| Next changeset 1:5d0c44bc354d (2018-07-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a |
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added:
README.rst pathwaymatcher.xml test-data/genes.txt test-data/genes_search.tsv test-data/proteoforms.txt test-data/proteoforms_graphs/geneExternalEdges.tsv test-data/proteoforms_graphs/geneInternalEdges.tsv test-data/proteoforms_graphs/geneVertices.tsv test-data/proteoforms_graphs/proteinExternalEdges.tsv test-data/proteoforms_graphs/proteinInternalEdges.tsv test-data/proteoforms_graphs/proteinVertices.tsv test-data/proteoforms_graphs/proteoformExternalEdges.tsv test-data/proteoforms_graphs/proteoformInternalEdges.tsv test-data/proteoforms_graphs/proteoformVertices.tsv |
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| diff -r 000000000000 -r f66af2b04a98 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Jun 20 14:21:10 2018 -0400 |
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| @@ -0,0 +1,41 @@ +PathwayMatcher +======================= + +- Home: <https://github.com/LuisFranciscoHS/PathwayMatcher/> +- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/pathwaymatcher> +- Tools ID: `pathwaymatcher` + + +Description +----------- + +PathwayMatcher is a software tool written in Java to search for pathways related to a list of proteins in Reactome. + + +General Requirements +-------------------- + +This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: + + export _JAVA_OPTIONS='-Xmx1500M' + +On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example: + + export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M' + +It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. + + +License +------- + +PathwayMatcher is a free open-source project, following an Apache License 2.0. + + +Authors +------- + +Authors and contributors: + +* Luis Francisco Hernández Sánchez <luis.sanchez@uib.no> +* Carlos Horro Marcos <carlos.horro@uib.no> |
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| diff -r 000000000000 -r f66af2b04a98 pathwaymatcher.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pathwaymatcher.xml Wed Jun 20 14:21:10 2018 -0400 |
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| b'@@ -0,0 +1,383 @@\n+<tool id="reactome_pathwaymatcher" name="Pathway Matcher" version="@PATHWAYMATCHER_VERSION@.@TOOL_SUBVERSION@">\n+ <description>\n+ PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.\n+ </description>\n+ <macros>\n+ <token name="@PATHWAYMATCHER_VERSION@">1.8</token>\n+ <token name="@TOOL_SUBVERSION@">0</token>\n+ <xml name="input_fasta">\n+ <param format="fasta" name="input_database" type="data" label="Protein Database"\n+ help="Select FASTA database from history"/>\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@PATHWAYMATCHER_VERSION@">pathwaymatcher</requirement>\n+ <requirement type="package" version="3.0">zip</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Job Failed" />\n+ <regex match="java.*Exception" level="fatal" description="Java Exception"/>\n+ <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>\n+ </stdio>\n+ <command>\n+<![CDATA[\n+ #from datetime import datetime\n+ #import json\n+ #import os\n+ #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n+ #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n+ #set $temp_stderr = "pathwaym_stderr"\n+ #set $bin_dir = "bin"\n+\n+ mkdir output;\n+ cwd=`pwd`;\n+ export HOME=\\$cwd;\n+\n+ #####################\n+ ## Pathway Matcher ##\n+ #####################\n+ (pathwaymatcher src.main.java.no.uib.pap.pathwaymatcher.PathwayMatcher\n+\n+ #for $i, $s in enumerate($input_types)\n+\n+ ## GENETIC VARIANTS\n+\n+ #if $s.input_type.input_type_selector == "rsid"\n+ -t rsid -i \'${s.input_type.input_rsid}\'\n+ #end if\n+\n+ #if $s.input_type.input_type_selector == "chrbp"\n+ -t chrbp -i \'${s.input_type.input_chrbp}\'\n+ #end if\n+\n+ #if $s.input_type.input_type_selector == "vcf"\n+ -t vcf -i \'${s.input_type.input_vcf}\'\n+ #end if\n+\n+ ## GENES\n+\n+ #if $s.input_type.input_type_selector == "gene"\n+ -t gene -i \'${s.input_type.input_gene}\'\n+ #end if\n+\n+ ## PEPTIDES\n+\n+ #if $s.input_type.input_type_selector == "peptide"\n+ -t peptide -i \'${s.input_type.input_peptide}\'\n+ -f \'${s.input_type.input_database}\'\n+ -r \'${s.input_type.ptm_range}\'\n+ #end if\n+\n+ #if $s.input_type.input_type_selector == "modifiedpeptide"\n+ -t modifiedpeptide -i \'${s.input_type.input_modifiedpeptide}\'\n+ -f \'${s.input_type.input_database}\'\n+ -r \'${s.input_type.ptm_range}\'\n+ #end if\n+\n+ ## PROTEINS\n+\n+ #if $s.input_type.input_type_selector == "uniprot"\n+ -t uniprot -i \'${s.input_type.input_uniprot}\'\n+ #end if\n+\n+ #if $s.input_type.input_type_selector == "ensembl"\n+ -t ensembl -i \'${s.input_type.input_ensembl}\'\n+ #end if\n+\n+ ## PROTEOFORMS\n+\n+ #if $s.input_type.input_type_selector == "proteoforms"\n+\n+ #if $s.input_type.proteoform_match_criteria:\n+ -t proteoform -m \'${s.input_type.proteoform_match_criteria}\' -i \'${s.input_type.input_proteoforms}\'\n+ #else:\n+ -t proteoform -i \'${s.input_type.input_proteoforms}\'\n+ #end if\n+\n+ #end if\n+\n+ #end for\n+\n+ ## OUTPUT OPTIONS\n+\n+ #if $output_options.search_top_level_info:\n+ -tl'..b'ement name="proteinExternalEdges" ftype="tsv" file="proteoforms_graphs/proteinExternalEdges.tsv" compare="sim_size" delta="10000"/>\n+ <element name="proteinInternalEdges" ftype="tsv" file="proteoforms_graphs/proteinInternalEdges.tsv" compare="sim_size" delta="1000"/>\n+ <element name="proteinVertices" ftype="tsv" file="proteoforms_graphs/proteinVertices.tsv" compare="sim_size" delta="1000"/>\n+ <element name="proteoformExternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformExternalEdges.tsv" compare="sim_size" delta="1000"/>\n+ <element name="proteoformInternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformInternalEdges.tsv" compare="sim_size" delta="1000"/>\n+ <element name="proteoformVertices" ftype="tsv" file="proteoforms_graphs/proteoformVertices.tsv" compare="sim_size" delta="1000"/>\n+ </output_collection>\n+ </test>\n+\n+ </tests>\n+ <help>\n+\n+.. class:: infomark\n+\n+**Introduction**\n+\n+Biological pathways are an excellent resource to analyze the causes and consequences of certain phenotypes.\n+Most of the components of the pathways are proteins. When searching for relevant pathways to perform analysis\n+of a patient sample proteins, it is very common to lose information due to lack of precision in the search.\n+\n+This leads to result sets with many extra selected pathways that are not really related to the input sample.\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+We present more fine grained approach to search, not only with the gene names, but also with post translational\n+modifications of the proteins, such as phosphorylation.\n+\n+Ultimately, any omics dataset with its mutations and\n+modifications will be mapped directly to the functional knowledgebases allowing the functional interpretation by\n+researchers and clinicians.\n+\n+The reference database used is Reactome, a free, open source, curated and peer reviewed database of biological reactions, that contains the quality data needed for this type of fine grained search. database of biological reactions. It can be readily queried with omics datasets, and we are improving its features by extending the matching the clinical data to the biological pathways. Not only will the gene names be used, but also mutations or post translational modifications such as phosphorylation.\n+\n+\n+.. class:: infomark\n+\n+**Inputs and outputs**\n+\n+PathwayMatcher can search for reactions and pathways with various input types, and generates mapping files to the database.\n+\n+The input can be:\n+\n+- Genetic variants\n+- Genes\n+- Peptides\n+- Protein\n+- Proteoforms\n+\n+The output of PathwayMatcher is composed of two files, the Reaction and Pathway mapping and the statistical analysis of the relevant pathways.\n+\n+.. class:: infomark\n+\n+Information included with this tool is a brief summary of the main one included in PathwayMatcher_.\n+\n+Specific information about PathwayMatcher\'s Input_ and Output_ may also be found there.\n+\n+\n+.. class:: infomark\n+\n+**References**\n+\n+[1] dbSNP_\n+\n+[2] VCF v4.3:\n+http://samtools.github.io/hts-specs/VCFv4.3.pdf\n+\n+[3] genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015 Jan;43(Database issue):D1079-85. doi: 10.1093/nar/gku1071. :\n+https://www.ncbi.nlm.nih.gov/pubmed/25361968\n+\n+[4] UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45: D158-D169 (2017):\n+http://dx.doi.org/doi:10.1093/nar/gkw1099\n+\n+[5] Ensembl:\n+https://www.ensembl.org/info/genome/stable_ids/index.html\n+\n+[6] The PSI-MOD community standard for representation of protein modification data. Nature Biotechnology 26, 864 - 866 (2008):\n+http://www.nature.com/nbt/journal/v26/n8/full/nbt0808-864.html\n+\n+.. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/\n+.. _PathwayMatcher: https://github.com/LuisFranciscoHS/PathwayMatcher\n+.. _Input: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Input\n+.. _Output: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Output\n+\n+ </help>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r f66af2b04a98 test-data/genes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes.txt Wed Jun 20 14:21:10 2018 -0400 |
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| @@ -0,0 +1,11 @@ +CFTR +TGFB1 +FCGR2A +DCTN4 +SCNN1B +SCNN1G +SCNN1A +TNFRSF1A +CLCA4 +STX1A +CXCL8 |
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| diff -r 000000000000 -r f66af2b04a98 test-data/genes_search.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes_search.tsv Wed Jun 20 14:21:10 2018 -0400 |
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| b'@@ -0,0 +1,539 @@\n+GENE\tUNIPROT\tREACTION_STID\tREACTION_DISPLAY_NAME\tPATHWAY_STID\tPATHWAY_DISPLAY_NAME\tTOP_LEVEL_PATHWAY_STID\tTOP_LEVEL_PATHWAY_DISPLAY_NAME\n+CFTR\tP13569\tR-HSA-1454916\tThe ABCC family mediates organic anion transport\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-1454916\tThe ABCC family mediates organic anion transport\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-383190\tHCO3- transport through ion channel\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-383190\tHCO3- transport through ion channel\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-5678863\tCFTR transports Cl- from cytosol to extracellular region\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-5678863\tCFTR transports Cl- from cytosol to extracellular region\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-5627071\tRHOQ positively regulates trafficking of GOPC:CFTR to the plasma membrane\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n+CFTR\tP13569\tR-HSA-5627071\tRHOQ positively regulates trafficking of GOPC:CFTR to the plasma membrane\tR-HSA-194315\tSignaling by Rho GTPases\tR-HSA-162582\tSignal Transduction\n+CFTR\tP13569\tR-HSA-5627071\tRHOQ positively regulates trafficking of GOPC:CFTR to the plasma membrane\tR-HSA-195258\tRHO GTPase Effectors\tR-HSA-162582\tSignal Transduction\n+CFTR\tP13569\tR-HSA-5627071\tRHOQ positively regulates trafficking of GOPC:CFTR to the plasma membrane\tR-HSA-5627083\tRHO GTPases regulate CFTR trafficking\tR-HSA-162582\tSignal Transduction\n+CFTR\tP13569\tR-HSA-8866542\tVCP-catalyzed ATP hydrolysis promotes the translocation of misfolded CFTR into the cytosol\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-8866542\tVCP-catalyzed ATP hydrolysis promotes the translocation of misfolded CFTR into the cytosol\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-8866546\tRNF5 and RNF185 ubiquitinate misfolded CFTR\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-8866546\tRNF5 and RNF185 ubiquitinate misfolded CFTR\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-8866551\tCFTR binds components of the ERAD machinery for ubiquitination and degradation\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-8866551\tCFTR binds components of the ERAD machinery for ubiquitination and degradation\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n+CFTR\tP13569\tR-HSA-5678992\tIvacaftor:CFTR G551D transports Cl- from cytosol to extracellular region\tR-HSA-1643685\tDisease\tR-HSA-1643685\tDisease\n+CFTR\tP13569\tR-HSA-5678992\tIvacaftor:CFTR G551D transports Cl- from cytosol to extracellular region\tR-HSA-5619115\tDisorders of transmembrane transporters\tR-HSA-1643685\tDisease\n+CFTR\tP13569\tR-HSA-5678992\tIvacaftor:CFTR G551D transports Cl- from cytosol to extracellular region\tR-HSA-5619084\tABC transporter disorders\tR-HSA-1643685\tDisease\n+CFTR\tP13569\tR-HSA-5678992\tIvacaftor:CFTR G551D transports Cl- from cytosol to extracellular region\tR-HSA-5678895\tDefective CFTR causes cystic fibrosis\tR-HSA-1643685\tDisease\n+CFTR\tP13569\tR-HSA-5679000\tIvacaftor binds CFTR G551D\tR-HSA-1643685\tDisease\tR-HSA-1643685\tDisease\n+CFTR\tP13569\tR-HSA-5679000\tIvacaftor binds CFTR G551D\tR-HSA-5619115\tDisorders of transmembrane transporters\tR-HSA-1643685\tDisease\n+CFTR\tP13569\tR-HSA-5679000\tIvacaftor binds CFTR G551D\tR-HSA-5619084\tABC transporter disorders\tR-HSA-1643685\tDisease\n+CFTR\tP13569\tR-HSA-5679000\tIvacaftor binds CFTR '..b'582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-380073\tLiganded Gi-activating GPCR acts as a GEF for Gi\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-380073\tLiganded Gi-activating GPCR acts as a GEF for Gi\tR-HSA-388396\tGPCR downstream signalling\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-749456\tLiganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi\tR-HSA-418594\tG alpha (i) signalling events\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-749456\tLiganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-749456\tLiganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-749456\tLiganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi\tR-HSA-388396\tGPCR downstream signalling\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-749454\tThe Ligand:GPCR:Gi complex dissociates\tR-HSA-418594\tG alpha (i) signalling events\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-749454\tThe Ligand:GPCR:Gi complex dissociates\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-749454\tThe Ligand:GPCR:Gi complex dissociates\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-749454\tThe Ligand:GPCR:Gi complex dissociates\tR-HSA-388396\tGPCR downstream signalling\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-373076\tClass A/1 (Rhodopsin-like receptors)\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-375276\tPeptide ligand-binding receptors\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-380108\tChemokine receptors bind chemokines\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-500792\tGPCR ligand binding\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-373076\tClass A/1 (Rhodopsin-like receptors)\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-375276\tPeptide ligand-binding receptors\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-380108\tChemokine receptors bind chemokines\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-500792\tGPCR ligand binding\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-374251\tDARC is a non-specific receptor for many chemokines\tR-HSA-373076\tClass A/1 (Rhodopsin-like receptors)\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-374251\tDARC is a non-specific receptor for many chemokines\tR-HSA-375276\tPeptide ligand-binding receptors\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-374251\tDARC is a non-specific receptor for many chemokines\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-374251\tDARC is a non-specific receptor for many chemokines\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n+CXCL8\tP10145\tR-HSA-374251\tDARC is a non-specific receptor for many chemokines\tR-HSA-500792\tGPCR ligand binding\tR-HSA-162582\tSignal Transduction\n' |
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| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms.txt Wed Jun 20 14:21:10 2018 -0400 |
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| @@ -0,0 +1,15 @@ +P00519;00046:245,00048:412 +P31749;00047:473,00047:308 +P11274;00187:177 +P22681;0098:774 +P22681 +P16220;00046:133 +P46109;01192:207 +P27361;00047:202,00048:204 +Q9UQC2;00000:452 +Q15759;00048:182,00047:180 +O15530;00048:241 +P62753;00048:235,00049:236,00126:240 +P12931;00048:419 +P40763;00046:705,00046:727 +P42229;00048:694 |
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| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/geneExternalEdges.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/geneExternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 |
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| @@ -0,0 +1,1 @@ +id1 id2 type container_id role1 role2 |
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| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/geneInternalEdges.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/geneInternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,411 @@\n+id1\tid2\ttype\tcontainer_id\trole1\trole2\n+PDK1\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n+PDPK1\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n+PDK1\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n+PDK1\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n+PDK1\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n+PDPK1\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n+PDPK1\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n+PDPK1\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n+AKT1\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n+AKT1\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n+PKB\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n+PKB\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n+RAC\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n+RAC\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n+AKT1\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n+AKT1\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n+PKB\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n+PKB\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n+RAC\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n+RAC\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n+PDK1\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n+PDK1\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n+PDPK1\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n+PDPK1\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n+AKT1\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n+AKT1\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n+PKB\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n+PKB\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n+RAC\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n+RAC\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n+GAB2\tPDK1\tReaction\tR-HSA-198284\tregulator\tinput\n+GAB2\tPDPK1\tReaction\tR-HSA-198284\tregulator\tinput\n+KIAA0571\tPDK1\tReaction\tR-HSA-198284\tregulator\tinput\n+KIAA0571\tPDPK1\tReaction\tR-HSA-198284\tregulator\tinput\n+GAB2\tAKT1\tReaction\tR-HSA-198284\tregulator\tinput\n+GAB2\tPKB\tReaction\tR-HSA-198284\tregulator\tinput\n+GAB2\tRAC\tReaction\tR-HSA-198284\tregulator\tinput\n+KIAA0571\tAKT1\tReaction\tR-HSA-198284\tregulator\tinput\n+KIAA0571\tPKB\tReaction\tR-HSA-198284\tregulator\tinput\n+KIAA0571\tRAC\tReaction\tR-HSA-198284\tregulator\tinput\n+GAB2\tKIAA0571\tReaction\tR-HSA-198284\tregulator\tregulator\n+KIAA0571\tGAB2\tReaction\tR-HSA-198284\tregulator\tregulator\n+AKT1\tAKT1\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n+PKB\tPKB\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n+RAC\tRAC\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n+PDK1\tPDK1\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n+PDPK1\tPDPK1\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n+PDK1\tPDK1\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n+PDPK1\tPDPK1\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n+AKT1\tAKT1\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n+PKB\tPKB\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n+RAC\tRAC\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n+ABL\tABL1\tReaction\tR-HSA-8985227\tregulator\tregulator\n+ABL\tJTK7\tReaction\tR-HSA-8985227\tregulator\tregulator\n+ABL1\tABL\tReaction\tR-HSA-8985227\tregulator\tregulator\n+ABL1\tJTK7\tReaction\tR-HSA-8985227\tregulator\tregulator\n+JTK7\tABL\tReaction\tR-HSA-8985227\tregulator\tregulator\n+JTK7\tABL1\tReaction\tR-HSA-8985227\tregulator\tregulator\n+SRC\tSRC1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+SRC1\tSRC\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+SRC\tABL\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+SRC\tABL1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+SRC\tJTK7\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+SRC1\tABL\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+SRC1\tABL1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+SRC1\tJTK7\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+ABL\tSRC\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+ABL\tSRC1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+ABL1\tSRC\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+ABL1\tSRC1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+JTK7\tSRC\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+JTK7\tSRC1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n+MAPK11\tPRKM11\tReaction\tR-HSA-448957\tinput\tinput\n+MAPK11\tSAPK2\tReaction\tR-HSA-448957\tinput\tinput\n+MAPK11\tSAPK2B\tReaction\tR-HSA-448957\tinput\tinput\n+PRKM11\tMAPK11\tReaction\tR-HSA-448957\tinput\tinput\n+PRKM11\tSAPK2\tReaction\tR-HSA-448957\tinput\tinput\n+PRKM11\tSAPK2B\tReaction\tR-HSA-448957\tinput\tinput\n+SAPK2\tMAPK11\tReactio'..b'r/candidate\tmember/candidate\n+PRKM11\tPRKM11\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n+SAPK2\tSAPK2\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n+SAPK2B\tSAPK2B\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n+AKT1\tPKB\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n+AKT1\tRAC\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n+PKB\tAKT1\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n+PKB\tRAC\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n+RAC\tAKT1\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n+RAC\tPKB\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n+AKT1\tAKT1\tComplex\tR-HSA-2317310\tcomponent\tcomponent\n+PKB\tPKB\tComplex\tR-HSA-2317310\tcomponent\tcomponent\n+RAC\tRAC\tComplex\tR-HSA-2317310\tcomponent\tcomponent\n+AKT1\tAKT1\tSet\tR-HSA-202074\tmember/candidate\tmember/candidate\n+PKB\tPKB\tSet\tR-HSA-202074\tmember/candidate\tmember/candidate\n+RAC\tRAC\tSet\tR-HSA-202074\tmember/candidate\tmember/candidate\n+APRF\tSTAT3\tReaction\tR-HSA-8875816\tinput\tinput\n+STAT3\tAPRF\tReaction\tR-HSA-8875816\tinput\tinput\n+STAT5\tSTAT5A\tReaction\tR-HSA-380782\tinput\tinput\n+STAT5A\tSTAT5\tReaction\tR-HSA-380782\tinput\tinput\n+STAT5\tAPRF\tReaction\tR-HSA-380782\tinput\tinput\n+STAT5\tSTAT3\tReaction\tR-HSA-380782\tinput\tinput\n+STAT5A\tAPRF\tReaction\tR-HSA-380782\tinput\tinput\n+STAT5A\tSTAT3\tReaction\tR-HSA-380782\tinput\tinput\n+APRF\tSTAT5\tReaction\tR-HSA-380782\tinput\tinput\n+APRF\tSTAT5A\tReaction\tR-HSA-380782\tinput\tinput\n+STAT3\tSTAT5\tReaction\tR-HSA-380782\tinput\tinput\n+STAT3\tSTAT5A\tReaction\tR-HSA-380782\tinput\tinput\n+APRF\tAPRF\tComplex\tR-HSA-1112576\tcomponent\tcomponent\n+STAT3\tSTAT3\tComplex\tR-HSA-1112576\tcomponent\tcomponent\n+STAT5\tSTAT5\tComplex\tR-HSA-1469975\tcomponent\tcomponent\n+STAT5A\tSTAT5A\tComplex\tR-HSA-1469975\tcomponent\tcomponent\n+APRF\tAPRF\tSet\tR-HSA-1112559\tmember/candidate\tmember/candidate\n+STAT3\tSTAT3\tSet\tR-HSA-1112559\tmember/candidate\tmember/candidate\n+STAT5\tSTAT5\tSet\tR-HSA-1433551\tmember/candidate\tmember/candidate\n+STAT5A\tSTAT5A\tSet\tR-HSA-1433551\tmember/candidate\tmember/candidate\n+STAT5\tSTAT5A\tReaction\tR-HSA-1671691\tinput\tinput\n+STAT5A\tSTAT5\tReaction\tR-HSA-1671691\tinput\tinput\n+STAT5\tSTAT5\tComplex\tR-HSA-507927\tcomponent\tcomponent\n+STAT5A\tSTAT5A\tComplex\tR-HSA-507927\tcomponent\tcomponent\n+STAT5\tSTAT5\tSet\tR-HSA-452094\tmember/candidate\tmember/candidate\n+STAT5A\tSTAT5A\tSet\tR-HSA-452094\tmember/candidate\tmember/candidate\n+CRKL\tCRKL\tComplex\tR-HSA-8875574\tcomponent\tcomponent\n+CRKL\tCRKL\tSet\tR-HSA-381945\tmember/candidate\tmember/candidate\n+OK/SW-cl.2\tRPS6\tReaction\tR-HSA-165726\tinput\tinput\n+RPS6\tOK/SW-cl.2\tReaction\tR-HSA-165726\tinput\tinput\n+OK/SW-cl.2\tOK/SW-cl.2\tComplex\tR-HSA-72505\tcomponent\tcomponent\n+RPS6\tRPS6\tComplex\tR-HSA-72505\tcomponent\tcomponent\n+MAPK11\tPRKM11\tReaction\tR-HSA-450257\tinput\tinput\n+MAPK11\tSAPK2\tReaction\tR-HSA-450257\tinput\tinput\n+MAPK11\tSAPK2B\tReaction\tR-HSA-450257\tinput\tinput\n+PRKM11\tMAPK11\tReaction\tR-HSA-450257\tinput\tinput\n+PRKM11\tSAPK2\tReaction\tR-HSA-450257\tinput\tinput\n+PRKM11\tSAPK2B\tReaction\tR-HSA-450257\tinput\tinput\n+SAPK2\tMAPK11\tReaction\tR-HSA-450257\tinput\tinput\n+SAPK2\tPRKM11\tReaction\tR-HSA-450257\tinput\tinput\n+SAPK2\tSAPK2B\tReaction\tR-HSA-450257\tinput\tinput\n+SAPK2B\tMAPK11\tReaction\tR-HSA-450257\tinput\tinput\n+SAPK2B\tPRKM11\tReaction\tR-HSA-450257\tinput\tinput\n+SAPK2B\tSAPK2\tReaction\tR-HSA-450257\tinput\tinput\n+MAPK11\tMAPK11\tComplex\tR-HSA-450254\tcomponent\tcomponent\n+PRKM11\tPRKM11\tComplex\tR-HSA-450254\tcomponent\tcomponent\n+SAPK2\tSAPK2\tComplex\tR-HSA-450254\tcomponent\tcomponent\n+SAPK2B\tSAPK2B\tComplex\tR-HSA-450254\tcomponent\tcomponent\n+MAPK11\tMAPK11\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n+PRKM11\tPRKM11\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n+SAPK2\tSAPK2\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n+SAPK2B\tSAPK2B\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n+GAB2\tKIAA0571\tReaction\tR-HSA-2730870\tcatalyst\tcatalyst\n+KIAA0571\tGAB2\tReaction\tR-HSA-2730870\tcatalyst\tcatalyst\n+GAB2\tGAB2\tComplex\tR-HSA-2685700\tcomponent\tcomponent\n+KIAA0571\tKIAA0571\tComplex\tR-HSA-2685700\tcomponent\tcomponent\n+GAB2\tGAB2\tSet\tR-HSA-912533\tmember/candidate\tmember/candidate\n+KIAA0571\tKIAA0571\tSet\tR-HSA-912533\tmember/candidate\tmember/candidate\n' |
| b |
| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/geneVertices.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/geneVertices.tsv Wed Jun 20 14:21:10 2018 -0400 |
| [ |
| @@ -0,0 +1,36 @@ +id name +ABL Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber +ABL1 Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber +AKT1 RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber +APRF fullName evidence="52"Signal transducer and activator of transcription 3 +BCR Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber +BCR1 Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber +CBL E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber +CBL2 E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber +CREB1 Cyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ] +CRKL Crk-like protein ] +D22S11 Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber +ERK1 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber +GAB2 GRB2-associated-binding protein 2 +JTK7 Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber +KIAA0571 GRB2-associated-binding protein 2 +MAPK11 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber +MAPK3 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber +OK/SW-cl.2 40S ribosomal protein S6 +PDK1 3-phosphoinositide-dependent protein kinase 1 shortName:hPDK1 ecNumber2.7.11.1/ecNumber ] +PDK1 [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial ecNumber2.7.11.2/ecNumber +PDPK1 3-phosphoinositide-dependent protein kinase 1 shortName:hPDK1 ecNumber2.7.11.1/ecNumber ] +PKB RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber +PRKM11 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber +PRKM3 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber +RAC RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber +RNF55 E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber +RPS6 40S ribosomal protein S6 +SAPK2 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber +SAPK2B Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber +SRC Proto-oncogene tyrosine-protein kinase Src ecNumber evidence="28 42 49 63 65 66"2.7.10.2/ecNumber +SRC1 Proto-oncogene tyrosine-protein kinase Src ecNumber evidence="28 42 49 63 65 66"2.7.10.2/ecNumber +SRC1 Nuclear receptor coactivator 1 shortName:NCoA-1 ecNumber2.3.1.48/ecNumber +STAT3 fullName evidence="52"Signal transducer and activator of transcription 3 +STAT5 Signal transducer and activator of transcription 5A ] +STAT5A Signal transducer and activator of transcription 5A ] |
| b |
| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/proteinExternalEdges.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/proteinExternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,49968 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|
| b |
| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/proteinInternalEdges.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/proteinInternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 |
| b |
| b'@@ -0,0 +1,365 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omponent\tcomponent\n+P12931\tP40763\tComplex\tR-HSA-1470000\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802672\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802669\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802667\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802662\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802664\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802666\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802645\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802647\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802648\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802625\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802637\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802636\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802710\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802711\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-6802695\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-418179\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-418103\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-418144\tcomponent\tcomponent\n+P12931\tP27361\tComplex\tR-HSA-418210\tcomponent\tcomponent\n+P12931\tQ9UQC2\tSet\tR-HSA-9031773\tmember/candidate\tmember/candidate\n+P16220\tP31749\tReaction\tR-HSA-199298\tinput\tcatalyst\n+P16220\tP31749\tReaction\tR-HSA-199298\toutput\tcatalyst\n+P16220\tP31749\tReaction\tR-HSA-2399996\tinput\tcatalyst\n+P16220\tP31749\tReaction\tR-HSA-2399996\toutput\tcatalyst\n+P22681\tP46109\tReaction\tR-HSA-912790\tinput\tinput\n+P22681\tP46109\tReaction\tR-HSA-912790\tinput\toutput\n+P22681\tP46109\tReaction\tR-HSA-912790\toutput\tinput\n+P22681\tP46109\tReaction\tR-HSA-912790\toutput\toutput\n+P22681\tP46109\tReaction\tR-HSA-912734\tinput\tinput\n+P22681\tP46109\tReaction\tR-HSA-912734\tinput\toutput\n+P22681\tP46109\tReaction\tR-HSA-912734\toutput\tinput\n+P22681\tP46109\tReaction\tR-HSA-912734\toutput\toutput\n+P22681\tP46109\tComplex\tR-HSA-912774\tcomponent\tcomponent\n+P22681\tP46109\tComplex\tR-HSA-914209\tcomponent\tcomponent\n+P27361\tQ15759\tReaction\tR-HSA-168053\tcatalyst\tcatalyst\n+P27361\tQ15759\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n+P40763\tP42229\tReaction\tR-HSA-380782\tinput\tinput\n+P40763\tP42229\tReaction\tR-HSA-380782\tinput\toutput\n+P40763\tP42229\tReaction\tR-HSA-380782\toutput\tinput\n+P40763\tP42229\tReaction\tR-HSA-380782\toutput\toutput\n+P40763\tP42229\tComplex\tR-HSA-1469975\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-1566924\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-380766\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8983118\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-9007112\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8983137\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8983180\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8983197\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-9006875\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8987135\tcomponent\tcomponent\n+P40763\tP42229\tSet\tR-HSA-1433551\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-1433413\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-1469979\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-380756\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9007142\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9007110\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9006868\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9006876\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9009216\tmember/candidate\tmember/candidate\n' |
| b |
| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/proteinVertices.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/proteinVertices.tsv Wed Jun 20 14:21:10 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ +id name +O15530 3-phosphoinositide-dependent protein kinase 1 shortName:hPDK1 ecNumber2.7.11.1/ecNumber ] +P00519 Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber +P11274 Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber +P12931 Proto-oncogene tyrosine-protein kinase Src ecNumber evidence="28 42 49 63 65 66"2.7.10.2/ecNumber +P16220 Cyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ] +P22681 E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber +P27361 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber +P31749 RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber +P40763 fullName evidence="52"Signal transducer and activator of transcription 3 +P42229 Signal transducer and activator of transcription 5A ] +P46109 Crk-like protein ] +P62753 40S ribosomal protein S6 +Q15759 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber +Q9UQC2 GRB2-associated-binding protein 2 |
| b |
| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/proteoformExternalEdges.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/proteoformExternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +id1 id2 type container_id role1 role2 |
| b |
| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/proteoformInternalEdges.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/proteoformInternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +id1 id2 type container_id role1 role2 |
| b |
| diff -r 000000000000 -r f66af2b04a98 test-data/proteoforms_graphs/proteoformVertices.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteoforms_graphs/proteoformVertices.tsv Wed Jun 20 14:21:10 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +id name |