG pathway name(s)</option> + <option value="pathways_ids">KEGG pathway IDs</option> + <option value="pathways_file">KEGG pathway IDs from file</option> + </param> + <when value="pathways_names"> + <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> + <options from_data_table="rno_pathways"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="pathways_ids"> + <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + <when value="pathways_file"> + <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> + <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> + <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> + </conditional> + </when> + </conditional> + <!--/section--> + <!--section name="genes_section" title="Genes/prot" expanded="True"--> + <param name="id_type" type="select" label="Select ID type for genes to map to the pathway(s):"> + <option value="geneID" selected="true">Entrez Gene ID</option> + <option value="keggid">KEGG Genes ID</option> + <option value="uniprotID">UniProt Accession number</option> + </param> + <conditional name="input" > + <param name="ids" type="select" label="Enter your IDs" help="Copy/paste or ID from file (e.g. table)" > + <option value="text">Copy/paste your IDs</option> + <option value="file" selected="true">Input file containing your IDs</option> + </param> + <when value="text" > + <param name="txt" type="text" label="Copy/paste your IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' > + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> + <param name="ncol" type="text" value="c1" label="Column if IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <conditional name="foldchange" > + <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Map quantitative data on the pathway?"/> + <when value="true"> + <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4"/> + </when> + <when value="false"/> + </conditional> + </when> + </conditional> + <!--/section--> + <param name="native" type="select" label="Graphical format"> + <option value="true">KEGG map (.png)</option> + <option value="false">Graphviz layout engine (.pdf)</option> + </param> + </inputs> + <outputs> + <data name="text_output" format="tsv" label="KEGG maps visualization text output"/> + <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="graphviz_output_from_file"> + <filter>native=="false" and input["ids"] == "file"</filter> + <discover_datasets pattern="(?P<designation>.+\..*)\.pdf" ext="pdf" /> + </collection> + <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="kegg_graph_output_from_file"> + <filter>native=="true" and input["ids"] == "file"</filter> + <discover_datasets pattern="(?P<designation>.+\..*)\.png" ext="png"/> + </collection> + <collection type="list" label="KEGG maps visualization" name="graphviz_output_from_list"> + <filter>native=="false" and input["ids"] == "text"</filter> + <discover_datasets pattern="(?P<designation>.+\..*)\.pdf" ext="pdf" /> + </collection> + <collection type="list" label="KEGG maps visualization" name="kegg_graph_output_from_list"> + <filter>native=="true" and input["ids"] == "text"</filter> + <discover_datasets pattern="(?P<designation>.+\..*)\.png" ext="png" /> + </collection> + </outputs> + <tests> + <!--test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="Lacombe_et_al_2017_OK.txt"/> + <param name="header" value="true"/> + <param name="ncol" value="c1"/> + </conditional> + <conditional name="pathways"> + <param name="pathways_id" value="pathways_ids"/> + <param name="pids" value="04514,05167,00010"/> + </conditional> + <param name="id_type" value="uniprotID"/> + <param name="species" value="hsa"/> + <param name="native" value="true"/> + <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/> + <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/> + <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/> + </test--> + </tests> + <help><![CDATA[ + +**Description** + +This tool based on the Pathview R package, is set for pathway based data integration and visualization. + +It maps and renders a wide variety of biological data on relevant KEGG pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. + +**Input** + +1. "Enter your pathway(s)": target KEGG Pathways to be specify can be set by: + + - choosing from the KEGG pathways name list + - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode) + - selecting a list from a dataset (column) - for instance, output from the "KEGG pathways identification and coverage" tool can be used (1st column, c1) +2. "Select ID type for genes to map on the pathway(s)": Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number. IDs to be mapped can be either provided by copy/paste or a file (tabular, tsv, txt) with a column containing the IDs. +3. "Map quantitative data on the pathway ?": Yes/No (default is No). Fold change values (up to three columns) from a dataset (same file as identifiers to map) can be graphically represented on the final figure (using a range of color representing the fold-change values). + +Below is an example of an input file with identifiers (uniprot_AC) and fold_change values. + +.. csv-table:: Simulated data + :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3" + + "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759" + "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064" + "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729" + "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788" + +| + +.. class:: warningmark + +If there's more than one ID per line in the specified column, it will be splitted resulting in one unique ID per line. For example this table: + +.. csv-table:: Simulated data + :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" + + "ENSG00000136881","Q14032","BAAT_HUMAN" + "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000244731","P0C0L4","CO4A_HUMAN" + +| + +will be converted as follow: + +.. csv-table:: Simulated data + :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" + + "ENSG00000136881","Q14032","BAAT_HUMAN" + "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000244731","P0C0L4","CO4A_HUMAN" + +| + +----- + +**Output:** + +- a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway. + +- a **summary text file** (.tsv) of the mapping(s) with the following columns + - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids + - **pathway name**: name(s) of KEGG pathway(s) used for mapping + - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs + - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping + - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway + - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway + - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs + - **Entrez gene ID mapped**: list of mapped Entrez gene IDs + - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs + +----- + +.. class:: infomark + +**Data source (release date)** + +KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/ + +User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html + +----- + +.. class:: infomark + +**Authors** + +Luo, Weijun, Brouwer, Cory (2013). “Pathview: an R/Bioconductor package for pathway-based data integration and visualization.” Bioinformatics, 29(14), 1830-1831. doi: 10.1093/bioinformatics/btt285. + +----- + +.. class:: infomark + +**Galaxy integration** + +David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + ]]></help> + <citations> + <citation type="doi">10.1093/nar/gkx372</citation> + <citation type="bibtex"> +@misc{renameTODO, + author = {Weijun Luo}, + year = {2013}, + title = {pathview}, + url = {https://bioconductor.org/packages/release/bioc/html/pathview.html}, +}</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_pathways_list_index.loc.sample Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,4 @@ +#value name path +hsa Homo sapiens tool-data/hsa_pathways.loc +mmu Mus musculus tool-data/mmu_pathways.loc +rno Rattus norvegicus tool-data/rno_pathways.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Lacombe_et_al_2017_OK.txt Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,165 @@ +Protein accession number (UniProt) Protein name Number of peptides (razor + unique) +P15924 Desmoplakin 69 +P02538 Keratin, type II cytoskeletal 6A 53 +P02768 Serum albumin 44 +P08779 Keratin, type I cytoskeletal 16 29 +Q02413 Desmoglein-1 24 +P07355 "Annexin A2;Putative annexin A2-like protein" 22 +P14923 Junction plakoglobin 22 +P02788 Lactotransferrin 21 +Q9HC84 Mucin-5B 21 +P29508 Serpin B3 20 +P63261 Actin, cytoplasmic 2 19 +Q8N1N4 Keratin, type II cytoskeletal 78 18 +Q04695 Keratin, type I cytoskeletal 17 18 +P01876 Ig alpha-1 chain C region 16 +Q01469 Fatty acid-binding protein 5, epidermal 15 +P31944 Caspase-14 15 +P01833 Polymeric immunoglobulin receptor 15 +P06733 Alpha-enolase 15 +P25311 Zinc-alpha-2-glycoprotein 15 +Q15149 Plectin 15 +P19013 Keratin, type II cytoskeletal 4 13 +Q6KB66 Keratin, type II cytoskeletal 80 13 +Q08188 Protein-glutamine gamma-glutamyltransferase E 12 +P13646 Keratin, type I cytoskeletal 13 11 +Q86YZ3 Hornerin 11 +P04259 Keratin, type II cytoskeletal 6B 10 +P02545 "Prelamin-A/C;Lamin-A/C" 10 +P04083 Annexin A1 10 +P11021 78 kDa glucose-regulated protein 10 +P02787 Serotransferrin 9 +P04040 Catalase 9 +P31151 Protein S100-A7 9 +P31947 14-3-3 protein sigma 9 +Q96P63 Serpin B12 9 +P14618 Pyruvate kinase PKM 9 +P60174 Triosephosphate isomerase 9 +Q06830 Peroxiredoxin-1 9 +P01040 Cystatin-A 8 +P05089 Arginase-1 8 +P01834 Ig kappa chain C region 8 +P04406 Glyceraldehyde-3-phosphate dehydrogenase 8 +P0DMV9 Heat shock 70 kDa protein 1B 8 +P13639 Elongation factor 2 8 +P35579 Myosin-9 8 +P68371 Tubulin beta-4B chain 8 +Q8WVV4 Protein POF1B 8 +O75635 Serpin B7 7 +P01857 Ig gamma-1 chain C region 7 +P61626 Lysozyme C 7 +P68363 Tubulin alpha-1B chain 7 +P01009 "Alpha-1-antitrypsin;Short peptide from AAT" 6 +P07900 Heat shock protein HSP 90-alpha 6 +Q9NZH8 Interleukin-36 gamma 6 +O43707 "Alpha-actinin-4;Alpha-actinin-1" 6 +O75223 Gamma-glutamylcyclotransferase 6 +P00338 L-lactate dehydrogenase A chain 6 +P07339 Cathepsin D 6 +P62987 Ubiquitin-60S ribosomal protein L40 6 +P10599 Thioredoxin 6 +Q9UGM3 Deleted in malignant brain tumors 1 protein 6 +Q9UI42 Carboxypeptidase A4 6 +P47929 Galectin-7 5 +Q13867 Bleomycin hydrolase 5 +Q6P4A8 Phospholipase B-like 1 5 +O75369 Filamin-B 5 +P00441 Superoxide dismutase [Cu-Zn] 5 +P04792 Heat shock protein beta-1 5 +P11142 Heat shock cognate 71 kDa protein 5 +P58107 Epiplakin 5 +P60842 Eukaryotic initiation factor 4A-I 5 +P62937 Peptidyl-prolyl cis-trans isomerase A 5 +P63104 14-3-3 protein zeta/delta 5 +Q92820 Gamma-glutamyl hydrolase 5 +O75342 Arachidonate 12-lipoxygenase, 12R-type 4 +P09211 Glutathione S-transferase P 4 +P31025 Lipocalin-1 4 +P48594 Serpin B4 4 +Q14574 Desmocollin-3 4 +Q5T750 Skin-specific protein 32 4 +Q6UWP8 Suprabasin 4 +O60911 Cathepsin L2 4 +P00558 Phosphoglycerate kinase 1 4 +P04075 Fructose-bisphosphate aldolase A 4 +P07384 Calpain-1 catalytic subunit 4 +P0CG05 Ig lambda-2 chain C regions 4 +P18206 Vinculin 4 +P62258 14-3-3 protein epsilon 4 +P68871 Hemoglobin subunit beta 4 +Q9C075 Keratin, type I cytoskeletal 23 4 +A8K2U0 Alpha-2-macroglobulin-like protein 1 3 +P00738 Haptoglobin 3 +P01011 Alpha-1-antichymotrypsin 3 +P02763 Alpha-1-acid glycoprotein 1 3 +P18510 Interleukin-1 receptor antagonist protein 3 +P22528 Cornifin-B 3 +P30740 Leukocyte elastase inhibitor 3 +P80188 Neutrophil gelatinase-associated lipocalin 3 +Q15828 Cystatin-M 3 +Q9HCY8 Protein S100-A14 3 +P01623 Ig kappa chain V-III region 3 +P01877 Ig alpha-2 chain C region 3 +P06396 Gelsolin 3 +P14735 Insulin-degrading enzyme 3 +P20933 N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase 3 +P25788 Proteasome subunit alpha type-3 3 +P26641 Elongation factor 1-gamma 3 +P36952 Serpin B5 3 +P40926 Malate dehydrogenase, mitochondrial 3 +Q9Y6R7 IgGFc-binding protein 3 +O95274 Ly6/PLAUR domain-containing protein 3 2 +P00491 Purine nucleoside phosphorylase 2 +P04080 Cystatin-B 2 +P09972 Fructose-bisphosphate aldolase C 2 +P19012 Keratin, type I cytoskeletal 15 2 +P20930 Filaggrin 2 +Q96FX8 p53 apoptosis effector related to PMP-22 2 +Q9UIV8 Serpin B13 2 +P01625 Ig kappa chain V-IV region Len 2 +P01765 Ig heavy chain V-III region TIL 2 +P01766 Ig heavy chain V-III region BRO 2 +P01860 Ig gamma-3 chain C region 2 +P01871 Ig mu chain C region 2 +P05090 Apolipoprotein D 2 +P06870 Kallikrein-1 2 +P07858 Cathepsin B 2 +P08865 40S ribosomal protein SA 2 +P11279 Lysosome-associated membrane glycoprotein 1 2 +P13473 Lysosome-associated membrane glycoprotein 2 2 +P19971 Thymidine phosphorylase 2 +P23284 Peptidyl-prolyl cis-trans isomerase B 2 +P23396 40S ribosomal protein S3 2 +P25705 ATP synthase subunit alpha, mitochondrial 2 +P27482 Calmodulin-like protein 3 2 +P31949 Protein S100-A11 2 +P40121 Macrophage-capping protein 2 +P42357 Histidine ammonia-lyase 2 +P47756 F-actin-capping protein subunit beta 2 +P48637 Glutathione synthetase 2 +P49720 Proteasome subunit beta type-3 2 +P50395 Rab GDP dissociation inhibitor beta 2 +P59998 Actin-related protein 2/3 complex subunit 4 2 +P61160 Actin-related protein 2 2 +P61916 Epididymal secretory protein E1 2 +P04745 Alpha-amylase 1 23 +Q9NZT1 Calmodulin-like protein 5 8 +P12273 Prolactin-inducible protein 6 +Q96DA0 Zymogen granule protein 16 homolog B 5 +P01036 Cystatin-S 5 +Q8TAX7 Mucin-7 2 +P01037 Cystatin-SN 2 +P09228 Cystatin-SA 2 +P04264 Keratin, type II cytoskeletal 1 61 +P35908 Keratin, type II cytoskeletal 2 epidermal 40 +P13645 Keratin, type I cytoskeletal 10 40 +Q5D862 Filaggrin-2 14 +Q5T749 Keratinocyte proline-rich protein 13 +Q8IW75 Serpin A12 3 +P81605 Dermcidin 3 +P22531 Small proline-rich protein 2E 3 +P59666 Neutrophil defensin 3 2 +P78386 Keratin, type II cuticular Hb5 2 + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/hsa_pathways.loc Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,330 @@ +#value name +hsa00010 Glycolysis / Gluconeogenesis +hsa00020 Citrate cycle (TCA cycle) +hsa00030 Pentose phosphate pathway +hsa00040 Pentose and glucuronate interconversions +hsa00051 Fructose and mannose metabolism +hsa00052 Galactose metabolism +hsa00053 Ascorbate and aldarate metabolism +hsa00061 Fatty acid biosynthesis +hsa00062 Fatty acid elongation +hsa00071 Fatty acid degradation +hsa00072 Synthesis and degradation of ketone bodies +hsa00100 Steroid biosynthesis +hsa00120 Primary bile acid biosynthesis +hsa00130 Ubiquinone and other terpenoid-quinone biosynthesis +hsa00140 Steroid hormone biosynthesis +hsa00190 Oxidative phosphorylation +hsa00220 Arginine biosynthesis +hsa00230 Purine metabolism +hsa00232 Caffeine metabolism +hsa00240 Pyrimidine metabolism +hsa00250 Alanine, aspartate and glutamate metabolism +hsa00260 Glycine, serine and threonine metabolism +hsa00270 Cysteine and methionine metabolism +hsa00280 Valine, leucine and isoleucine degradation +hsa00290 Valine, leucine and isoleucine biosynthesis +hsa00310 Lysine degradation +hsa00330 Arginine and proline metabolism +hsa00340 Histidine metabolism +hsa00350 Tyrosine metabolism +hsa00360 Phenylalanine metabolism +hsa00380 Tryptophan metabolism +hsa00400 Phenylalanine, tyrosine and tryptophan biosynthesis +hsa00410 beta-Alanine metabolism +hsa00430 Taurine and hypotaurine metabolism +hsa00440 Phosphonate and phosphinate metabolism +hsa00450 Selenocompound metabolism +hsa00471 D-Glutamine and D-glutamate metabolism +hsa00472 D-Arginine and D-ornithine metabolism +hsa00480 Glutathione metabolism +hsa00500 Starch and sucrose metabolism +hsa00510 N-Glycan biosynthesis +hsa00511 Other glycan degradation +hsa00512 Mucin type O-glycan biosynthesis +hsa00514 Other types of O-glycan biosynthesis +hsa00515 Mannose type O-glycan biosynthesis +hsa00520 Amino sugar and nucleotide sugar metabolism +hsa00524 Neomycin, kanamycin and gentamicin biosynthesis +hsa00531 Glycosaminoglycan degradation +hsa00532 Glycosaminoglycan biosynthesis +hsa00533 Glycosaminoglycan biosynthesis +hsa00534 Glycosaminoglycan biosynthesis +hsa00561 Glycerolipid metabolism +hsa00562 Inositol phosphate metabolism +hsa00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +hsa00564 Glycerophospholipid metabolism +hsa00565 Ether lipid metabolism +hsa00590 Arachidonic acid metabolism +hsa00591 Linoleic acid metabolism +hsa00592 alpha-Linolenic acid metabolism +hsa00600 Sphingolipid metabolism +hsa00601 Glycosphingolipid biosynthesis +hsa00603 Glycosphingolipid biosynthesis +hsa00604 Glycosphingolipid biosynthesis +hsa00620 Pyruvate metabolism +hsa00630 Glyoxylate and dicarboxylate metabolism +hsa00640 Propanoate metabolism +hsa00650 Butanoate metabolism +hsa00670 One carbon pool by folate +hsa00730 Thiamine metabolism +hsa00740 Riboflavin metabolism +hsa00750 Vitamin B6 metabolism +hsa00760 Nicotinate and nicotinamide metabolism +hsa00770 Pantothenate and CoA biosynthesis +hsa00780 Biotin metabolism +hsa00785 Lipoic acid metabolism +hsa00790 Folate biosynthesis +hsa00830 Retinol metabolism +hsa00860 Porphyrin and chlorophyll metabolism +hsa00900 Terpenoid backbone biosynthesis +hsa00910 Nitrogen metabolism +hsa00920 Sulfur metabolism +hsa00970 Aminoacyl-tRNA biosynthesis +hsa00980 Metabolism of xenobiotics by cytochrome P450 +hsa00982 Drug metabolism +hsa00983 Drug metabolism +hsa01040 Biosynthesis of unsaturated fatty acids +hsa01100 Metabolic pathways +hsa01200 Carbon metabolism +hsa01210 2-Oxocarboxylic acid metabolism +hsa01212 Fatty acid metabolism +hsa01230 Biosynthesis of amino acids +hsa01521 EGFR tyrosine kinase inhibitor resistance +hsa01522 Endocrine resistance +hsa01523 Antifolate resistance +hsa01524 Platinum drug resistance +hsa02010 ABC transporters +hsa03008 Ribosome biogenesis in eukaryotes +hsa03010 Ribosome +hsa03013 RNA transport +hsa03015 mRNA surveillance pathway +hsa03018 RNA degradation +hsa03020 RNA polymerase +hsa03022 Basal transcription factors +hsa03030 DNA replication +hsa03040 Spliceosome +hsa03050 Proteasome +hsa03060 Protein export +hsa03320 PPAR signaling pathway +hsa03410 Base excision repair +hsa03420 Nucleotide excision repair +hsa03430 Mismatch repair +hsa03440 Homologous recombination +hsa03450 Non-homologous end-joining +hsa03460 Fanconi anemia pathway +hsa04010 MAPK signaling pathway +hsa04012 ErbB signaling pathway +hsa04014 Ras signaling pathway +hsa04015 Rap1 signaling pathway +hsa04020 Calcium signaling pathway +hsa04022 cGMP-PKG signaling pathway +hsa04024 cAMP signaling pathway +hsa04060 Cytokine-cytokine receptor interaction +hsa04062 Chemokine signaling pathway +hsa04064 NF-kappa B signaling pathway +hsa04066 HIF-1 signaling pathway +hsa04068 FoxO signaling pathway +hsa04070 Phosphatidylinositol signaling system +hsa04071 Sphingolipid signaling pathway +hsa04072 Phospholipase D signaling pathway +hsa04080 Neuroactive ligand-receptor interaction +hsa04110 Cell cycle +hsa04114 Oocyte meiosis +hsa04115 p53 signaling pathway +hsa04120 Ubiquitin mediated proteolysis +hsa04122 Sulfur relay system +hsa04130 SNARE interactions in vesicular transport +hsa04136 Autophagy +hsa04137 Mitophagy +hsa04140 Autophagy +hsa04141 Protein processing in endoplasmic reticulum +hsa04142 Lysosome +hsa04144 Endocytosis +hsa04145 Phagosome +hsa04146 Peroxisome +hsa04150 mTOR signaling pathway +hsa04151 PI3K-Akt signaling pathway +hsa04152 AMPK signaling pathway +hsa04210 Apoptosis +hsa04211 Longevity regulating pathway +hsa04213 Longevity regulating pathway +hsa04215 Apoptosis +hsa04216 Ferroptosis +hsa04217 Necroptosis +hsa04218 Cellular senescence +hsa04260 Cardiac muscle contraction +hsa04261 Adrenergic signaling in cardiomyocytes +hsa04270 Vascular smooth muscle contraction +hsa04310 Wnt signaling pathway +hsa04330 Notch signaling pathway +hsa04340 Hedgehog signaling pathway +hsa04350 TGF-beta signaling pathway +hsa04360 Axon guidance +hsa04370 VEGF signaling pathway +hsa04371 Apelin signaling pathway +hsa04380 Osteoclast differentiation +hsa04390 Hippo signaling pathway +hsa04392 Hippo signaling pathway +hsa04510 Focal adhesion +hsa04512 ECM-receptor interaction +hsa04514 Cell adhesion molecules (CAMs) +hsa04520 Adherens junction +hsa04530 Tight junction +hsa04540 Gap junction +hsa04550 Signaling pathways regulating pluripotency of stem cells +hsa04610 Complement and coagulation cascades +hsa04611 Platelet activation +hsa04612 Antigen processing and presentation +hsa04614 Renin-angiotensin system +hsa04620 Toll-like receptor signaling pathway +hsa04621 NOD-like receptor signaling pathway +hsa04622 RIG-I-like receptor signaling pathway +hsa04623 Cytosolic DNA-sensing pathway +hsa04625 C-type lectin receptor signaling pathway +hsa04630 Jak-STAT signaling pathway +hsa04640 Hematopoietic cell lineage +hsa04650 Natural killer cell mediated cytotoxicity +hsa04657 IL-17 signaling pathway +hsa04658 Th1 and Th2 cell differentiation +hsa04659 Th17 cell differentiation +hsa04660 T cell receptor signaling pathway +hsa04662 B cell receptor signaling pathway +hsa04664 Fc epsilon RI signaling pathway +hsa04666 Fc gamma R-mediated phagocytosis +hsa04668 TNF signaling pathway +hsa04670 Leukocyte transendothelial migration +hsa04672 Intestinal immune network for IgA production +hsa04710 Circadian rhythm +hsa04713 Circadian entrainment +hsa04714 Thermogenesis +hsa04720 Long-term potentiation +hsa04721 Synaptic vesicle cycle +hsa04722 Neurotrophin signaling pathway +hsa04723 Retrograde endocannabinoid signaling +hsa04724 Glutamatergic synapse +hsa04725 Cholinergic synapse +hsa04726 Serotonergic synapse +hsa04727 GABAergic synapse +hsa04728 Dopaminergic synapse +hsa04730 Long-term depression +hsa04740 Olfactory transduction +hsa04742 Taste transduction +hsa04744 Phototransduction +hsa04750 Inflammatory mediator regulation of TRP channels +hsa04810 Regulation of actin cytoskeleton +hsa04910 Insulin signaling pathway +hsa04911 Insulin secretion +hsa04912 GnRH signaling pathway +hsa04913 Ovarian steroidogenesis +hsa04914 Progesterone-mediated oocyte maturation +hsa04915 Estrogen signaling pathway +hsa04916 Melanogenesis +hsa04917 Prolactin signaling pathway +hsa04918 Thyroid hormone synthesis +hsa04919 Thyroid hormone signaling pathway +hsa04920 Adipocytokine signaling pathway +hsa04921 Oxytocin signaling pathway +hsa04922 Glucagon signaling pathway +hsa04923 Regulation of lipolysis in adipocytes +hsa04924 Renin secretion +hsa04925 Aldosterone synthesis and secretion +hsa04926 Relaxin signaling pathway +hsa04927 Cortisol synthesis and secretion +hsa04928 Parathyroid hormone synthesis, secretion and action +hsa04930 Type II diabetes mellitus +hsa04931 Insulin resistance +hsa04932 Non-alcoholic fatty liver disease (NAFLD) +hsa04933 AGE-RAGE signaling pathway in diabetic complications +hsa04934 Cushing's syndrome +hsa04940 Type I diabetes mellitus +hsa04950 Maturity onset diabetes of the young +hsa04960 Aldosterone-regulated sodium reabsorption +hsa04961 Endocrine and other factor-regulated calcium reabsorption +hsa04962 Vasopressin-regulated water reabsorption +hsa04964 Proximal tubule bicarbonate reclamation +hsa04966 Collecting duct acid secretion +hsa04970 Salivary secretion +hsa04971 Gastric acid secretion +hsa04972 Pancreatic secretion +hsa04973 Carbohydrate digestion and absorption +hsa04974 Protein digestion and absorption +hsa04975 Fat digestion and absorption +hsa04976 Bile secretion +hsa04977 Vitamin digestion and absorption +hsa04978 Mineral absorption +hsa04979 Cholesterol metabolism +hsa05010 Alzheimer's disease +hsa05012 Parkinson's disease +hsa05014 Amyotrophic lateral sclerosis (ALS) +hsa05016 Huntington's disease +hsa05020 Prion diseases +hsa05030 Cocaine addiction +hsa05031 Amphetamine addiction +hsa05032 Morphine addiction +hsa05033 Nicotine addiction +hsa05034 Alcoholism +hsa05100 Bacterial invasion of epithelial cells +hsa05110 Vibrio cholerae infection +hsa05120 Epithelial cell signaling in Helicobacter pylori infection +hsa05130 Pathogenic Escherichia coli infection +hsa05131 Shigellosis +hsa05132 Salmonella infection +hsa05133 Pertussis +hsa05134 Legionellosis +hsa05140 Leishmaniasis +hsa05142 Chagas disease (American trypanosomiasis) +hsa05143 African trypanosomiasis +hsa05144 Malaria +hsa05145 Toxoplasmosis +hsa05146 Amoebiasis +hsa05150 Staphylococcus aureus infection +hsa05152 Tuberculosis +hsa05160 Hepatitis C +hsa05161 Hepatitis B +hsa05162 Measles +hsa05163 Human cytomegalovirus infection +hsa05164 Influenza A +hsa05165 Human papillomavirus infection +hsa05166 HTLV-I infection +hsa05167 Kaposi's sarcoma-associated herpesvirus infection +hsa05168 Herpes simplex infection +hsa05169 Epstein-Barr virus infection +hsa05200 Pathways in cancer +hsa05202 Transcriptional misregulation in cancer +hsa05203 Viral carcinogenesis +hsa05204 Chemical carcinogenesis +hsa05205 Proteoglycans in cancer +hsa05206 MicroRNAs in cancer +hsa05210 Colorectal cancer +hsa05211 Renal cell carcinoma +hsa05212 Pancreatic cancer +hsa05213 Endometrial cancer +hsa05214 Glioma +hsa05215 Prostate cancer +hsa05216 Thyroid cancer +hsa05217 Basal cell carcinoma +hsa05218 Melanoma +hsa05219 Bladder cancer +hsa05220 Chronic myeloid leukemia +hsa05221 Acute myeloid leukemia +hsa05222 Small cell lung cancer +hsa05223 Non-small cell lung cancer +hsa05224 Breast cancer +hsa05225 Hepatocellular carcinoma +hsa05226 Gastric cancer +hsa05230 Central carbon metabolism in cancer +hsa05231 Choline metabolism in cancer +hsa05310 Asthma +hsa05320 Autoimmune thyroid disease +hsa05321 Inflammatory bowel disease (IBD) +hsa05322 Systemic lupus erythematosus +hsa05323 Rheumatoid arthritis +hsa05330 Allograft rejection +hsa05332 Graft-versus-host disease +hsa05340 Primary immunodeficiency +hsa05410 Hypertrophic cardiomyopathy (HCM) +hsa05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +hsa05414 Dilated cardiomyopathy (DCM) +hsa05416 Viral myocarditis +hsa05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/hsa_pathways.loc.sample Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,330 @@ +#value name +hsa00010 Glycolysis / Gluconeogenesis +hsa00020 Citrate cycle (TCA cycle) +hsa00030 Pentose phosphate pathway +hsa00040 Pentose and glucuronate interconversions +hsa00051 Fructose and mannose metabolism +hsa00052 Galactose metabolism +hsa00053 Ascorbate and aldarate metabolism +hsa00061 Fatty acid biosynthesis +hsa00062 Fatty acid elongation +hsa00071 Fatty acid degradation +hsa00072 Synthesis and degradation of ketone bodies +hsa00100 Steroid biosynthesis +hsa00120 Primary bile acid biosynthesis +hsa00130 Ubiquinone and other terpenoid-quinone biosynthesis +hsa00140 Steroid hormone biosynthesis +hsa00190 Oxidative phosphorylation +hsa00220 Arginine biosynthesis +hsa00230 Purine metabolism +hsa00232 Caffeine metabolism +hsa00240 Pyrimidine metabolism +hsa00250 Alanine, aspartate and glutamate metabolism +hsa00260 Glycine, serine and threonine metabolism +hsa00270 Cysteine and methionine metabolism +hsa00280 Valine, leucine and isoleucine degradation +hsa00290 Valine, leucine and isoleucine biosynthesis +hsa00310 Lysine degradation +hsa00330 Arginine and proline metabolism +hsa00340 Histidine metabolism +hsa00350 Tyrosine metabolism +hsa00360 Phenylalanine metabolism +hsa00380 Tryptophan metabolism +hsa00400 Phenylalanine, tyrosine and tryptophan biosynthesis +hsa00410 beta-Alanine metabolism +hsa00430 Taurine and hypotaurine metabolism +hsa00440 Phosphonate and phosphinate metabolism +hsa00450 Selenocompound metabolism +hsa00471 D-Glutamine and D-glutamate metabolism +hsa00472 D-Arginine and D-ornithine metabolism +hsa00480 Glutathione metabolism +hsa00500 Starch and sucrose metabolism +hsa00510 N-Glycan biosynthesis +hsa00511 Other glycan degradation +hsa00512 Mucin type O-glycan biosynthesis +hsa00514 Other types of O-glycan biosynthesis +hsa00515 Mannose type O-glycan biosynthesis +hsa00520 Amino sugar and nucleotide sugar metabolism +hsa00524 Neomycin, kanamycin and gentamicin biosynthesis +hsa00531 Glycosaminoglycan degradation +hsa00532 Glycosaminoglycan biosynthesis +hsa00533 Glycosaminoglycan biosynthesis +hsa00534 Glycosaminoglycan biosynthesis +hsa00561 Glycerolipid metabolism +hsa00562 Inositol phosphate metabolism +hsa00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +hsa00564 Glycerophospholipid metabolism +hsa00565 Ether lipid metabolism +hsa00590 Arachidonic acid metabolism +hsa00591 Linoleic acid metabolism +hsa00592 alpha-Linolenic acid metabolism +hsa00600 Sphingolipid metabolism +hsa00601 Glycosphingolipid biosynthesis +hsa00603 Glycosphingolipid biosynthesis +hsa00604 Glycosphingolipid biosynthesis +hsa00620 Pyruvate metabolism +hsa00630 Glyoxylate and dicarboxylate metabolism +hsa00640 Propanoate metabolism +hsa00650 Butanoate metabolism +hsa00670 One carbon pool by folate +hsa00730 Thiamine metabolism +hsa00740 Riboflavin metabolism +hsa00750 Vitamin B6 metabolism +hsa00760 Nicotinate and nicotinamide metabolism +hsa00770 Pantothenate and CoA biosynthesis +hsa00780 Biotin metabolism +hsa00785 Lipoic acid metabolism +hsa00790 Folate biosynthesis +hsa00830 Retinol metabolism +hsa00860 Porphyrin and chlorophyll metabolism +hsa00900 Terpenoid backbone biosynthesis +hsa00910 Nitrogen metabolism +hsa00920 Sulfur metabolism +hsa00970 Aminoacyl-tRNA biosynthesis +hsa00980 Metabolism of xenobiotics by cytochrome P450 +hsa00982 Drug metabolism +hsa00983 Drug metabolism +hsa01040 Biosynthesis of unsaturated fatty acids +hsa01100 Metabolic pathways +hsa01200 Carbon metabolism +hsa01210 2-Oxocarboxylic acid metabolism +hsa01212 Fatty acid metabolism +hsa01230 Biosynthesis of amino acids +hsa01521 EGFR tyrosine kinase inhibitor resistance +hsa01522 Endocrine resistance +hsa01523 Antifolate resistance +hsa01524 Platinum drug resistance +hsa02010 ABC transporters +hsa03008 Ribosome biogenesis in eukaryotes +hsa03010 Ribosome +hsa03013 RNA transport +hsa03015 mRNA surveillance pathway +hsa03018 RNA degradation +hsa03020 RNA polymerase +hsa03022 Basal transcription factors +hsa03030 DNA replication +hsa03040 Spliceosome +hsa03050 Proteasome +hsa03060 Protein export +hsa03320 PPAR signaling pathway +hsa03410 Base excision repair +hsa03420 Nucleotide excision repair +hsa03430 Mismatch repair +hsa03440 Homologous recombination +hsa03450 Non-homologous end-joining +hsa03460 Fanconi anemia pathway +hsa04010 MAPK signaling pathway +hsa04012 ErbB signaling pathway +hsa04014 Ras signaling pathway +hsa04015 Rap1 signaling pathway +hsa04020 Calcium signaling pathway +hsa04022 cGMP-PKG signaling pathway +hsa04024 cAMP signaling pathway +hsa04060 Cytokine-cytokine receptor interaction +hsa04062 Chemokine signaling pathway +hsa04064 NF-kappa B signaling pathway +hsa04066 HIF-1 signaling pathway +hsa04068 FoxO signaling pathway +hsa04070 Phosphatidylinositol signaling system +hsa04071 Sphingolipid signaling pathway +hsa04072 Phospholipase D signaling pathway +hsa04080 Neuroactive ligand-receptor interaction +hsa04110 Cell cycle +hsa04114 Oocyte meiosis +hsa04115 p53 signaling pathway +hsa04120 Ubiquitin mediated proteolysis +hsa04122 Sulfur relay system +hsa04130 SNARE interactions in vesicular transport +hsa04136 Autophagy +hsa04137 Mitophagy +hsa04140 Autophagy +hsa04141 Protein processing in endoplasmic reticulum +hsa04142 Lysosome +hsa04144 Endocytosis +hsa04145 Phagosome +hsa04146 Peroxisome +hsa04150 mTOR signaling pathway +hsa04151 PI3K-Akt signaling pathway +hsa04152 AMPK signaling pathway +hsa04210 Apoptosis +hsa04211 Longevity regulating pathway +hsa04213 Longevity regulating pathway +hsa04215 Apoptosis +hsa04216 Ferroptosis +hsa04217 Necroptosis +hsa04218 Cellular senescence +hsa04260 Cardiac muscle contraction +hsa04261 Adrenergic signaling in cardiomyocytes +hsa04270 Vascular smooth muscle contraction +hsa04310 Wnt signaling pathway +hsa04330 Notch signaling pathway +hsa04340 Hedgehog signaling pathway +hsa04350 TGF-beta signaling pathway +hsa04360 Axon guidance +hsa04370 VEGF signaling pathway +hsa04371 Apelin signaling pathway +hsa04380 Osteoclast differentiation +hsa04390 Hippo signaling pathway +hsa04392 Hippo signaling pathway +hsa04510 Focal adhesion +hsa04512 ECM-receptor interaction +hsa04514 Cell adhesion molecules (CAMs) +hsa04520 Adherens junction +hsa04530 Tight junction +hsa04540 Gap junction +hsa04550 Signaling pathways regulating pluripotency of stem cells +hsa04610 Complement and coagulation cascades +hsa04611 Platelet activation +hsa04612 Antigen processing and presentation +hsa04614 Renin-angiotensin system +hsa04620 Toll-like receptor signaling pathway +hsa04621 NOD-like receptor signaling pathway +hsa04622 RIG-I-like receptor signaling pathway +hsa04623 Cytosolic DNA-sensing pathway +hsa04625 C-type lectin receptor signaling pathway +hsa04630 Jak-STAT signaling pathway +hsa04640 Hematopoietic cell lineage +hsa04650 Natural killer cell mediated cytotoxicity +hsa04657 IL-17 signaling pathway +hsa04658 Th1 and Th2 cell differentiation +hsa04659 Th17 cell differentiation +hsa04660 T cell receptor signaling pathway +hsa04662 B cell receptor signaling pathway +hsa04664 Fc epsilon RI signaling pathway +hsa04666 Fc gamma R-mediated phagocytosis +hsa04668 TNF signaling pathway +hsa04670 Leukocyte transendothelial migration +hsa04672 Intestinal immune network for IgA production +hsa04710 Circadian rhythm +hsa04713 Circadian entrainment +hsa04714 Thermogenesis +hsa04720 Long-term potentiation +hsa04721 Synaptic vesicle cycle +hsa04722 Neurotrophin signaling pathway +hsa04723 Retrograde endocannabinoid signaling +hsa04724 Glutamatergic synapse +hsa04725 Cholinergic synapse +hsa04726 Serotonergic synapse +hsa04727 GABAergic synapse +hsa04728 Dopaminergic synapse +hsa04730 Long-term depression +hsa04740 Olfactory transduction +hsa04742 Taste transduction +hsa04744 Phototransduction +hsa04750 Inflammatory mediator regulation of TRP channels +hsa04810 Regulation of actin cytoskeleton +hsa04910 Insulin signaling pathway +hsa04911 Insulin secretion +hsa04912 GnRH signaling pathway +hsa04913 Ovarian steroidogenesis +hsa04914 Progesterone-mediated oocyte maturation +hsa04915 Estrogen signaling pathway +hsa04916 Melanogenesis +hsa04917 Prolactin signaling pathway +hsa04918 Thyroid hormone synthesis +hsa04919 Thyroid hormone signaling pathway +hsa04920 Adipocytokine signaling pathway +hsa04921 Oxytocin signaling pathway +hsa04922 Glucagon signaling pathway +hsa04923 Regulation of lipolysis in adipocytes +hsa04924 Renin secretion +hsa04925 Aldosterone synthesis and secretion +hsa04926 Relaxin signaling pathway +hsa04927 Cortisol synthesis and secretion +hsa04928 Parathyroid hormone synthesis, secretion and action +hsa04930 Type II diabetes mellitus +hsa04931 Insulin resistance +hsa04932 Non-alcoholic fatty liver disease (NAFLD) +hsa04933 AGE-RAGE signaling pathway in diabetic complications +hsa04934 Cushing's syndrome +hsa04940 Type I diabetes mellitus +hsa04950 Maturity onset diabetes of the young +hsa04960 Aldosterone-regulated sodium reabsorption +hsa04961 Endocrine and other factor-regulated calcium reabsorption +hsa04962 Vasopressin-regulated water reabsorption +hsa04964 Proximal tubule bicarbonate reclamation +hsa04966 Collecting duct acid secretion +hsa04970 Salivary secretion +hsa04971 Gastric acid secretion +hsa04972 Pancreatic secretion +hsa04973 Carbohydrate digestion and absorption +hsa04974 Protein digestion and absorption +hsa04975 Fat digestion and absorption +hsa04976 Bile secretion +hsa04977 Vitamin digestion and absorption +hsa04978 Mineral absorption +hsa04979 Cholesterol metabolism +hsa05010 Alzheimer's disease +hsa05012 Parkinson's disease +hsa05014 Amyotrophic lateral sclerosis (ALS) +hsa05016 Huntington's disease +hsa05020 Prion diseases +hsa05030 Cocaine addiction +hsa05031 Amphetamine addiction +hsa05032 Morphine addiction +hsa05033 Nicotine addiction +hsa05034 Alcoholism +hsa05100 Bacterial invasion of epithelial cells +hsa05110 Vibrio cholerae infection +hsa05120 Epithelial cell signaling in Helicobacter pylori infection +hsa05130 Pathogenic Escherichia coli infection +hsa05131 Shigellosis +hsa05132 Salmonella infection +hsa05133 Pertussis +hsa05134 Legionellosis +hsa05140 Leishmaniasis +hsa05142 Chagas disease (American trypanosomiasis) +hsa05143 African trypanosomiasis +hsa05144 Malaria +hsa05145 Toxoplasmosis +hsa05146 Amoebiasis +hsa05150 Staphylococcus aureus infection +hsa05152 Tuberculosis +hsa05160 Hepatitis C +hsa05161 Hepatitis B +hsa05162 Measles +hsa05163 Human cytomegalovirus infection +hsa05164 Influenza A +hsa05165 Human papillomavirus infection +hsa05166 HTLV-I infection +hsa05167 Kaposi's sarcoma-associated herpesvirus infection +hsa05168 Herpes simplex infection +hsa05169 Epstein-Barr virus infection +hsa05200 Pathways in cancer +hsa05202 Transcriptional misregulation in cancer +hsa05203 Viral carcinogenesis +hsa05204 Chemical carcinogenesis +hsa05205 Proteoglycans in cancer +hsa05206 MicroRNAs in cancer +hsa05210 Colorectal cancer +hsa05211 Renal cell carcinoma +hsa05212 Pancreatic cancer +hsa05213 Endometrial cancer +hsa05214 Glioma +hsa05215 Prostate cancer +hsa05216 Thyroid cancer +hsa05217 Basal cell carcinoma +hsa05218 Melanoma +hsa05219 Bladder cancer +hsa05220 Chronic myeloid leukemia +hsa05221 Acute myeloid leukemia +hsa05222 Small cell lung cancer +hsa05223 Non-small cell lung cancer +hsa05224 Breast cancer +hsa05225 Hepatocellular carcinoma +hsa05226 Gastric cancer +hsa05230 Central carbon metabolism in cancer +hsa05231 Choline metabolism in cancer +hsa05310 Asthma +hsa05320 Autoimmune thyroid disease +hsa05321 Inflammatory bowel disease (IBD) +hsa05322 Systemic lupus erythematosus +hsa05323 Rheumatoid arthritis +hsa05330 Allograft rejection +hsa05332 Graft-versus-host disease +hsa05340 Primary immunodeficiency +hsa05410 Hypertrophic cardiomyopathy (HCM) +hsa05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +hsa05414 Dilated cardiomyopathy (DCM) +hsa05416 Viral myocarditis +hsa05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mmu_pathways.loc Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,326 @@ +#value name +mmu00010 Glycolysis / Gluconeogenesis +mmu00020 Citrate cycle (TCA cycle) +mmu00030 Pentose phosphate pathway +mmu00040 Pentose and glucuronate interconversions +mmu00051 Fructose and mannose metabolism +mmu00052 Galactose metabolism +mmu00053 Ascorbate and aldarate metabolism +mmu00061 Fatty acid biosynthesis +mmu00062 Fatty acid elongation +mmu00071 Fatty acid degradation +mmu00072 Synthesis and degradation of ketone bodies +mmu00100 Steroid biosynthesis +mmu00120 Primary bile acid biosynthesis +mmu00130 Ubiquinone and other terpenoid-quinone biosynthesis +mmu00140 Steroid hormone biosynthesis +mmu00190 Oxidative phosphorylation +mmu00220 Arginine biosynthesis +mmu00230 Purine metabolism +mmu00232 Caffeine metabolism +mmu00240 Pyrimidine metabolism +mmu00250 Alanine, aspartate and glutamate metabolism +mmu00260 Glycine, serine and threonine metabolism +mmu00270 Cysteine and methionine metabolism +mmu00280 Valine, leucine and isoleucine degradation +mmu00290 Valine, leucine and isoleucine biosynthesis +mmu00310 Lysine degradation +mmu00330 Arginine and proline metabolism +mmu00340 Histidine metabolism +mmu00350 Tyrosine metabolism +mmu00360 Phenylalanine metabolism +mmu00380 Tryptophan metabolism +mmu00400 Phenylalanine, tyrosine and tryptophan biosynthesis +mmu00410 beta-Alanine metabolism +mmu00430 Taurine and hypotaurine metabolism +mmu00440 Phosphonate and phosphinate metabolism +mmu00450 Selenocompound metabolism +mmu00471 D-Glutamine and D-glutamate metabolism +mmu00472 D-Arginine and D-ornithine metabolism +mmu00480 Glutathione metabolism +mmu00500 Starch and sucrose metabolism +mmu00510 N-Glycan biosynthesis +mmu00511 Other glycan degradation +mmu00512 Mucin type O-glycan biosynthesis +mmu00514 Other types of O-glycan biosynthesis +mmu00515 Mannose type O-glycan biosynthesis +mmu00520 Amino sugar and nucleotide sugar metabolism +mmu00524 Neomycin, kanamycin and gentamicin biosynthesis +mmu00531 Glycosaminoglycan degradation +mmu00532 Glycosaminoglycan biosynthesis +mmu00533 Glycosaminoglycan biosynthesis +mmu00534 Glycosaminoglycan biosynthesis +mmu00561 Glycerolipid metabolism +mmu00562 Inositol phosphate metabolism +mmu00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +mmu00564 Glycerophospholipid metabolism +mmu00565 Ether lipid metabolism +mmu00590 Arachidonic acid metabolism +mmu00591 Linoleic acid metabolism +mmu00592 alpha-Linolenic acid metabolism +mmu00600 Sphingolipid metabolism +mmu00601 Glycosphingolipid biosynthesis +mmu00603 Glycosphingolipid biosynthesis +mmu00604 Glycosphingolipid biosynthesis +mmu00620 Pyruvate metabolism +mmu00630 Glyoxylate and dicarboxylate metabolism +mmu00640 Propanoate metabolism +mmu00650 Butanoate metabolism +mmu00670 One carbon pool by folate +mmu00730 Thiamine metabolism +mmu00740 Riboflavin metabolism +mmu00750 Vitamin B6 metabolism +mmu00760 Nicotinate and nicotinamide metabolism +mmu00770 Pantothenate and CoA biosynthesis +mmu00780 Biotin metabolism +mmu00785 Lipoic acid metabolism +mmu00790 Folate biosynthesis +mmu00830 Retinol metabolism +mmu00860 Porphyrin and chlorophyll metabolism +mmu00900 Terpenoid backbone biosynthesis +mmu00910 Nitrogen metabolism +mmu00920 Sulfur metabolism +mmu00970 Aminoacyl-tRNA biosynthesis +mmu00980 Metabolism of xenobiotics by cytochrome P450 +mmu00982 Drug metabolism +mmu00983 Drug metabolism +mmu01040 Biosynthesis of unsaturated fatty acids +mmu01100 Metabolic pathways +mmu01200 Carbon metabolism +mmu01210 2-Oxocarboxylic acid metabolism +mmu01212 Fatty acid metabolism +mmu01230 Biosynthesis of amino acids +mmu01521 EGFR tyrosine kinase inhibitor resistance +mmu01522 Endocrine resistance +mmu01523 Antifolate resistance +mmu01524 Platinum drug resistance +mmu02010 ABC transporters +mmu03008 Ribosome biogenesis in eukaryotes +mmu03010 Ribosome +mmu03013 RNA transport +mmu03015 mRNA surveillance pathway +mmu03018 RNA degradation +mmu03020 RNA polymerase +mmu03022 Basal transcription factors +mmu03030 DNA replication +mmu03040 Spliceosome +mmu03050 Proteasome +mmu03060 Protein export +mmu03320 PPAR signaling pathway +mmu03410 Base excision repair +mmu03420 Nucleotide excision repair +mmu03430 Mismatch repair +mmu03440 Homologous recombination +mmu03450 Non-homologous end-joining +mmu03460 Fanconi anemia pathway +mmu04010 MAPK signaling pathway +mmu04012 ErbB signaling pathway +mmu04014 Ras signaling pathway +mmu04015 Rap1 signaling pathway +mmu04020 Calcium signaling pathway +mmu04022 cGMP-PKG signaling pathway +mmu04024 cAMP signaling pathway +mmu04060 Cytokine-cytokine receptor interaction +mmu04062 Chemokine signaling pathway +mmu04064 NF-kappa B signaling pathway +mmu04066 HIF-1 signaling pathway +mmu04068 FoxO signaling pathway +mmu04070 Phosphatidylinositol signaling system +mmu04071 Sphingolipid signaling pathway +mmu04072 Phospholipase D signaling pathway +mmu04080 Neuroactive ligand-receptor interaction +mmu04110 Cell cycle +mmu04114 Oocyte meiosis +mmu04115 p53 signaling pathway +mmu04120 Ubiquitin mediated proteolysis +mmu04122 Sulfur relay system +mmu04130 SNARE interactions in vesicular transport +mmu04136 Autophagy +mmu04137 Mitophagy +mmu04140 Autophagy +mmu04141 Protein processing in endoplasmic reticulum +mmu04142 Lysosome +mmu04144 Endocytosis +mmu04145 Phagosome +mmu04146 Peroxisome +mmu04150 mTOR signaling pathway +mmu04151 PI3K-Akt signaling pathway +mmu04152 AMPK signaling pathway +mmu04210 Apoptosis +mmu04211 Longevity regulating pathway +mmu04213 Longevity regulating pathway +mmu04215 Apoptosis +mmu04216 Ferroptosis +mmu04217 Necroptosis +mmu04218 Cellular senescence +mmu04260 Cardiac muscle contraction +mmu04261 Adrenergic signaling in cardiomyocytes +mmu04270 Vascular smooth muscle contraction +mmu04310 Wnt signaling pathway +mmu04330 Notch signaling pathway +mmu04340 Hedgehog signaling pathway +mmu04350 TGF-beta signaling pathway +mmu04360 Axon guidance +mmu04370 VEGF signaling pathway +mmu04371 Apelin signaling pathway +mmu04380 Osteoclast differentiation +mmu04390 Hippo signaling pathway +mmu04392 Hippo signaling pathway +mmu04510 Focal adhesion +mmu04512 ECM-receptor interaction +mmu04514 Cell adhesion molecules (CAMs) +mmu04520 Adherens junction +mmu04530 Tight junction +mmu04540 Gap junction +mmu04550 Signaling pathways regulating pluripotency of stem cells +mmu04610 Complement and coagulation cascades +mmu04611 Platelet activation +mmu04612 Antigen processing and presentation +mmu04614 Renin-angiotensin system +mmu04620 Toll-like receptor signaling pathway +mmu04621 NOD-like receptor signaling pathway +mmu04622 RIG-I-like receptor signaling pathway +mmu04623 Cytosolic DNA-sensing pathway +mmu04625 C-type lectin receptor signaling pathway +mmu04630 Jak-STAT signaling pathway +mmu04640 Hematopoietic cell lineage +mmu04650 Natural killer cell mediated cytotoxicity +mmu04657 IL-17 signaling pathway +mmu04658 Th1 and Th2 cell differentiation +mmu04659 Th17 cell differentiation +mmu04660 T cell receptor signaling pathway +mmu04662 B cell receptor signaling pathway +mmu04664 Fc epsilon RI signaling pathway +mmu04666 Fc gamma R-mediated phagocytosis +mmu04668 TNF signaling pathway +mmu04670 Leukocyte transendothelial migration +mmu04672 Intestinal immune network for IgA production +mmu04710 Circadian rhythm +mmu04713 Circadian entrainment +mmu04714 Thermogenesis +mmu04720 Long-term potentiation +mmu04721 Synaptic vesicle cycle +mmu04722 Neurotrophin signaling pathway +mmu04723 Retrograde endocannabinoid signaling +mmu04724 Glutamatergic synapse +mmu04725 Cholinergic synapse +mmu04726 Serotonergic synapse +mmu04727 GABAergic synapse +mmu04728 Dopaminergic synapse +mmu04730 Long-term depression +mmu04740 Olfactory transduction +mmu04742 Taste transduction +mmu04744 Phototransduction +mmu04750 Inflammatory mediator regulation of TRP channels +mmu04810 Regulation of actin cytoskeleton +mmu04910 Insulin signaling pathway +mmu04911 Insulin secretion +mmu04912 GnRH signaling pathway +mmu04913 Ovarian steroidogenesis +mmu04914 Progesterone-mediated oocyte maturation +mmu04915 Estrogen signaling pathway +mmu04916 Melanogenesis +mmu04917 Prolactin signaling pathway +mmu04918 Thyroid hormone synthesis +mmu04919 Thyroid hormone signaling pathway +mmu04920 Adipocytokine signaling pathway +mmu04921 Oxytocin signaling pathway +mmu04922 Glucagon signaling pathway +mmu04923 Regulation of lipolysis in adipocytes +mmu04924 Renin secretion +mmu04925 Aldosterone synthesis and secretion +mmu04926 Relaxin signaling pathway +mmu04927 Cortisol synthesis and secretion +mmu04928 Parathyroid hormone synthesis, secretion and action +mmu04930 Type II diabetes mellitus +mmu04931 Insulin resistance +mmu04932 Non-alcoholic fatty liver disease (NAFLD) +mmu04933 AGE-RAGE signaling pathway in diabetic complications +mmu04934 Cushing's syndrome +mmu04940 Type I diabetes mellitus +mmu04950 Maturity onset diabetes of the young +mmu04960 Aldosterone-regulated sodium reabsorption +mmu04961 Endocrine and other factor-regulated calcium reabsorption +mmu04962 Vasopressin-regulated water reabsorption +mmu04964 Proximal tubule bicarbonate reclamation +mmu04966 Collecting duct acid secretion +mmu04970 Salivary secretion +mmu04971 Gastric acid secretion +mmu04972 Pancreatic secretion +mmu04973 Carbohydrate digestion and absorption +mmu04974 Protein digestion and absorption +mmu04975 Fat digestion and absorption +mmu04976 Bile secretion +mmu04977 Vitamin digestion and absorption +mmu04978 Mineral absorption +mmu04979 Cholesterol metabolism +mmu05010 Alzheimer's disease +mmu05012 Parkinson's disease +mmu05014 Amyotrophic lateral sclerosis (ALS) +mmu05016 Huntington's disease +mmu05020 Prion diseases +mmu05030 Cocaine addiction +mmu05031 Amphetamine addiction +mmu05032 Morphine addiction +mmu05033 Nicotine addiction +mmu05034 Alcoholism +mmu05100 Bacterial invasion of epithelial cells +mmu05132 Salmonella infection +mmu05133 Pertussis +mmu05134 Legionellosis +mmu05140 Leishmaniasis +mmu05142 Chagas disease (American trypanosomiasis) +mmu05143 African trypanosomiasis +mmu05144 Malaria +mmu05145 Toxoplasmosis +mmu05146 Amoebiasis +mmu05150 Staphylococcus aureus infection +mmu05152 Tuberculosis +mmu05160 Hepatitis C +mmu05161 Hepatitis B +mmu05162 Measles +mmu05163 Human cytomegalovirus infection +mmu05164 Influenza A +mmu05165 Human papillomavirus infection +mmu05166 HTLV-I infection +mmu05167 Kaposi's sarcoma-associated herpesvirus infection +mmu05168 Herpes simplex infection +mmu05169 Epstein-Barr virus infection +mmu05200 Pathways in cancer +mmu05202 Transcriptional misregulation in cancer +mmu05203 Viral carcinogenesis +mmu05204 Chemical carcinogenesis +mmu05205 Proteoglycans in cancer +mmu05206 MicroRNAs in cancer +mmu05210 Colorectal cancer +mmu05211 Renal cell carcinoma +mmu05212 Pancreatic cancer +mmu05213 Endometrial cancer +mmu05214 Glioma +mmu05215 Prostate cancer +mmu05216 Thyroid cancer +mmu05217 Basal cell carcinoma +mmu05218 Melanoma +mmu05219 Bladder cancer +mmu05220 Chronic myeloid leukemia +mmu05221 Acute myeloid leukemia +mmu05222 Small cell lung cancer +mmu05223 Non-small cell lung cancer +mmu05224 Breast cancer +mmu05225 Hepatocellular carcinoma +mmu05226 Gastric cancer +mmu05230 Central carbon metabolism in cancer +mmu05231 Choline metabolism in cancer +mmu05310 Asthma +mmu05320 Autoimmune thyroid disease +mmu05321 Inflammatory bowel disease (IBD) +mmu05322 Systemic lupus erythematosus +mmu05323 Rheumatoid arthritis +mmu05330 Allograft rejection +mmu05332 Graft-versus-host disease +mmu05340 Primary immunodeficiency +mmu05410 Hypertrophic cardiomyopathy (HCM) +mmu05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +mmu05414 Dilated cardiomyopathy (DCM) +mmu05416 Viral myocarditis +mmu05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mmu_pathways.loc.sample Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,326 @@ +#value name +mmu00010 Glycolysis / Gluconeogenesis +mmu00020 Citrate cycle (TCA cycle) +mmu00030 Pentose phosphate pathway +mmu00040 Pentose and glucuronate interconversions +mmu00051 Fructose and mannose metabolism +mmu00052 Galactose metabolism +mmu00053 Ascorbate and aldarate metabolism +mmu00061 Fatty acid biosynthesis +mmu00062 Fatty acid elongation +mmu00071 Fatty acid degradation +mmu00072 Synthesis and degradation of ketone bodies +mmu00100 Steroid biosynthesis +mmu00120 Primary bile acid biosynthesis +mmu00130 Ubiquinone and other terpenoid-quinone biosynthesis +mmu00140 Steroid hormone biosynthesis +mmu00190 Oxidative phosphorylation +mmu00220 Arginine biosynthesis +mmu00230 Purine metabolism +mmu00232 Caffeine metabolism +mmu00240 Pyrimidine metabolism +mmu00250 Alanine, aspartate and glutamate metabolism +mmu00260 Glycine, serine and threonine metabolism +mmu00270 Cysteine and methionine metabolism +mmu00280 Valine, leucine and isoleucine degradation +mmu00290 Valine, leucine and isoleucine biosynthesis +mmu00310 Lysine degradation +mmu00330 Arginine and proline metabolism +mmu00340 Histidine metabolism +mmu00350 Tyrosine metabolism +mmu00360 Phenylalanine metabolism +mmu00380 Tryptophan metabolism +mmu00400 Phenylalanine, tyrosine and tryptophan biosynthesis +mmu00410 beta-Alanine metabolism +mmu00430 Taurine and hypotaurine metabolism +mmu00440 Phosphonate and phosphinate metabolism +mmu00450 Selenocompound metabolism +mmu00471 D-Glutamine and D-glutamate metabolism +mmu00472 D-Arginine and D-ornithine metabolism +mmu00480 Glutathione metabolism +mmu00500 Starch and sucrose metabolism +mmu00510 N-Glycan biosynthesis +mmu00511 Other glycan degradation +mmu00512 Mucin type O-glycan biosynthesis +mmu00514 Other types of O-glycan biosynthesis +mmu00515 Mannose type O-glycan biosynthesis +mmu00520 Amino sugar and nucleotide sugar metabolism +mmu00524 Neomycin, kanamycin and gentamicin biosynthesis +mmu00531 Glycosaminoglycan degradation +mmu00532 Glycosaminoglycan biosynthesis +mmu00533 Glycosaminoglycan biosynthesis +mmu00534 Glycosaminoglycan biosynthesis +mmu00561 Glycerolipid metabolism +mmu00562 Inositol phosphate metabolism +mmu00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +mmu00564 Glycerophospholipid metabolism +mmu00565 Ether lipid metabolism +mmu00590 Arachidonic acid metabolism +mmu00591 Linoleic acid metabolism +mmu00592 alpha-Linolenic acid metabolism +mmu00600 Sphingolipid metabolism +mmu00601 Glycosphingolipid biosynthesis +mmu00603 Glycosphingolipid biosynthesis +mmu00604 Glycosphingolipid biosynthesis +mmu00620 Pyruvate metabolism +mmu00630 Glyoxylate and dicarboxylate metabolism +mmu00640 Propanoate metabolism +mmu00650 Butanoate metabolism +mmu00670 One carbon pool by folate +mmu00730 Thiamine metabolism +mmu00740 Riboflavin metabolism +mmu00750 Vitamin B6 metabolism +mmu00760 Nicotinate and nicotinamide metabolism +mmu00770 Pantothenate and CoA biosynthesis +mmu00780 Biotin metabolism +mmu00785 Lipoic acid metabolism +mmu00790 Folate biosynthesis +mmu00830 Retinol metabolism +mmu00860 Porphyrin and chlorophyll metabolism +mmu00900 Terpenoid backbone biosynthesis +mmu00910 Nitrogen metabolism +mmu00920 Sulfur metabolism +mmu00970 Aminoacyl-tRNA biosynthesis +mmu00980 Metabolism of xenobiotics by cytochrome P450 +mmu00982 Drug metabolism +mmu00983 Drug metabolism +mmu01040 Biosynthesis of unsaturated fatty acids +mmu01100 Metabolic pathways +mmu01200 Carbon metabolism +mmu01210 2-Oxocarboxylic acid metabolism +mmu01212 Fatty acid metabolism +mmu01230 Biosynthesis of amino acids +mmu01521 EGFR tyrosine kinase inhibitor resistance +mmu01522 Endocrine resistance +mmu01523 Antifolate resistance +mmu01524 Platinum drug resistance +mmu02010 ABC transporters +mmu03008 Ribosome biogenesis in eukaryotes +mmu03010 Ribosome +mmu03013 RNA transport +mmu03015 mRNA surveillance pathway +mmu03018 RNA degradation +mmu03020 RNA polymerase +mmu03022 Basal transcription factors +mmu03030 DNA replication +mmu03040 Spliceosome +mmu03050 Proteasome +mmu03060 Protein export +mmu03320 PPAR signaling pathway +mmu03410 Base excision repair +mmu03420 Nucleotide excision repair +mmu03430 Mismatch repair +mmu03440 Homologous recombination +mmu03450 Non-homologous end-joining +mmu03460 Fanconi anemia pathway +mmu04010 MAPK signaling pathway +mmu04012 ErbB signaling pathway +mmu04014 Ras signaling pathway +mmu04015 Rap1 signaling pathway +mmu04020 Calcium signaling pathway +mmu04022 cGMP-PKG signaling pathway +mmu04024 cAMP signaling pathway +mmu04060 Cytokine-cytokine receptor interaction +mmu04062 Chemokine signaling pathway +mmu04064 NF-kappa B signaling pathway +mmu04066 HIF-1 signaling pathway +mmu04068 FoxO signaling pathway +mmu04070 Phosphatidylinositol signaling system +mmu04071 Sphingolipid signaling pathway +mmu04072 Phospholipase D signaling pathway +mmu04080 Neuroactive ligand-receptor interaction +mmu04110 Cell cycle +mmu04114 Oocyte meiosis +mmu04115 p53 signaling pathway +mmu04120 Ubiquitin mediated proteolysis +mmu04122 Sulfur relay system +mmu04130 SNARE interactions in vesicular transport +mmu04136 Autophagy +mmu04137 Mitophagy +mmu04140 Autophagy +mmu04141 Protein processing in endoplasmic reticulum +mmu04142 Lysosome +mmu04144 Endocytosis +mmu04145 Phagosome +mmu04146 Peroxisome +mmu04150 mTOR signaling pathway +mmu04151 PI3K-Akt signaling pathway +mmu04152 AMPK signaling pathway +mmu04210 Apoptosis +mmu04211 Longevity regulating pathway +mmu04213 Longevity regulating pathway +mmu04215 Apoptosis +mmu04216 Ferroptosis +mmu04217 Necroptosis +mmu04218 Cellular senescence +mmu04260 Cardiac muscle contraction +mmu04261 Adrenergic signaling in cardiomyocytes +mmu04270 Vascular smooth muscle contraction +mmu04310 Wnt signaling pathway +mmu04330 Notch signaling pathway +mmu04340 Hedgehog signaling pathway +mmu04350 TGF-beta signaling pathway +mmu04360 Axon guidance +mmu04370 VEGF signaling pathway +mmu04371 Apelin signaling pathway +mmu04380 Osteoclast differentiation +mmu04390 Hippo signaling pathway +mmu04392 Hippo signaling pathway +mmu04510 Focal adhesion +mmu04512 ECM-receptor interaction +mmu04514 Cell adhesion molecules (CAMs) +mmu04520 Adherens junction +mmu04530 Tight junction +mmu04540 Gap junction +mmu04550 Signaling pathways regulating pluripotency of stem cells +mmu04610 Complement and coagulation cascades +mmu04611 Platelet activation +mmu04612 Antigen processing and presentation +mmu04614 Renin-angiotensin system +mmu04620 Toll-like receptor signaling pathway +mmu04621 NOD-like receptor signaling pathway +mmu04622 RIG-I-like receptor signaling pathway +mmu04623 Cytosolic DNA-sensing pathway +mmu04625 C-type lectin receptor signaling pathway +mmu04630 Jak-STAT signaling pathway +mmu04640 Hematopoietic cell lineage +mmu04650 Natural killer cell mediated cytotoxicity +mmu04657 IL-17 signaling pathway +mmu04658 Th1 and Th2 cell differentiation +mmu04659 Th17 cell differentiation +mmu04660 T cell receptor signaling pathway +mmu04662 B cell receptor signaling pathway +mmu04664 Fc epsilon RI signaling pathway +mmu04666 Fc gamma R-mediated phagocytosis +mmu04668 TNF signaling pathway +mmu04670 Leukocyte transendothelial migration +mmu04672 Intestinal immune network for IgA production +mmu04710 Circadian rhythm +mmu04713 Circadian entrainment +mmu04714 Thermogenesis +mmu04720 Long-term potentiation +mmu04721 Synaptic vesicle cycle +mmu04722 Neurotrophin signaling pathway +mmu04723 Retrograde endocannabinoid signaling +mmu04724 Glutamatergic synapse +mmu04725 Cholinergic synapse +mmu04726 Serotonergic synapse +mmu04727 GABAergic synapse +mmu04728 Dopaminergic synapse +mmu04730 Long-term depression +mmu04740 Olfactory transduction +mmu04742 Taste transduction +mmu04744 Phototransduction +mmu04750 Inflammatory mediator regulation of TRP channels +mmu04810 Regulation of actin cytoskeleton +mmu04910 Insulin signaling pathway +mmu04911 Insulin secretion +mmu04912 GnRH signaling pathway +mmu04913 Ovarian steroidogenesis +mmu04914 Progesterone-mediated oocyte maturation +mmu04915 Estrogen signaling pathway +mmu04916 Melanogenesis +mmu04917 Prolactin signaling pathway +mmu04918 Thyroid hormone synthesis +mmu04919 Thyroid hormone signaling pathway +mmu04920 Adipocytokine signaling pathway +mmu04921 Oxytocin signaling pathway +mmu04922 Glucagon signaling pathway +mmu04923 Regulation of lipolysis in adipocytes +mmu04924 Renin secretion +mmu04925 Aldosterone synthesis and secretion +mmu04926 Relaxin signaling pathway +mmu04927 Cortisol synthesis and secretion +mmu04928 Parathyroid hormone synthesis, secretion and action +mmu04930 Type II diabetes mellitus +mmu04931 Insulin resistance +mmu04932 Non-alcoholic fatty liver disease (NAFLD) +mmu04933 AGE-RAGE signaling pathway in diabetic complications +mmu04934 Cushing's syndrome +mmu04940 Type I diabetes mellitus +mmu04950 Maturity onset diabetes of the young +mmu04960 Aldosterone-regulated sodium reabsorption +mmu04961 Endocrine and other factor-regulated calcium reabsorption +mmu04962 Vasopressin-regulated water reabsorption +mmu04964 Proximal tubule bicarbonate reclamation +mmu04966 Collecting duct acid secretion +mmu04970 Salivary secretion +mmu04971 Gastric acid secretion +mmu04972 Pancreatic secretion +mmu04973 Carbohydrate digestion and absorption +mmu04974 Protein digestion and absorption +mmu04975 Fat digestion and absorption +mmu04976 Bile secretion +mmu04977 Vitamin digestion and absorption +mmu04978 Mineral absorption +mmu04979 Cholesterol metabolism +mmu05010 Alzheimer's disease +mmu05012 Parkinson's disease +mmu05014 Amyotrophic lateral sclerosis (ALS) +mmu05016 Huntington's disease +mmu05020 Prion diseases +mmu05030 Cocaine addiction +mmu05031 Amphetamine addiction +mmu05032 Morphine addiction +mmu05033 Nicotine addiction +mmu05034 Alcoholism +mmu05100 Bacterial invasion of epithelial cells +mmu05132 Salmonella infection +mmu05133 Pertussis +mmu05134 Legionellosis +mmu05140 Leishmaniasis +mmu05142 Chagas disease (American trypanosomiasis) +mmu05143 African trypanosomiasis +mmu05144 Malaria +mmu05145 Toxoplasmosis +mmu05146 Amoebiasis +mmu05150 Staphylococcus aureus infection +mmu05152 Tuberculosis +mmu05160 Hepatitis C +mmu05161 Hepatitis B +mmu05162 Measles +mmu05163 Human cytomegalovirus infection +mmu05164 Influenza A +mmu05165 Human papillomavirus infection +mmu05166 HTLV-I infection +mmu05167 Kaposi's sarcoma-associated herpesvirus infection +mmu05168 Herpes simplex infection +mmu05169 Epstein-Barr virus infection +mmu05200 Pathways in cancer +mmu05202 Transcriptional misregulation in cancer +mmu05203 Viral carcinogenesis +mmu05204 Chemical carcinogenesis +mmu05205 Proteoglycans in cancer +mmu05206 MicroRNAs in cancer +mmu05210 Colorectal cancer +mmu05211 Renal cell carcinoma +mmu05212 Pancreatic cancer +mmu05213 Endometrial cancer +mmu05214 Glioma +mmu05215 Prostate cancer +mmu05216 Thyroid cancer +mmu05217 Basal cell carcinoma +mmu05218 Melanoma +mmu05219 Bladder cancer +mmu05220 Chronic myeloid leukemia +mmu05221 Acute myeloid leukemia +mmu05222 Small cell lung cancer +mmu05223 Non-small cell lung cancer +mmu05224 Breast cancer +mmu05225 Hepatocellular carcinoma +mmu05226 Gastric cancer +mmu05230 Central carbon metabolism in cancer +mmu05231 Choline metabolism in cancer +mmu05310 Asthma +mmu05320 Autoimmune thyroid disease +mmu05321 Inflammatory bowel disease (IBD) +mmu05322 Systemic lupus erythematosus +mmu05323 Rheumatoid arthritis +mmu05330 Allograft rejection +mmu05332 Graft-versus-host disease +mmu05340 Primary immunodeficiency +mmu05410 Hypertrophic cardiomyopathy (HCM) +mmu05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +mmu05414 Dilated cardiomyopathy (DCM) +mmu05416 Viral myocarditis +mmu05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rno_pathways.loc Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,326 @@ +rno00010 Glycolysis / Gluconeogenesis +rno00020 Citrate cycle (TCA cycle) +rno00030 Pentose phosphate pathway +rno00040 Pentose and glucuronate interconversions +rno00051 Fructose and mannose metabolism +rno00052 Galactose metabolism +rno00053 Ascorbate and aldarate metabolism +rno00061 Fatty acid biosynthesis +rno00062 Fatty acid elongation +rno00071 Fatty acid degradation +rno00072 Synthesis and degradation of ketone bodies +rno00100 Steroid biosynthesis +rno00120 Primary bile acid biosynthesis +rno00130 Ubiquinone and other terpenoid-quinone biosynthesis +rno00140 Steroid hormone biosynthesis +rno00190 Oxidative phosphorylation +rno00220 Arginine biosynthesis +rno00230 Purine metabolism +rno00232 Caffeine metabolism +rno00240 Pyrimidine metabolism +rno00250 Alanine, aspartate and glutamate metabolism +rno00260 Glycine, serine and threonine metabolism +rno00270 Cysteine and methionine metabolism +rno00280 Valine, leucine and isoleucine degradation +rno00290 Valine, leucine and isoleucine biosynthesis +rno00310 Lysine degradation +rno00330 Arginine and proline metabolism +rno00340 Histidine metabolism +rno00350 Tyrosine metabolism +rno00360 Phenylalanine metabolism +rno00380 Tryptophan metabolism +rno00400 Phenylalanine, tyrosine and tryptophan biosynthesis +rno00410 beta-Alanine metabolism +rno00430 Taurine and hypotaurine metabolism +rno00440 Phosphonate and phosphinate metabolism +rno00450 Selenocompound metabolism +rno00471 D-Glutamine and D-glutamate metabolism +rno00472 D-Arginine and D-ornithine metabolism +rno00480 Glutathione metabolism +rno00500 Starch and sucrose metabolism +rno00510 N-Glycan biosynthesis +rno00511 Other glycan degradation +rno00512 Mucin type O-glycan biosynthesis +rno00514 Other types of O-glycan biosynthesis +rno00515 Mannose type O-glycan biosynthesis +rno00520 Amino sugar and nucleotide sugar metabolism +rno00524 Neomycin, kanamycin and gentamicin biosynthesis +rno00531 Glycosaminoglycan degradation +rno00532 Glycosaminoglycan biosynthesis +rno00533 Glycosaminoglycan biosynthesis +rno00534 Glycosaminoglycan biosynthesis +rno00561 Glycerolipid metabolism +rno00562 Inositol phosphate metabolism +rno00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +rno00564 Glycerophospholipid metabolism +rno00565 Ether lipid metabolism +rno00590 Arachidonic acid metabolism +rno00591 Linoleic acid metabolism +rno00592 alpha-Linolenic acid metabolism +rno00600 Sphingolipid metabolism +rno00601 Glycosphingolipid biosynthesis +rno00603 Glycosphingolipid biosynthesis +rno00604 Glycosphingolipid biosynthesis +rno00620 Pyruvate metabolism +rno00630 Glyoxylate and dicarboxylate metabolism +rno00640 Propanoate metabolism +rno00650 Butanoate metabolism +rno00670 One carbon pool by folate +rno00730 Thiamine metabolism +rno00740 Riboflavin metabolism +rno00750 Vitamin B6 metabolism +rno00760 Nicotinate and nicotinamide metabolism +rno00770 Pantothenate and CoA biosynthesis +rno00780 Biotin metabolism +rno00785 Lipoic acid metabolism +rno00790 Folate biosynthesis +rno00830 Retinol metabolism +rno00860 Porphyrin and chlorophyll metabolism +rno00900 Terpenoid backbone biosynthesis +rno00910 Nitrogen metabolism +rno00920 Sulfur metabolism +rno00970 Aminoacyl-tRNA biosynthesis +rno00980 Metabolism of xenobiotics by cytochrome P450 +rno00982 Drug metabolism +rno00983 Drug metabolism +rno01040 Biosynthesis of unsaturated fatty acids +rno01100 Metabolic pathways +rno01200 Carbon metabolism +rno01210 2-Oxocarboxylic acid metabolism +rno01212 Fatty acid metabolism +rno01230 Biosynthesis of amino acids +rno01521 EGFR tyrosine kinase inhibitor resistance +rno01522 Endocrine resistance +rno01523 Antifolate resistance +rno01524 Platinum drug resistance +rno02010 ABC transporters +rno03008 Ribosome biogenesis in eukaryotes +rno03010 Ribosome +rno03013 RNA transport +rno03015 mRNA surveillance pathway +rno03018 RNA degradation +rno03020 RNA polymerase +rno03022 Basal transcription factors +rno03030 DNA replication +rno03040 Spliceosome +rno03050 Proteasome +rno03060 Protein export +rno03320 PPAR signaling pathway +rno03410 Base excision repair +rno03420 Nucleotide excision repair +rno03430 Mismatch repair +rno03440 Homologous recombination +rno03450 Non-homologous end-joining +rno03460 Fanconi anemia pathway +rno04010 MAPK signaling pathway +rno04012 ErbB signaling pathway +rno04014 Ras signaling pathway +rno04015 Rap1 signaling pathway +rno04020 Calcium signaling pathway +rno04022 cGMP-PKG signaling pathway +rno04024 cAMP signaling pathway +rno04060 Cytokine-cytokine receptor interaction +rno04062 Chemokine signaling pathway +rno04064 NF-kappa B signaling pathway +rno04066 HIF-1 signaling pathway +rno04068 FoxO signaling pathway +rno04070 Phosphatidylinositol signaling system +rno04071 Sphingolipid signaling pathway +rno04072 Phospholipase D signaling pathway +rno04080 Neuroactive ligand-receptor interaction +rno04110 Cell cycle +rno04114 Oocyte meiosis +rno04115 p53 signaling pathway +rno04120 Ubiquitin mediated proteolysis +rno04122 Sulfur relay system +rno04130 SNARE interactions in vesicular transport +rno04136 Autophagy +rno04137 Mitophagy +rno04140 Autophagy +rno04141 Protein processing in endoplasmic reticulum +rno04142 Lysosome +rno04144 Endocytosis +rno04145 Phagosome +rno04146 Peroxisome +rno04150 mTOR signaling pathway +rno04151 PI3K-Akt signaling pathway +rno04152 AMPK signaling pathway +rno04210 Apoptosis +rno04211 Longevity regulating pathway +rno04213 Longevity regulating pathway +rno04215 Apoptosis +rno04216 Ferroptosis +rno04217 Necroptosis +rno04218 Cellular senescence +rno04260 Cardiac muscle contraction +rno04261 Adrenergic signaling in cardiomyocytes +rno04270 Vascular smooth muscle contraction +rno04310 Wnt signaling pathway +rno04330 Notch signaling pathway +rno04340 Hedgehog signaling pathway +rno04350 TGF-beta signaling pathway +rno04360 Axon guidance +rno04370 VEGF signaling pathway +rno04371 Apelin signaling pathway +rno04380 Osteoclast differentiation +rno04390 Hippo signaling pathway +rno04392 Hippo signaling pathway +rno04510 Focal adhesion +rno04512 ECM-receptor interaction +rno04514 Cell adhesion molecules (CAMs) +rno04520 Adherens junction +rno04530 Tight junction +rno04540 Gap junction +rno04550 Signaling pathways regulating pluripotency of stem cells +rno04610 Complement and coagulation cascades +rno04611 Platelet activation +rno04612 Antigen processing and presentation +rno04614 Renin-angiotensin system +rno04620 Toll-like receptor signaling pathway +rno04621 NOD-like receptor signaling pathway +rno04622 RIG-I-like receptor signaling pathway +rno04623 Cytosolic DNA-sensing pathway +rno04625 C-type lectin receptor signaling pathway +rno04630 JAK-STAT signaling pathway +rno04640 Hematopoietic cell lineage +rno04650 Natural killer cell mediated cytotoxicity +rno04657 IL-17 signaling pathway +rno04658 Th1 and Th2 cell differentiation +rno04659 Th17 cell differentiation +rno04660 T cell receptor signaling pathway +rno04662 B cell receptor signaling pathway +rno04664 Fc epsilon RI signaling pathway +rno04666 Fc gamma R-mediated phagocytosis +rno04668 TNF signaling pathway +rno04670 Leukocyte transendothelial migration +rno04672 Intestinal immune network for IgA production +rno04710 Circadian rhythm +rno04713 Circadian entrainment +rno04714 Thermogenesis +rno04720 Long-term potentiation +rno04721 Synaptic vesicle cycle +rno04722 Neurotrophin signaling pathway +rno04723 Retrograde endocannabinoid signaling +rno04724 Glutamatergic synapse +rno04725 Cholinergic synapse +rno04726 Serotonergic synapse +rno04727 GABAergic synapse +rno04728 Dopaminergic synapse +rno04730 Long-term depression +rno04740 Olfactory transduction +rno04742 Taste transduction +rno04744 Phototransduction +rno04750 Inflammatory mediator regulation of TRP channels +rno04810 Regulation of actin cytoskeleton +rno04910 Insulin signaling pathway +rno04911 Insulin secretion +rno04912 GnRH signaling pathway +rno04913 Ovarian steroidogenesis +rno04914 Progesterone-mediated oocyte maturation +rno04915 Estrogen signaling pathway +rno04916 Melanogenesis +rno04917 Prolactin signaling pathway +rno04918 Thyroid hormone synthesis +rno04919 Thyroid hormone signaling pathway +rno04920 Adipocytokine signaling pathway +rno04921 Oxytocin signaling pathway +rno04922 Glucagon signaling pathway +rno04923 Regulation of lipolysis in adipocytes +rno04924 Renin secretion +rno04925 Aldosterone synthesis and secretion +rno04926 Relaxin signaling pathway +rno04927 Cortisol synthesis and secretion +rno04928 Parathyroid hormone synthesis, secretion and action +rno04930 Type II diabetes mellitus +rno04931 Insulin resistance +rno04932 Non-alcoholic fatty liver disease (NAFLD) +rno04933 AGE-RAGE signaling pathway in diabetic complications +rno04934 Cushing syndrome +rno04940 Type I diabetes mellitus +rno04950 Maturity onset diabetes of the young +rno04960 Aldosterone-regulated sodium reabsorption +rno04961 Endocrine and other factor-regulated calcium reabsorption +rno04962 Vasopressin-regulated water reabsorption +rno04964 Proximal tubule bicarbonate reclamation +rno04966 Collecting duct acid secretion +rno04970 Salivary secretion +rno04971 Gastric acid secretion +rno04972 Pancreatic secretion +rno04973 Carbohydrate digestion and absorption +rno04974 Protein digestion and absorption +rno04975 Fat digestion and absorption +rno04976 Bile secretion +rno04977 Vitamin digestion and absorption +rno04978 Mineral absorption +rno04979 Cholesterol metabolism +rno05010 Alzheimer disease +rno05012 Parkinson disease +rno05014 Amyotrophic lateral sclerosis (ALS) +rno05016 Huntington disease +rno05020 Prion diseases +rno05030 Cocaine addiction +rno05031 Amphetamine addiction +rno05032 Morphine addiction +rno05033 Nicotine addiction +rno05034 Alcoholism +rno05100 Bacterial invasion of epithelial cells +rno05132 Salmonella infection +rno05133 Pertussis +rno05134 Legionellosis +rno05140 Leishmaniasis +rno05142 Chagas disease (American trypanosomiasis) +rno05143 African trypanosomiasis +rno05144 Malaria +rno05145 Toxoplasmosis +rno05146 Amoebiasis +rno05150 Staphylococcus aureus infection +rno05152 Tuberculosis +rno05160 Hepatitis C +rno05161 Hepatitis B +rno05162 Measles +rno05163 Human cytomegalovirus infection +rno05164 Influenza A +rno05165 Human papillomavirus infection +rno05166 Human T-cell leukemia virus 1 infection +rno05167 Kaposi sarcoma-associated herpesvirus infection +rno05168 Herpes simplex infection +rno05169 Epstein-Barr virus infection +rno05170 Human immunodeficiency virus 1 infection +rno05200 Pathways in cancer +rno05202 Transcriptional misregulation in cancer +rno05203 Viral carcinogenesis +rno05204 Chemical carcinogenesis +rno05205 Proteoglycans in cancer +rno05206 MicroRNAs in cancer +rno05210 Colorectal cancer +rno05211 Renal cell carcinoma +rno05212 Pancreatic cancer +rno05213 Endometrial cancer +rno05214 Glioma +rno05215 Prostate cancer +rno05216 Thyroid cancer +rno05217 Basal cell carcinoma +rno05218 Melanoma +rno05219 Bladder cancer +rno05220 Chronic myeloid leukemia +rno05221 Acute myeloid leukemia +rno05222 Small cell lung cancer +rno05223 Non-small cell lung cancer +rno05224 Breast cancer +rno05225 Hepatocellular carcinoma +rno05226 Gastric cancer +rno05230 Central carbon metabolism in cancer +rno05231 Choline metabolism in cancer +rno05310 Asthma +rno05320 Autoimmune thyroid disease +rno05321 Inflammatory bowel disease (IBD) +rno05322 Systemic lupus erythematosus +rno05323 Rheumatoid arthritis +rno05330 Allograft rejection +rno05332 Graft-versus-host disease +rno05340 Primary immunodeficiency +rno05410 Hypertrophic cardiomyopathy (HCM) +rno05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +rno05414 Dilated cardiomyopathy (DCM) +rno05416 Viral myocarditis +rno05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rno_pathways.loc.sample Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,326 @@ +rno00010 Glycolysis / Gluconeogenesis +rno00020 Citrate cycle (TCA cycle) +rno00030 Pentose phosphate pathway +rno00040 Pentose and glucuronate interconversions +rno00051 Fructose and mannose metabolism +rno00052 Galactose metabolism +rno00053 Ascorbate and aldarate metabolism +rno00061 Fatty acid biosynthesis +rno00062 Fatty acid elongation +rno00071 Fatty acid degradation +rno00072 Synthesis and degradation of ketone bodies +rno00100 Steroid biosynthesis +rno00120 Primary bile acid biosynthesis +rno00130 Ubiquinone and other terpenoid-quinone biosynthesis +rno00140 Steroid hormone biosynthesis +rno00190 Oxidative phosphorylation +rno00220 Arginine biosynthesis +rno00230 Purine metabolism +rno00232 Caffeine metabolism +rno00240 Pyrimidine metabolism +rno00250 Alanine, aspartate and glutamate metabolism +rno00260 Glycine, serine and threonine metabolism +rno00270 Cysteine and methionine metabolism +rno00280 Valine, leucine and isoleucine degradation +rno00290 Valine, leucine and isoleucine biosynthesis +rno00310 Lysine degradation +rno00330 Arginine and proline metabolism +rno00340 Histidine metabolism +rno00350 Tyrosine metabolism +rno00360 Phenylalanine metabolism +rno00380 Tryptophan metabolism +rno00400 Phenylalanine, tyrosine and tryptophan biosynthesis +rno00410 beta-Alanine metabolism +rno00430 Taurine and hypotaurine metabolism +rno00440 Phosphonate and phosphinate metabolism +rno00450 Selenocompound metabolism +rno00471 D-Glutamine and D-glutamate metabolism +rno00472 D-Arginine and D-ornithine metabolism +rno00480 Glutathione metabolism +rno00500 Starch and sucrose metabolism +rno00510 N-Glycan biosynthesis +rno00511 Other glycan degradation +rno00512 Mucin type O-glycan biosynthesis +rno00514 Other types of O-glycan biosynthesis +rno00515 Mannose type O-glycan biosynthesis +rno00520 Amino sugar and nucleotide sugar metabolism +rno00524 Neomycin, kanamycin and gentamicin biosynthesis +rno00531 Glycosaminoglycan degradation +rno00532 Glycosaminoglycan biosynthesis +rno00533 Glycosaminoglycan biosynthesis +rno00534 Glycosaminoglycan biosynthesis +rno00561 Glycerolipid metabolism +rno00562 Inositol phosphate metabolism +rno00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +rno00564 Glycerophospholipid metabolism +rno00565 Ether lipid metabolism +rno00590 Arachidonic acid metabolism +rno00591 Linoleic acid metabolism +rno00592 alpha-Linolenic acid metabolism +rno00600 Sphingolipid metabolism +rno00601 Glycosphingolipid biosynthesis +rno00603 Glycosphingolipid biosynthesis +rno00604 Glycosphingolipid biosynthesis +rno00620 Pyruvate metabolism +rno00630 Glyoxylate and dicarboxylate metabolism +rno00640 Propanoate metabolism +rno00650 Butanoate metabolism +rno00670 One carbon pool by folate +rno00730 Thiamine metabolism +rno00740 Riboflavin metabolism +rno00750 Vitamin B6 metabolism +rno00760 Nicotinate and nicotinamide metabolism +rno00770 Pantothenate and CoA biosynthesis +rno00780 Biotin metabolism +rno00785 Lipoic acid metabolism +rno00790 Folate biosynthesis +rno00830 Retinol metabolism +rno00860 Porphyrin and chlorophyll metabolism +rno00900 Terpenoid backbone biosynthesis +rno00910 Nitrogen metabolism +rno00920 Sulfur metabolism +rno00970 Aminoacyl-tRNA biosynthesis +rno00980 Metabolism of xenobiotics by cytochrome P450 +rno00982 Drug metabolism +rno00983 Drug metabolism +rno01040 Biosynthesis of unsaturated fatty acids +rno01100 Metabolic pathways +rno01200 Carbon metabolism +rno01210 2-Oxocarboxylic acid metabolism +rno01212 Fatty acid metabolism +rno01230 Biosynthesis of amino acids +rno01521 EGFR tyrosine kinase inhibitor resistance +rno01522 Endocrine resistance +rno01523 Antifolate resistance +rno01524 Platinum drug resistance +rno02010 ABC transporters +rno03008 Ribosome biogenesis in eukaryotes +rno03010 Ribosome +rno03013 RNA transport +rno03015 mRNA surveillance pathway +rno03018 RNA degradation +rno03020 RNA polymerase +rno03022 Basal transcription factors +rno03030 DNA replication +rno03040 Spliceosome +rno03050 Proteasome +rno03060 Protein export +rno03320 PPAR signaling pathway +rno03410 Base excision repair +rno03420 Nucleotide excision repair +rno03430 Mismatch repair +rno03440 Homologous recombination +rno03450 Non-homologous end-joining +rno03460 Fanconi anemia pathway +rno04010 MAPK signaling pathway +rno04012 ErbB signaling pathway +rno04014 Ras signaling pathway +rno04015 Rap1 signaling pathway +rno04020 Calcium signaling pathway +rno04022 cGMP-PKG signaling pathway +rno04024 cAMP signaling pathway +rno04060 Cytokine-cytokine receptor interaction +rno04062 Chemokine signaling pathway +rno04064 NF-kappa B signaling pathway +rno04066 HIF-1 signaling pathway +rno04068 FoxO signaling pathway +rno04070 Phosphatidylinositol signaling system +rno04071 Sphingolipid signaling pathway +rno04072 Phospholipase D signaling pathway +rno04080 Neuroactive ligand-receptor interaction +rno04110 Cell cycle +rno04114 Oocyte meiosis +rno04115 p53 signaling pathway +rno04120 Ubiquitin mediated proteolysis +rno04122 Sulfur relay system +rno04130 SNARE interactions in vesicular transport +rno04136 Autophagy +rno04137 Mitophagy +rno04140 Autophagy +rno04141 Protein processing in endoplasmic reticulum +rno04142 Lysosome +rno04144 Endocytosis +rno04145 Phagosome +rno04146 Peroxisome +rno04150 mTOR signaling pathway +rno04151 PI3K-Akt signaling pathway +rno04152 AMPK signaling pathway +rno04210 Apoptosis +rno04211 Longevity regulating pathway +rno04213 Longevity regulating pathway +rno04215 Apoptosis +rno04216 Ferroptosis +rno04217 Necroptosis +rno04218 Cellular senescence +rno04260 Cardiac muscle contraction +rno04261 Adrenergic signaling in cardiomyocytes +rno04270 Vascular smooth muscle contraction +rno04310 Wnt signaling pathway +rno04330 Notch signaling pathway +rno04340 Hedgehog signaling pathway +rno04350 TGF-beta signaling pathway +rno04360 Axon guidance +rno04370 VEGF signaling pathway +rno04371 Apelin signaling pathway +rno04380 Osteoclast differentiation +rno04390 Hippo signaling pathway +rno04392 Hippo signaling pathway +rno04510 Focal adhesion +rno04512 ECM-receptor interaction +rno04514 Cell adhesion molecules (CAMs) +rno04520 Adherens junction +rno04530 Tight junction +rno04540 Gap junction +rno04550 Signaling pathways regulating pluripotency of stem cells +rno04610 Complement and coagulation cascades +rno04611 Platelet activation +rno04612 Antigen processing and presentation +rno04614 Renin-angiotensin system +rno04620 Toll-like receptor signaling pathway +rno04621 NOD-like receptor signaling pathway +rno04622 RIG-I-like receptor signaling pathway +rno04623 Cytosolic DNA-sensing pathway +rno04625 C-type lectin receptor signaling pathway +rno04630 JAK-STAT signaling pathway +rno04640 Hematopoietic cell lineage +rno04650 Natural killer cell mediated cytotoxicity +rno04657 IL-17 signaling pathway +rno04658 Th1 and Th2 cell differentiation +rno04659 Th17 cell differentiation +rno04660 T cell receptor signaling pathway +rno04662 B cell receptor signaling pathway +rno04664 Fc epsilon RI signaling pathway +rno04666 Fc gamma R-mediated phagocytosis +rno04668 TNF signaling pathway +rno04670 Leukocyte transendothelial migration +rno04672 Intestinal immune network for IgA production +rno04710 Circadian rhythm +rno04713 Circadian entrainment +rno04714 Thermogenesis +rno04720 Long-term potentiation +rno04721 Synaptic vesicle cycle +rno04722 Neurotrophin signaling pathway +rno04723 Retrograde endocannabinoid signaling +rno04724 Glutamatergic synapse +rno04725 Cholinergic synapse +rno04726 Serotonergic synapse +rno04727 GABAergic synapse +rno04728 Dopaminergic synapse +rno04730 Long-term depression +rno04740 Olfactory transduction +rno04742 Taste transduction +rno04744 Phototransduction +rno04750 Inflammatory mediator regulation of TRP channels +rno04810 Regulation of actin cytoskeleton +rno04910 Insulin signaling pathway +rno04911 Insulin secretion +rno04912 GnRH signaling pathway +rno04913 Ovarian steroidogenesis +rno04914 Progesterone-mediated oocyte maturation +rno04915 Estrogen signaling pathway +rno04916 Melanogenesis +rno04917 Prolactin signaling pathway +rno04918 Thyroid hormone synthesis +rno04919 Thyroid hormone signaling pathway +rno04920 Adipocytokine signaling pathway +rno04921 Oxytocin signaling pathway +rno04922 Glucagon signaling pathway +rno04923 Regulation of lipolysis in adipocytes +rno04924 Renin secretion +rno04925 Aldosterone synthesis and secretion +rno04926 Relaxin signaling pathway +rno04927 Cortisol synthesis and secretion +rno04928 Parathyroid hormone synthesis, secretion and action +rno04930 Type II diabetes mellitus +rno04931 Insulin resistance +rno04932 Non-alcoholic fatty liver disease (NAFLD) +rno04933 AGE-RAGE signaling pathway in diabetic complications +rno04934 Cushing syndrome +rno04940 Type I diabetes mellitus +rno04950 Maturity onset diabetes of the young +rno04960 Aldosterone-regulated sodium reabsorption +rno04961 Endocrine and other factor-regulated calcium reabsorption +rno04962 Vasopressin-regulated water reabsorption +rno04964 Proximal tubule bicarbonate reclamation +rno04966 Collecting duct acid secretion +rno04970 Salivary secretion +rno04971 Gastric acid secretion +rno04972 Pancreatic secretion +rno04973 Carbohydrate digestion and absorption +rno04974 Protein digestion and absorption +rno04975 Fat digestion and absorption +rno04976 Bile secretion +rno04977 Vitamin digestion and absorption +rno04978 Mineral absorption +rno04979 Cholesterol metabolism +rno05010 Alzheimer disease +rno05012 Parkinson disease +rno05014 Amyotrophic lateral sclerosis (ALS) +rno05016 Huntington disease +rno05020 Prion diseases +rno05030 Cocaine addiction +rno05031 Amphetamine addiction +rno05032 Morphine addiction +rno05033 Nicotine addiction +rno05034 Alcoholism +rno05100 Bacterial invasion of epithelial cells +rno05132 Salmonella infection +rno05133 Pertussis +rno05134 Legionellosis +rno05140 Leishmaniasis +rno05142 Chagas disease (American trypanosomiasis) +rno05143 African trypanosomiasis +rno05144 Malaria +rno05145 Toxoplasmosis +rno05146 Amoebiasis +rno05150 Staphylococcus aureus infection +rno05152 Tuberculosis +rno05160 Hepatitis C +rno05161 Hepatitis B +rno05162 Measles +rno05163 Human cytomegalovirus infection +rno05164 Influenza A +rno05165 Human papillomavirus infection +rno05166 Human T-cell leukemia virus 1 infection +rno05167 Kaposi sarcoma-associated herpesvirus infection +rno05168 Herpes simplex infection +rno05169 Epstein-Barr virus infection +rno05170 Human immunodeficiency virus 1 infection +rno05200 Pathways in cancer +rno05202 Transcriptional misregulation in cancer +rno05203 Viral carcinogenesis +rno05204 Chemical carcinogenesis +rno05205 Proteoglycans in cancer +rno05206 MicroRNAs in cancer +rno05210 Colorectal cancer +rno05211 Renal cell carcinoma +rno05212 Pancreatic cancer +rno05213 Endometrial cancer +rno05214 Glioma +rno05215 Prostate cancer +rno05216 Thyroid cancer +rno05217 Basal cell carcinoma +rno05218 Melanoma +rno05219 Bladder cancer +rno05220 Chronic myeloid leukemia +rno05221 Acute myeloid leukemia +rno05222 Small cell lung cancer +rno05223 Non-small cell lung cancer +rno05224 Breast cancer +rno05225 Hepatocellular carcinoma +rno05226 Gastric cancer +rno05230 Central carbon metabolism in cancer +rno05231 Choline metabolism in cancer +rno05310 Asthma +rno05320 Autoimmune thyroid disease +rno05321 Inflammatory bowel disease (IBD) +rno05322 Systemic lupus erythematosus +rno05323 Rheumatoid arthritis +rno05330 Allograft rejection +rno05332 Graft-versus-host disease +rno05340 Primary immunodeficiency +rno05410 Hypertrophic cardiomyopathy (HCM) +rno05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +rno05414 Dilated cardiomyopathy (DCM) +rno05416 Viral myocarditis +rno05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Dec 18 10:02:54 2018 -0500 @@ -0,0 +1,19 @@ +<tables> + <!-- Location kegg_pathways file for pathview tool --> + <table name="kegg_pathways_list_index" comment_char="#"> + <columns>value,name,path</columns> + <file path="tool-data/kegg_pathways_list_index.loc"/> + </table> + <table name="hsa_pathways" comment_char="#"> + <columns>value,name</columns> + <file path="tool-data/hsa_pathways.loc" /> + </table> + <table name="mmu_pathways" comment_char="#"> + <columns>value,name</columns> + <file path="tool-data/mmu_pathways.loc" /> + </table> + <table name="rno_pathways" comment_char="#"> + <columns>value,name</columns> + <file path="tool-data/rno_pathways.loc" /> + </table> +</tables>