| Next changeset 1:09ba28df72ad (2018-03-01) |
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planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty |
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GO-enrich.R README.rst cluster_profiler.xml test-data/Lacombe_et_al_2017_OK.txt test-data/clusterProfiler_diagram_outputs__GGO.CC.png test-data/clusterProfiler_text_output.tabular |
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| diff -r 000000000000 -r bd052861852b GO-enrich.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GO-enrich.R Thu Mar 01 10:05:18 2018 -0500 |
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| @@ -0,0 +1,167 @@ +library(clusterProfiler) + +#library(org.Sc.sgd.db) +library(org.Hs.eg.db) +library(org.Mm.eg.db) + +# Read file and return file content as data.frame? +readfile = function(filename, header) { + if (header == "true") { + # Read only the first line of the files as data (without headers): + headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE) + #Read the data of the files (skipping the first row): + file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE) + # Remove empty rows + file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] + #And assign the headers of step two to the data: + names(file) <- headers + } + else { + file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE) + file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] + } + return(file) +} + +repartition.GO <- function(geneid, orgdb, ontology, level=3, readable=TRUE) { + ggo<-groupGO(gene=geneid, + OrgDb = orgdb, + ont=ontology, + level=level, + readable=TRUE) + name <- paste("GGO.", ontology, ".png", sep = "") + png(name) + p <- barplot(ggo) + print(p) + dev.off() + return(ggo) +} + +# GO over-representation test +enrich.GO <- function(geneid, orgdb, ontology, pval_cutoff, qval_cutoff) { + ego<-enrichGO(gene=geneid, + OrgDb=orgdb, + keytype="ENTREZID", + ont=ontology, + pAdjustMethod="BH", + pvalueCutoff=pval_cutoff, + qvalueCutoff=qval_cutoff, + readable=TRUE) + bar_name <- paste("EGO.", ontology, ".bar.png", sep = "") + png(bar_name) + p <- barplot(ego) + print(p) + dev.off() + dot_name <- paste("EGO.", ontology, ".dot.png", sep = "") + png(dot_name) + p <- dotplot(ego) + print(p) + dev.off() + return(ego) +} + +clusterProfiler = function() { + args <- commandArgs(TRUE) + if(length(args)<1) { + args <- c("--help") + } + + # Help section + if("--help" %in% args) { + cat("clusterProfiler Enrichment Analysis + Arguments: + --input_type: type of input (list of id or filename) + --input: input + --ncol: the column number which you would like to apply... + --header: true/false if your file contains a header + --id_type: the type of input IDs (UniProt/EntrezID) + --species + --onto_opt: ontology options + --go_function: groupGO/enrichGO + --level: 1-3 + --pval_cutoff + --qval_cutoff + --text_output: text output filename \n") + q(save="no") + } + # Parse arguments + 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 + + input_type = args$input_type + if (input_type == "text") { + input = args$input + } + else if (input_type == "file") { + filename = args$input + ncol = args$ncol + # Check ncol + if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) { + stop("Please enter an integer for level") + } + else { + ncol = as.numeric(gsub("c", "", ncol)) + } + header = args$header + # Get file content + file = readfile(filename, header) + # Extract Protein IDs list + input = c() + for (row in as.character(file[,ncol])) { + input = c(input, strsplit(row, ";")[[1]][1]) + } + } + id_type = args$id_type + + + #ID format Conversion + #This case : from UNIPROT (protein id) to ENTREZ (gene id) + #bitr = conversion function from clusterProfiler + + if (args$species=="human") { + orgdb<-org.Hs.eg.db + } + else if (args$species=="mouse") { + orgdb<-org.Mm.eg.db + } + else if (args$species=="rat") { + orgdb<-org.Rn.eg.db + } + + ##to initialize + if (id_type=="Uniprot") { + idFrom<-"UNIPROT" + idTo<-"ENTREZID" + gene<-bitr(input, fromType=idFrom, toType=idTo, OrgDb=orgdb) + } + else if (id_type=="Entrez") { + gene<-input + } + + ontology <- strsplit(args$onto_opt, ",")[[1]] + if (args$go_represent == "true") { + go_represent <- args$go_represent + level <- as.numeric(args$level) + } + if (args$go_enrich == "true") { + go_enrich <- args$go_enrich + pval_cutoff <- as.numeric(args$pval_cutoff) + qval_cutoff <- as.numeric(args$qval_cutoff) + } + + ##enrichGO : GO over-representation test + for (onto in ontology) { + if (args$go_represent == "true") { + ggo<-repartition.GO(gene$ENTREZID, orgdb, onto, level, readable=TRUE) + write.table(ggo, args$text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE) + } + if (args$go_enrich == "true") { + ego<-enrich.GO(gene$ENTREZID, orgdb, onto, pval_cutoff, qval_cutoff) + write.table(ego, args$text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE) + } + } +} + +clusterProfiler() |
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| diff -r 000000000000 -r bd052861852b README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Mar 01 10:05:18 2018 -0500 |
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| @@ -0,0 +1,45 @@ +Wrapper for clusterProfiler Enrichment Analysis Tool +==================================================== + +**Authors** + +clusterProfiler R package reference : +G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. +OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. +doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118) + + +**Galaxy integration** + +T.P. Lien Nguyen, 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. + + +=================== + +**Galaxy component based on R package clusterProfiler (see ref below)** + +This component allows to perform GO enrichment-analyses. +Given a list of IDs, the tool either +(i) performs gene classification based on GO distribution at a specific level, or +(ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, +compared to a background (whole organism or user-defined list). + +**Input required** + +This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). +You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained. + + +**Output** + +Text (tables) and graphics representing the repartition and/or enrichment of GO categories. + +**User manual / Documentation** of the clusterProfiler R package (functions and parameters): +https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html +(Very well explained) \ No newline at end of file |
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| diff -r 000000000000 -r bd052861852b cluster_profiler.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cluster_profiler.xml Thu Mar 01 10:05:18 2018 -0500 |
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| b'@@ -0,0 +1,205 @@\n+<tool id="cluter_profiler" name="clusterProfiler Enrichment Analysis" version="0.1.0">\n+ <requirements>\n+ <requirement type="package" version="3.4.1">R</requirement>\n+ <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>\n+ <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>\n+ <requirement type="package" version="3.2.0">bioconductor-dose</requirement>\n+ <requirement type="package" version="3.0.5">bioconductor-clusterprofiler</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ Rscript "$__tool_directory__/GO-enrich.R"\n+ #if $input.ids == "text"\n+ --input_type="text"\n+ --input="$input.text"\n+ #else\n+ --input_type="file"\n+ --input="$input.file"\n+ --ncol="$input.ncol"\n+ --header="$input.header"\n+ #end if\n+ \n+ --id_type="$idti.idtypein"\n+\n+ --species="$species"\n+\n+ #if $ggo.go_represent == "true"\n+ --go_represent="true"\n+ --level="$ggo.level"\n+ #else\n+ --go_represent="false"\n+ #end if\n+\n+ #if $ego.go_enrich == "true"\n+ --go_enrich="true"\n+ --pval_cutoff="$ego.pval"\n+ --qval_cutoff="$ego.qval"\n+ #else\n+ --go_enrich="false"\n+ #end if\n+ \n+ --onto_opt="$ontology"\n+\n+ --text_output="$text_output"\n+ ]]></command>\n+ <inputs>\n+ <conditional name="input" >\n+ <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >\n+ <option value="text">Copy/paste your identifiers</option>\n+ <option value="file">Input file containing your identifiers</option>\n+ </param>\n+ <when value="text" >\n+ <param name="txt" type="text" label="Copy/paste your identifiers" help=\'IDs must be separated by spaces into the form field, for example: P31946 P62258\' >\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="'"/>\n+ </valid>\n+ <mapping initial="none">\n+ <add source="'" target="__sq__"/>\n+ </mapping>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ <when value="file" >\n+ <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />\n+ <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />\n+ <param name="ncol" type="text" label="The column number of 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\' /> \n+ </when>\n+ </conditional>\n+ <conditional name="idti" >\n+ <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >\n+ <option value="Uniprot">UniProt accession number</option>\n+ <option value="Entrez">Entrez Gene ID</option>\n+ </param>\n+ <when value="Uniprot"/>\n+ <when value="Entrez"/>\n+ </conditional>\n+ <param name="species" type="select" label="Select a species" >\n+ <option value="human">Human</option>\n+ <option value="mouse">Mouse</option>\n+ <option value="rat">Rat</option>\n+ </param>\n+ <conditional name="ggo">\n+ <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories representation analysis?"/>\n+ '..b' <when value="ego" >\n+\t\t\t <param name="pval" type="float" value="0.01" label="P-value cut off"/>\n+\t\t\t <param name="qval" type="float" value="0.05" label="Q-value cut off"/>\n+\t\t </when>\n+\t </conditional-->\n+\t\t\t\t\n+\t\t<param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">\n+ <option value="CC">Cellular Component</option>\n+ <option value="BP">Biological Process</option>\n+ <option value="MF">Molecular Function</option>\n+ </param>\n+\t \n+\t \n+\t \n+ </inputs>\n+ <outputs>\n+ <data name="text_output" format="tabular" label="clusterProfiler text output" />\n+ <collection type="list" label="clusterProfiler diagram outputs" name="output" >\n+\t <discover_datasets pattern="(?P<designation>.+\\.png)" ext="png" />\n+\t</collection>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <conditional name="input">\n+ <param name="ids" value="file"/>\n+ <param name="file" value="Lacombe_et_al_2017_OK.txt"/>\n+ <param name="header" value="true"/>\n+ <param name="ncol" value="c1"/>\n+ </conditional>\n+ <conditional name="idti">\n+ <param name="idtypein" value="Uniprot"/>\n+ </conditional>\n+ <param name="species" value="human"/>\n+ <conditional name="ggo">\n+ <param name="go_represent" value="true"/>\n+ <param name="level" value="3"/>\n+ </conditional>\n+ <conditional name="ego">\n+ <param name="go_enrich" value="false"/>\n+ </conditional>\n+ <param name="ontology" value="CC"/>\n+ <output name="text_output" file="clusterProfiler_text_output.tabular"/>\n+ <output_collection name="output">\n+ <element name="clusterProfiler_diagram_outputs__GGO.CC.png" file="clusterProfiler_diagram_outputs__GGO.CC.png" ftype="png"/>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><\n+\n+\t\n+\t**Galaxy integration**\n+\n+\tT.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR\n+\n+\tSandra D\xc3\xa9rozier, Olivier Ru\xc3\xa9, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform\n+\n+\tThis work has been partially funded through the French National Agency for Research (ANR) IFB project.\n+\n+\tContact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.\n+\n+\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r bd052861852b test-data/Lacombe_et_al_2017_OK.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Lacombe_et_al_2017_OK.txt Thu Mar 01 10:05:18 2018 -0500 |
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| @@ -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 + + + |
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| diff -r 000000000000 -r bd052861852b test-data/clusterProfiler_text_output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clusterProfiler_text_output.tabular Thu Mar 01 10:05:18 2018 -0500 |
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| b'@@ -0,0 +1,378 @@\n+ID\tDescription\tCount\tGeneRatio\tgeneID\n+GO:0005886\tplasma membrane\t56\t56/153\tDSP/DSG1/ANXA2/JUP/MUC5B/ACTG1/FABP5/PIGR/ENO1/AZGP1/PLEC/TGM3/HRNR/ANXA1/HSPA5/TF/CAT/SERPINB12/CSTA/GAPDH/EEF2/MYH9/HSP90AA1/UBA52/FLNB/SOD1/HSPB1/HSPA8/EPPK1/GSTP1/DSC3/C1orf68/CTSV/CAPN1/VCL/YWHAE/IL1RN/SPRR1B/CST6/GSN/IDE/LYPD3/FLG/PERP/RPSA/LAMP1/LAMP2/RPS3/ATP5A1/PIP/MUC7/KRT1/KRT2/KRT10/SERPINA12/SPRR2E\n+GO:0005628\tprospore membrane\t0\t0/153\t\n+GO:0005789\tendoplasmic reticulum membrane\t1\t1/153\tHSPA5\n+GO:0019867\touter membrane\t2\t2/153\tARG1/UBA52\n+GO:0031090\torganelle membrane\t24\t24/153\tDSP/DSG1/ANXA2/FABP5/PIGR/LMNA/ANXA1/TF/CAT/SFN/SERPINB12/ARG1/GAPDH/SERPINA1/UBA52/DMBT1/HSPA8/YWHAZ/YWHAE/MDH2/LAMP1/LAMP2/RPS3/ATP5A1\n+GO:0034357\tphotosynthetic membrane\t0\t0/153\t\n+GO:0036362\tascus membrane\t0\t0/153\t\n+GO:0042175\tnuclear outer membrane-endoplasmic reticulum membrane network\t1\t1/153\tHSPA5\n+GO:0044425\tmembrane part\t28\t28/153\tDSP/DSG1/ANXA2/JUP/PIGR/TGM3/ANXA1/HSPA5/TF/EEF2/MYH9/TUBA1B/HSP90AA1/CTSD/DMBT1/FLNB/HSPA8/EPPK1/DSC3/CTSV/PGK1/LYPD3/PERP/LAMP1/LAMP2/RPS3/ATP5A1/PIP\n+GO:0048475\tcoated membrane\t0\t0/153\t\n+GO:0055036\tvirion membrane\t0\t0/153\t\n+GO:0098552\tside of membrane\t8\t8/153\tDSG1/JUP/TGM3/ANXA1/TF/HSPA8/CTSV/LAMP1\n+GO:0098589\tmembrane region\t7\t7/153\tANXA2/TF/EEF2/TUBA1B/CTSD/PGK1/LAMP2\n+GO:0098590\tplasma membrane region\t10\t10/153\tDSP/DSG1/ANXA2/JUP/ANXA1/TF/HSP90AA1/EPPK1/RPS3/PIP\n+GO:0098796\tmembrane protein complex\t3\t3/153\tJUP/MYH9/ATP5A1\n+GO:0098805\twhole membrane\t19\t19/153\tDSP/DSG1/ANXA2/FABP5/PIGR/ANXA1/TF/CAT/SERPINB12/ARG1/EEF2/TUBA1B/CTSD/UBA52/DMBT1/HSPA8/PGK1/LAMP1/LAMP2\n+GO:1990195\tmacrolide transmembrane transporter complex\t0\t0/153\t\n+GO:1990196\tMacAB-TolC complex\t0\t0/153\t\n+GO:1990578\tperinuclear endoplasmic reticulum membrane\t0\t0/153\t\n+GO:1990850\tH-gal-GP complex\t0\t0/153\t\n+GO:0010367\textracellular isoamylase complex\t0\t0/153\t\n+GO:0031012\textracellular matrix\t28\t28/153\tDSP/DSG1/ANXA2/JUP/ACTG1/CASP14/PLEC/LMNA/HSPA5/PKM/PRDX1/CSTA/GAPDH/EEF2/MYH9/TUBB4B/SERPINA1/CTSD/FLNB/SOD1/HSPB1/HSPA8/EIF4A1/SBSN/RPS3/ATP5A1/KRT1/DCD\n+GO:0043083\tsynaptic cleft\t0\t0/153\t\n+GO:0043230\textracellular organelle\t130\t130/153\tDSP/KRT6A/ALB/KRT16/DSG1/ANXA2/JUP/LTF/MUC5B/SERPINB3/ACTG1/KRT78/KRT17/FABP5/CASP14/PIGR/ENO1/AZGP1/PLEC/TGM3/KRT13/HRNR/KRT6B/ANXA1/HSPA5/TF/CAT/S100A7/SFN/SERPINB12/PKM/TPI1/PRDX1/CSTA/ARG1/GAPDH/HSPA1A/HSPA1B/EEF2/MYH9/TUBB4B/LYZ/TUBA1B/SERPINA1/HSP90AA1/ACTN4/GGCT/LDHA/CTSD/UBA52/TXN/DMBT1/LGALS7B/BLMH/FLNB/SOD1/HSPB1/HSPA8/EIF4A1/PPIA/YWHAZ/GGH/GSTP1/LCN1/SERPINB4/C1orf68/SBSN/CTSV/PGK1/ALDOA/CAPN1/VCL/YWHAE/HBB/A2ML1/HP/SERPINA3/ORM1/IL1RN/SPRR1B/SERPINB1/LCN2/CST6/S100A14/GSN/AGA/PSMA3/EEF1G/SERPINB5/MDH2/FCGBP/PNP/CSTB/ALDOC/KRT15/SERPINB13/APOD/KLK1/CTSB/RPSA/LAMP1/LAMP2/PPIB/RPS3/ATP5A1/CALML3/S100A11/CAPG/CAPZB/GSS/PSMB3/GDI2/ARPC4/ACTR2/NPC2/AMY1A/AMY1B/AMY1C/CALML5/PIP/ZG16B/CST4/MUC7/KRT1/KRT2/KRT10/FLG2/KPRP/DCD/DEFA3\n+GO:0044421\textracellular region part\t141\t141/153\tDSP/KRT6A/ALB/KRT16/DSG1/ANXA2/JUP/LTF/MUC5B/SERPINB3/ACTG1/KRT78/KRT17/FABP5/CASP14/PIGR/ENO1/AZGP1/PLEC/TGM3/KRT13/HRNR/KRT6B/LMNA/ANXA1/HSPA5/TF/CAT/S100A7/SFN/SERPINB12/PKM/TPI1/PRDX1/CSTA/ARG1/GAPDH/HSPA1A/HSPA1B/EEF2/MYH9/TUBB4B/SERPINB7/LYZ/TUBA1B/SERPINA1/HSP90AA1/IL36G/ACTN4/GGCT/LDHA/CTSD/UBA52/TXN/DMBT1/CPA4/LGALS7B/BLMH/PLBD1/FLNB/SOD1/HSPB1/HSPA8/EIF4A1/PPIA/YWHAZ/GGH/GSTP1/LCN1/SERPINB4/C1orf68/SBSN/CTSV/PGK1/ALDOA/CAPN1/VCL/YWHAE/HBB/A2ML1/HP/SERPINA3/ORM1/IL1RN/SPRR1B/SERPINB1/LCN2/CST6/S100A14/GSN/IDE/AGA/PSMA3/EEF1G/SERPINB5/MDH2/FCGBP/LYPD3/PNP/CSTB/ALDOC/KRT15/SERPINB13/APOD/KLK1/CTSB/RPSA/LAMP1/LAMP2/PPIB/RPS3/ATP5A1/CALML3/S100A11/CAPG/CAPZB/GSS/PSMB3/GDI2/ARPC4/ACTR2/NPC2/AMY1A/AMY1B/AMY1C/CALML5/PIP/ZG16B/CST4/MUC7/CST1/CST2/KRT1/KRT2/KRT10/FLG2/KPRP/SERPINA12/DCD/DEFA3/KRT85\n+GO:0048046\tapoplast\t0\t0/153\t\n+GO:0070062\textracellular exosome\t130\t130/153\tDSP/KRT6A/ALB/KRT16/DSG1/ANXA2/JUP/LTF/MUC5B/SERPINB3/ACTG1/KRT78/KRT17/FABP5/CASP14/PIGR/ENO1/AZGP1/PLEC/TGM3/KRT13/HRNR/KRT6B/ANXA1/HSPA5/TF/CAT/S100A7/SFN/SERPINB'..b'A2\n+GO:0043684\ttype IV secretion system complex\t0\t0/153\t\n+GO:0044099\tpolar tube\t0\t0/153\t\n+GO:0044297\tcell body\t6\t6/153\tARG1/FLNB/SOD1/CTSV/APOD/LAMP1\n+GO:0044424\tintracellular part\t133\t133/153\tDSP/KRT6A/ALB/KRT16/DSG1/ANXA2/JUP/LTF/MUC5B/SERPINB3/ACTG1/KRT78/KRT17/FABP5/CASP14/PIGR/ENO1/AZGP1/PLEC/KRT80/TGM3/KRT13/HRNR/KRT6B/LMNA/ANXA1/HSPA5/TF/CAT/S100A7/SFN/SERPINB12/PKM/TPI1/PRDX1/CSTA/ARG1/GAPDH/HSPA1A/HSPA1B/EEF2/MYH9/TUBB4B/SERPINB7/LYZ/TUBA1B/SERPINA1/HSP90AA1/ACTN4/GGCT/LDHA/CTSD/UBA52/TXN/DMBT1/LGALS7B/BLMH/PLBD1/FLNB/SOD1/HSPB1/HSPA8/EPPK1/EIF4A1/PPIA/YWHAZ/GGH/ALOX12B/GSTP1/SERPINB4/DSC3/C1orf68/CTSV/PGK1/ALDOA/CAPN1/VCL/YWHAE/HBB/KRT23/HP/SERPINA3/ORM1/IL1RN/SPRR1B/SERPINB1/LCN2/S100A14/GSN/IDE/AGA/PSMA3/EEF1G/SERPINB5/MDH2/PNP/CSTB/ALDOC/KRT15/FLG/PERP/SERPINB13/APOD/KLK1/CTSB/RPSA/LAMP1/LAMP2/TYMP/PPIB/RPS3/ATP5A1/S100A11/CAPG/HAL/CAPZB/GSS/PSMB3/GDI2/ARPC4/ACTR2/NPC2/CALML5/PIP/MUC7/KRT1/KRT2/KRT10/FLG2/KPRP/SPRR2E/DEFA3/KRT85\n+GO:0044457\tcell septum part\t0\t0/153\t\n+GO:0044462\texternal encapsulating structure part\t0\t0/153\t\n+GO:0044463\tcell projection part\t5\t5/153\tHSP90AA1/SOD1/HSPB1/YWHAE/RPS3\n+GO:0044697\tHICS complex\t0\t0/153\t\n+GO:0045177\tapical part of cell\t5\t5/153\tDSG1/ANXA1/TF/CTSV/PIP\n+GO:0045178\tbasal part of cell\t1\t1/153\tTF\n+GO:0051286\tcell tip\t0\t0/153\t\n+GO:0060187\tcell pole\t0\t0/153\t\n+GO:0061835\tventral surface of cell\t0\t0/153\t\n+GO:0070056\tprospore membrane leading edge\t0\t0/153\t\n+GO:0070258\tinner membrane complex\t0\t0/153\t\n+GO:0070331\tCD20-Lck-Fyn complex\t0\t0/153\t\n+GO:0070332\tCD20-Lck-Lyn-Fyn complex\t0\t0/153\t\n+GO:0070938\tcontractile ring\t1\t1/153\tMYH9\n+GO:0071944\tcell periphery\t59\t59/153\tDSP/DSG1/ANXA2/JUP/MUC5B/ACTG1/KRT17/FABP5/PIGR/ENO1/AZGP1/PLEC/TGM3/HRNR/ANXA1/HSPA5/TF/CAT/SERPINB12/CSTA/GAPDH/EEF2/MYH9/HSP90AA1/ACTN4/UBA52/FLNB/SOD1/HSPB1/HSPA8/EPPK1/GSTP1/DSC3/C1orf68/CTSV/CAPN1/VCL/YWHAE/IL1RN/SPRR1B/CST6/GSN/IDE/LYPD3/FLG/PERP/RPSA/LAMP1/LAMP2/RPS3/ATP5A1/ACTR2/PIP/MUC7/KRT1/KRT2/KRT10/SERPINA12/SPRR2E\n+GO:0072324\tascus epiplasm\t0\t0/153\t\n+GO:0090543\tFlemming body\t1\t1/153\tCAPG\n+GO:0090635\textracellular core region of desmosome\t0\t0/153\t\n+GO:0090636\touter dense plaque of desmosome\t0\t0/153\t\n+GO:0090637\tinner dense plaque of desmosome\t0\t0/153\t\n+GO:0097223\tsperm part\t0\t0/153\t\n+GO:0097268\tcytoophidium\t0\t0/153\t\n+GO:0097458\tneuron part\t10\t10/153\tARG1/ACTN4/FLNB/SOD1/HSPB1/HSPA8/CTSV/YWHAE/APOD/LAMP1\n+GO:0097569\tlateral shield\t0\t0/153\t\n+GO:0097574\tlateral part of cell\t0\t0/153\t\n+GO:0097610\tcell surface furrow\t1\t1/153\tMYH9\n+GO:0097613\tdinoflagellate epicone\t0\t0/153\t\n+GO:0097614\tdinoflagellate hypocone\t0\t0/153\t\n+GO:0097653\tunencapsulated part of cell\t0\t0/153\t\n+GO:0097683\tdinoflagellate apex\t0\t0/153\t\n+GO:0097684\tdinoflagellate antapex\t0\t0/153\t\n+GO:0098046\ttype V protein secretion system complex\t0\t0/153\t\n+GO:0098862\tcluster of actin-based cell projections\t4\t4/153\tPLEC/MYH9/ACTN4/FLNB\n+GO:1990015\tensheathing process\t0\t0/153\t\n+GO:1990016\tneck portion of tanycyte\t0\t0/153\t\n+GO:1990018\ttail portion of tanycyte\t0\t0/153\t\n+GO:1990225\trhoptry neck\t0\t0/153\t\n+GO:1990794\tbasolateral part of cell\t0\t0/153\t\n+GO:0031594\tneuromuscular junction\t1\t1/153\tMYH9\n+GO:0044456\tsynapse part\t3\t3/153\tHSPA8/LAMP1/ACTR2\n+GO:0060076\texcitatory synapse\t0\t0/153\t\n+GO:0060077\tinhibitory synapse\t0\t0/153\t\n+GO:0097470\tribbon synapse\t0\t0/153\t\n+GO:0098685\tSchaffer collateral - CA1 synapse\t0\t0/153\t\n+GO:0098686\thippocampal mossy fiber to CA3 synapse\t0\t0/153\t\n+GO:0098978\tglutamatergic synapse\t0\t0/153\t\n+GO:0098979\tpolyadic synapse\t0\t0/153\t\n+GO:0098981\tcholinergic synapse\t0\t0/153\t\n+GO:0098982\tGABA-ergic synapse\t0\t0/153\t\n+GO:0098984\tneuron to neuron synapse\t1\t1/153\tACTR2\n+GO:0009506\tplasmodesma\t0\t0/153\t\n+GO:0005818\taster\t0\t0/153\t\n+GO:0097740\tparaflagellar rod\t0\t0/153\t\n+GO:0097741\tmastigoneme\t0\t0/153\t\n+GO:0098644\tcomplex of collagen trimers\t0\t0/153\t\n+GO:0099081\tsupramolecular polymer\t30\t30/153\tDSP/KRT6A/KRT16/JUP/ACTG1/KRT78/KRT17/CASP14/ENO1/PLEC/KRT80/KRT13/KRT6B/LMNA/TUBB4B/TUBA1B/ACTN4/FLNB/HSPB1/EPPK1/ALDOA/VCL/KRT23/KRT15/FLG/CAPZB/KRT1/KRT2/KRT10/KRT85\n' |
