Mercurial > repos > proteore > proteore_pathview_mapping
changeset 0:097bb3ed2b4d draft
planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
| author | proteore |
|---|---|
| date | Wed, 22 Aug 2018 11:30:23 -0400 |
| parents | |
| children | 59c96f071853 |
| files | PathView.R Pathview.xml README.rst kegg_pathways.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_table_conf.xml.sample |
| diffstat | 9 files changed, 670 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PathView.R Wed Aug 22 11:30:23 2018 -0400 @@ -0,0 +1,234 @@ +#!/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. + +suppressMessages(library("pathview")) + +read_file <- function(path,header){ + file <- try(read.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote=""),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) +} + + +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 + --ouput Output filename + --expression_values1 Column containing expression values (first condition) + --expression_values2 Column containing expression values (second condition) + --expression_values3 Column containing expression values (third condition) + --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph + --species KEGG species (hsa, mmu, ...) + + Example: + ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n") + + q(save="no") + } + + + #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda") + #load("/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda") + 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) +} + +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){ + if (is.letter(substr(x,1,3))){ + x <- substr(x,4,nchar(x)) + } + return(x) +} + +clean_bad_character <- function(string) { + string <- gsub("X","",string) + string <- gsub(" ","",string) + return(string) +} + +args <- get_args() + +###save and load args in rda file for testing +#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda") +#load("/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda") + +###setting variables +if (!is.null(args$pathways_id)) { ids <- sapply(rapply(strsplit(clean_bad_character(args$pathways_id),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)} +#if (!is.null(args$pathways_name)) {names <- as.vector(sapply(strsplit(args$pathways_name,","), function(x) concat_string(x),USE.NAMES = FALSE))} +if (!is.null(args$id_list)) {id_list <- as.vector(strsplit(clean_bad_character(args$id_list),","))} +id_type <- tolower(args$id_type) +ncol <- as.numeric(gsub("c", "" ,args$id_column)) +header <- str2bool(args$header) +#output <- args$output +native_kegg <- str2bool(args$native_kegg) +species=args$species + + +#read input file or list +if (!is.null(args$input)){ + tab <- read_file(args$input,header) + tab <- tab[!apply(is.na(tab) | tab == "", 1, all),] #delete empty rows +} else { + tab <- data.frame(id_list) + ncol=1 +} + +e1 <- as.numeric(gsub("c", "" ,args$expression_values1)) +if (!is.null(args$expression_values1)) { colnames(tab)[e1] <- "e1" } +e2 <- as.numeric(gsub("c", "" ,args$expression_values2)) +if (!is.null(args$expression_values2)) { colnames(tab)[e2] <- "e2" } +e3 <- as.numeric(gsub("c", "" ,args$expression_values3)) +if (!is.null(args$expression_values3)) { colnames(tab)[e3] <- "e3" } + + +##### map uniprotID to entrez geneID +if (id_type == "uniprotid") { + + uniprotID = tab[,ncol] + mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = "Hs", pkg.name = NULL) + geneID = mapped2geneID[,2] + tab = cbind(tab,geneID) + +}else if (id_type == "geneid"){ + + colnames(tab)[ncol] <- "geneID" + +} + +geneID = tab$geneID[which(tab$geneID !="NA")] +geneID = gsub(" ","",geneID) +geneID = unlist(strsplit(geneID,"[;]")) + + +#### get hsa pathways list +#download.file(url = "http://rest.kegg.jp/link/pathway/hsa", destfile = "/home/dchristiany/proteore_project/ProteoRE/tools/pathview/geneID_to_hsa_pathways.csv") +#geneid_hsa_pathways <- read_file(path = "/home/dchristiany/proteore_project/ProteoRE/tools/pathview/geneID_to_hsa_pathways.csv",FALSE) +#names(geneid_hsa_pathways) <- c("geneID","pathway") + +##### build matrix to map on KEGG pathway (kgml : KEGG xml) +if (!is.null(args$expression_values1)&is.null(args$expression_values2)&is.null(args$expression_values3)){ + mat <- as.data.frame(cbind(tab$e1)[which(!is.na(tab$geneID)),]) + row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))] +} else if (!is.null(args$expression_values1)&!is.null(args$expression_values2)&is.null(args$expression_values3)){ + mat <- as.data.frame(cbind(tab$e1,tab$e2)[which(!is.na(tab$geneID)),]) + row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))] +}else if (!is.null(args$expression_values1)&!is.null(args$expression_values2)&!is.null(args$expression_values3)){ + mat <- as.data.frame(cbind(tab$e1,tab$e2,tab$e3)[which(!is.na(tab$geneID)),]) + row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))] +} else { + mat <- geneID +} + + +#### simulation data test +#exp1 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=100) +#exp2 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=50) +#exp3 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=10) +#tab <- cbind(tab,exp1,exp2,exp3) + +#write.table(tab, file='/home/dchristiany/proteore_project/ProteoRE/tools/pathview/Lacombe_sim_expression_data.tsv', quote=FALSE, sep='\t',row.names = FALSE) + +#mat <- exp1[1:nrow(tab)] +#names(mat) <- geneID + + +#####mapping geneID (with or without expression values) on KEGG pathway +for (id in ids) { + pathview(gene.data = mat, + #gene.idtype = "geneID", + #cpd.data = uniprotID, + #cpd.idtype = "uniprot", + pathway.id = id, + #pathway.name = "", + species = species, + kegg.dir = ".", + gene.idtype = "entrez", + #gene.annotpkg = NULL, + #min.nnodes = 3, + kegg.native = native_kegg, + #map.null = TRUE, + #expand.node = FALSE, + #split.group = FALSE, + #map.symbol = TRUE, + #map.cpdname = TRUE, + #node.sum = "sum", + #discrete=list(gene=FALSE,cpd=FALSE), + #limit = list(gene = 1, cpd = 1), + #bins = list(gene = 10, cpd = 10), + #both.dirs = list(gene = T, cpd = T), + #trans.fun = list(gene = NULL, cpd = NULL), + #low = list(gene = "green", cpd = "blue"), + #mid = list(gene = "gray", cpd = "gray"), + #high = list(gene = "red", cpd = "yellow"), + #na.col = "transparent", + #sign.pos="bottomleft", + #key.pos="topright", + #new.signature=TRUE, + #rankdir="LB", + #cex=0.3, + #text.width=15, + #res=300, + pdf.size=c(9,9)) + #is.signal=TRUE) +} + +########using keggview.native + +#xml.file=system.file("extdata", "hsa00010.xml", package = "pathview") +#node.data=node.info("/home/dchristiany/hsa00010.xml") +#plot.data.gene=node.map(mol.data=test, node.data, node.types="gene") +#colors =node.color(plot.data = plot.data.gene[,1:9]) \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Pathview.xml Wed Aug 22 11:30:23 2018 -0400 @@ -0,0 +1,234 @@ +<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.22"> + <requirements> + <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/PathView.R + #if $input.ids == "text" + --id_list="$input.txt" + #else + --input="$input.file" + --id_column="$input.ncol" + --header="$input.header" + #end if + #if $species.pathways.pathways_id == "pathways_ids" + --pathways_id="$species.pathways.pids" + #else + --pathways_id="$species.pathways.pids" + #end if + --id_type="$id_type" + --native_kegg="$native" + + #if $input.ids=="file" + #if $input.expression_values.nb_exp =="1" + --expression_values1="$input.expression_values.e1" + #else if $input.expression_values.nb_exp =="2" + --expression_values1="$input.expression_values.e1" + --expression_values2="$input.expression_values.e2" + #else if $input.expression_values.nb_exp =="3" + --expression_values1="$input.expression_values.e1" + --expression_values2="$input.expression_values.e2" + --expression_values3="$input.expression_values.e3" + #end if + #end if + + --species=${species.ref_file} + + ]]></command> + <inputs> + <conditional name="input" > + <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > + <option value="text">Copy/paste your identifiers</option> + <option value="file" selected="true">Input file containing your identifiers</option> + </param> + <when value="text" > + <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," 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 a file that contains your list of IDs" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> + <param name="ncol" type="text" value="c1" 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' /> + <conditional name="expression_values"> + <param name="nb_exp" type="select" label="How many expression values column in your file ?"> + <option value="0" >0</option> + <option value="1" >1</option> + <option value="2" >2</option> + <option value="3" >3</option> + </param> + <when value="0"> + </when> + <when value="1"> + <param name="e1" type="text" value="" label="First column number of your expression data" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'/> + </when> + <when value="2"> + <param name="e1" type="text" value="" label="First column number of your expression data"/> + <param name="e2" type="text" value="" label="Second column number of your expression data"/> + </when> + <when value="3"> + <param name="e1" type="text" value="" label="First column number of your expression data"/> + <param name="e2" type="text" value="" label="Second column number of your expression data"/> + <param name="e3" type="text" value="" label="Third column number of your expression data"/> + </when> + </conditional> + </when> + </conditional> + <param name="id_type" type="select" label="select your identifiers type :"> + <option value="uniprotID">Uniprot Accession number</option> + <option value="geneID">Entrez gene ID</option> + </param> + + <conditional name="species"> + <param name="ref_file" type="select" label="Select species" > + <options from_data_table="kegg_pathways"/> + <option value="hsa"/> + <option value="mmu"/> + </param> + <when value="hsa"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="Provide 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 id(s)</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="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 id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + </conditional> + </when> + <when value="mmu"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="Provide 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 id(s)</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 id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + </conditional> + </when> + </conditional> + <param name="native" type="select" label="Choose the output graph format"> + <option value="true">KEGG graph (.png)</option> + <option value="false">Graphviz layout engine (.pdf)</option> + </param> + </inputs> + <outputs> + <data name="graphviz_from_file" format="pdf" label="KEGG mapping with ${input.file.name}"> + <filter>native=="false" and input["ids"] == "file"</filter> + <discover_datasets pattern="(?P<designation>.+)\.pathview.*\.pdf" ext="pdf" visible="true" assign_primary_output="true"/> + </data> + <data name="kegg_from_file" format="png" label="KEGG mapping with ${input.file.name}"> + <filter>native=="true" and input["ids"] == "file"</filter> + <discover_datasets pattern="(?P<designation>.+)\.pathview.*\.png" ext="png" visible="true" assign_primary_output="true"/> + </data> + <data name="graphviz_from_list" format="pdf" label="KEGG mapping with given ids"> + <filter>native=="false" and input["ids"] == "text"</filter> + <discover_datasets pattern="(?P<designation>.+)\.pathview.*\.pdf" ext="pdf" visible="true" assign_primary_output="true"/> + </data> + <data name="kegg_from_list" format="png" label="KEGG mapping with given ids"> + <filter>native=="true" and input["ids"] == "text"</filter> + <discover_datasets pattern="(?P<designation>.+)\.pathview.*\.png" ext="png" visible="true" assign_primary_output="true"/> + </data> + </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[ +This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. + +Select an input file containing ids in a column, set header and column number or copy/paste your ids. + +Select your identifier type and a species of interest (for now only human available). + +Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) + +Select the graph format : KEGG or graphviz + +Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways. + +Output : One file (png or pdf) for each selected pathway. + +----- + +.. class:: infomark + +**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. + ]]></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/README.rst Wed Aug 22 11:30:23 2018 -0400 @@ -0,0 +1,28 @@ +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. + +Select an input file containing ids in a column, set header and column number or copy/paste your ids. + +Select your identifier type and a species of interest (for now only human available). + +Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) + +Select the graph format : KEGG or graphviz + +Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways. + +Output : One file (png or pdf) for each selected pathway. \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_pathways.loc.sample Wed Aug 22 11:30:23 2018 -0400 @@ -0,0 +1,2 @@ +hsa_pathways Human (hsa) hsa tool-data/hsa_pathways.csv +mmu_pathways Mouse (mmu) mmu tool-data/mmu_pathways.csv \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Lacombe_et_al_2017_OK.txt Wed Aug 22 11:30:23 2018 -0400 @@ -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_table_conf.xml.sample Wed Aug 22 11:30:23 2018 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Location kegg_pathways file for pathview tool --> + <table name="kegg_pathways" comment_char="#" > + <columns>dbkey,name,value,path</columns> + <file path="tool-data/kegg_pathways.loc" /> + </table> +</tables> \ No newline at end of file