Mercurial > repos > proteore > proteore_maps_visualization
changeset 0:789acaab8255 draft
planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
| author | proteore |
|---|---|
| date | Thu, 06 Dec 2018 08:27:31 -0500 |
| parents | |
| children | 48f302ae5545 |
| files | README.rst kegg_maps_visualization.R kegg_maps_visualization.xml kegg_pathways_list_index.loc.sample test-data/Lacombe_et_al_2017_OK.txt test-data/hsa00010.pathview.png test-data/hsa04514.pathview.png test-data/hsa05167.pathview.png tool-data/hsa_pathways.loc tool-data/hsa_pathways.loc.sample tool-data/mmu_pathways.loc tool-data/mmu_pathways.loc.sample tool-data/rno_pathways.loc tool-data/rno_pathways.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 15 files changed, 2924 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,94 @@ +Wrapper for Pathview tool +============================= + +**Authors** + +David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + +============================= + +This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. + +You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat. + +If your input have another type of IDs, please use the ID_Converter tool. + +**Input:** + + +- KEGG Pathways IDs to be used for mapping can be set by: + - chosing from the KEGG pathways name list + - giving a list (copy/paste) + - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column) +- Genes/proteins ids to map can be either a list of Entrez genes IDs / Uniprot accession number or a file (tabular, tsv, txt) containing at least one column of Entrez genes IDs / Uniprot accession number. +- fold change values (up to three columns) from a dataset (same dataset as for Genes/proteins ids to map) + +You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values. + +.. csv-table:: Simulated data + :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3" + + "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759" + "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064" + "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729" + "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788" + +| + + + +.. class:: warningmark + +If there's more than one id per line in the defined column, it will be split to have only one id per line. For example this table: + +.. csv-table:: Simulated data + :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" + + "ENSG00000136881","Q14032","BAAT_HUMAN" + "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000244731","P0C0L4","CO4A_HUMAN" + +| + +will become: + +.. csv-table:: Simulated data + :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" + + "ENSG00000136881","Q14032","BAAT_HUMAN" + "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000244731","P0C0L4","CO4A_HUMAN" + +| + +**Output:** + +- a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway. +- a **summary text file** (.tsv) of the mapping(s) with the following columns + - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids + - **pathway name**: name(s) of KEGG pathway(s) used for mapping + - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs + - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping + - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway + - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway + - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs + - **Entrez gene ID mapped**: list of mapped Entrez gene IDs + - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs + +----- + +.. class:: infomark + +**Database:** + +KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/ + +User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_maps_visualization.R Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,345 @@ +#!/usr/bin/Rscript +#Rscript made for mapping genesID on KEGG pathway with Pathview package +#input : csv file containing ids (uniprot or geneID) to map, plus parameters +#output : KEGG pathway : jpeg or pdf file. + +options(warn=-1) #TURN OFF WARNINGS !!!!!! +suppressMessages(library("pathview")) +suppressMessages(library(KEGGREST)) + +read_file <- function(path,header){ + file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F, comment.char = "#"),silent=TRUE) + if (inherits(file,"try-error")){ + stop("File not found !") + }else{ + return(file) + } +} + +##### fuction to clean and concatenate pathway name (allow more flexibility for user input) +concat_string <- function(x){ + x <- gsub(" - .*","",x) + x <- gsub(" ","",x) + x <- gsub("-","",x) + x <- gsub("_","",x) + x <- gsub(",","",x) + x <- gsub("\\'","",x) + x <- gsub("\\(.*)","",x) + x <- gsub("\\/","",x) + x <- tolower(x) + return(x) +} + +#return output suffix (pathway name) from id kegg (ex : hsa:00010) +get_suffix <- function(pathways_list,species,id){ + suffix = gsub("/","or",pathways_list[pathways_list[,1]==paste(species,id,sep=""),2]) + suffix = gsub(" ","_",suffix) + if (nchar(suffix) > 50){ + suffix = substr(suffix,1,50) + } + return(suffix) +} + +str2bool <- function(x){ + if (any(is.element(c("t","true"),tolower(x)))){ + return (TRUE) + }else if (any(is.element(c("f","false"),tolower(x)))){ + return (FALSE) + }else{ + return(NULL) + } +} + +is.letter <- function(x) grepl("[[:alpha:]]", x) + +#### hsa00010 -> 00010 +remove_kegg_prefix <- function(x){ + x = gsub(":","",x) + if (substr(x,1,4) == 'path'){ + x=substr(x,5,nchar(x)) + } + if (is.letter(substr(x,1,3))){ + x <- substr(x,4,nchar(x)) + } + return(x) +} + +kegg_to_geneID <- function(vector){ + vector <- sapply(vector, function(x) unlist(strsplit(x,":"))[2],USE.NAMES = F) + return (vector) +} + +clean_bad_character <- function(string) { + string <- gsub("X","",string) + return(string) +} + +get_list_from_cp <-function(list){ + list = strsplit(list, "[ \t\n]+")[[1]] + list = list[list != ""] #remove empty entry + list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2") + return(list) +} + +get_ref_pathways <- function(species){ + ##all available pathways for the species + pathways <-keggLink("pathway", species) + tot_path<-unique(pathways) + + ##formating the dat into a list object + ##key= pathway ID, value = genes of the pathway in the kegg format + pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway))) + return (pathways_list) +} + +mapping_summary <- function(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID){ + ref_pathways = get_ref_pathways(species) + names(ref_pathways) <- sapply(names(ref_pathways), function(x) gsub("path:[a-z]{3}","",x),USE.NAMES = F) + + #genes present in pathway + genes = ref_pathways[id][[1]] + nb_genes = length(genes) + + #genes mapped on pathway genes + mapped <- unlist(sapply(pv.out$plot.data.gene$all.mapped, function(x) strsplit(x,",")),use.names = F) + mapped = unique(mapped[mapped!=""]) + nb_mapped <- length(mapped) + + #compue ratio of mapping + ratio = round((nb_mapped/nb_genes)*100, 2) + if (is.nan(ratio)) { ratio = ""} + pathway_id = paste(species,id,sep="") + pathway_name = as.character(pathways_list[pathways_list[,1]==pathway_id,][2]) + + if (id_type=="geneid" || id_type=="keggid") { + row <- c(pathway_id,pathway_name,length(unique(geneID)),nb_mapped,nb_genes,ratio,paste(mapped,collapse=";")) + names(row) <- c("KEGG pathway ID","pathway name","nb of Entrez gene ID used","nb of Entrez gene ID mapped", + "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped") + } else if (id_type=="uniprotid") { + row <- c(pathway_id,pathway_name,length(unique(uniprotID)),length(unique(geneID)),nb_mapped,nb_genes,ratio,paste(mapped,collapse=";"),paste(mapped2geneID[which(mapped2geneID[,2] %in% mapped)],collapse=";")) + names(row) <- c("KEGG pathway ID","pathway name","nb of Uniprot_AC used","nb of Entrez gene ID used","nb of Entrez gene ID mapped", + "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped","uniprot_AC mapped") + } + return(row) +} + +#take data frame, return data frame +split_ids_per_line <- function(line,ncol){ + + #print (line) + header = colnames(line) + line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol]) + + if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) { + if (length(line)==1 ) { + lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F) + } else { + if (ncol==1) { #first column + lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)])) + } else if (ncol==length(line)) { #last column + lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";")))) + } else { + lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)])) + } + } + colnames(lines)=header + return(lines) + } else { + return(line) + } +} + +#create new lines if there's more than one id per cell in the columns in order to have only one id per line +one_id_one_line <-function(tab,ncol){ + + if (ncol(tab)>1){ + + tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x)) + header=colnames(tab) + res=as.data.frame(matrix(ncol=ncol(tab),nrow=0)) + for (i in 1:nrow(tab) ) { + lines = split_ids_per_line(tab[i,],ncol) + res = rbind(res,lines) + } + }else { + res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F) + res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F) + colnames(res)=colnames(tab) + } + return(res) +} + +get_args <- function(){ + + ## Collect arguments + args <- commandArgs(TRUE) + + ## Default setting when no arguments passed + if(length(args) < 1) { + args <- c("--help") + } + + ## Help section + if("--help" %in% args) { + cat("Pathview R script + Arguments: + --help Print this test + --input path of the input file (must contains a colum of uniprot and/or geneID accession number) + --id_list list of ids to use, ',' separated + --pathways_id Id(s) of pathway(s) to use, if several, semicolon separated list : hsa00010;hsa05412 + --id_type Type of accession number ('uniprotID' or 'geneID') + --id_column Column containing accesion number of interest (ex : 'c1') + --header Boolean, TRUE if header FALSE if not + --output Output filename + --fold_change_col Column(s) containing fold change values (comma separated) + --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph + --species KEGG species (hsa, mmu, ...) + --pathways_input Tab with pathways in a column, output format of find_pathways + --pathway_col Column of pathways to use + --header2 Boolean, TRUE if header FALSE if not + --pathways_list path of file containg the species pathways list (hsa_pathways.loc, mmu_pathways.loc, ...) + + Example: + ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n") + + q(save="no") + } + + parseArgs <- function(x) strsplit(sub("^--", "", x), "=") + argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) + args <- as.list(as.character(argsDF$V2)) + names(args) <- argsDF$V1 + + return(args) +} + +main <- function(){ + + args <- get_args() + + #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_maps_visualization/args.Rda") + #load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_maps_visualization/args.Rda") + + ###setting variables + if (!is.null(args$pathways_id)) { + ids <- get_list_from_cp(clean_bad_character(args$pathways_id)) + ids <- sapply(ids, function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) + }else if (!is.null(args$pathways_input)){ + header2 <- str2bool(args$header2) + pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col)) + pathways_file = read_file(args$pathways_input,header2) + ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) + } + pathways_list <- read_file(args$pathways_list,F) + if (!is.null(args$id_list)) { + id_list <- get_list_from_cp(args$id_list) + } + id_type <- tolower(args$id_type) + ncol <- as.numeric(gsub("c", "" ,args$id_column)) + header <- str2bool(args$header) + native_kegg <- str2bool(args$native_kegg) + species=args$species + fold_change_data = str2bool(args$fold_change_data) + + #org list used in mapped2geneID + org <- c('Hs','Mm','Rn') + names(org) <- c('hsa','mmu','rno') + + #read input file or list + if (!is.null(args$input)){ + tab <- read_file(args$input,header) + tab <- data.frame(tab[which(tab[ncol]!=""),],stringsAsFactors = F) + tab = one_id_one_line(tab,ncol) + } else { + id_list = gsub("[[:blank:]]|\u00A0|NA","",id_list) + id_list = unique(id_list[id_list!=""]) + tab <- data.frame(id_list,stringsAsFactors = F) + ncol=1 + } + + + ##### map uniprotID to entrez geneID and kegg to geneID + uniprotID="" + mapped2geneID="" + if (id_type == "uniprotid") { + uniprotID=tab[,ncol] + mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL) + geneID = mapped2geneID[,2] + tab = cbind(tab,geneID) + ncol=ncol(tab) + }else if (id_type == "keggid"){ + keggID = tab[,ncol] + geneID = kegg_to_geneID(keggID) + tab = cbind(tab,geneID) + ncol=ncol(tab) + }else if (id_type == "geneid"){ + colnames(tab)[ncol] <- "geneID" + } + + ##### build matrix to map on KEGG pathway (kgml : KEGG xml) + geneID_indices = which(!is.na(tab$geneID)) + if (fold_change_data) { + fold_change <- as.integer(unlist(strsplit(gsub("c","",args$fold_change_col),","))) + if (length(fold_change) > 3) { fold_change= fold_change[1:3] } + if (length(fold_change)==1){ + tab[,fold_change] <- as.double(gsub(",",".",as.character(tab[,fold_change]) )) + } else { + tab[,fold_change] <- apply(tab[,fold_change],2,function(x) as.double(gsub(",",".",as.character(x)))) + } + mat = tab[geneID_indices,c(ncol,fold_change)] + mat = mat[(!duplicated(mat$geneID)),] + geneID=mat$geneID + mat = as.data.frame(mat[,-1]) + row.names(mat)=geneID + } else { + mat = unique(as.character(tab$geneID[!is.na(tab$geneID[tab$geneID!=""])])) + geneID=mat + } + + #####mapping geneID (with or without expression values) on KEGG pathway + plot.col.key= TRUE + low_color = "green" + mid_color = "#F3F781" #yellow + high_color = "red" + if (!fold_change_data) { + plot.col.key= FALSE #if there's no exrepession data, we don't show the color key + high_color = "#81BEF7" #blue + } + + #create graph(s) and text output + for (id in ids) { + suffix= get_suffix(pathways_list,species,id) + pv.out <- suppressMessages(pathview(gene.data = mat, + gene.idtype = "entrez", + pathway.id = id, + species = species, + kegg.dir = ".", + out.suffix=suffix, + kegg.native = native_kegg, + low = list(gene = low_color, cpd = "blue"), + mid = list(gene = mid_color, cpd = "transparent"), + high = list(gene = high_color, cpd = "yellow"), + na.col="#D8D8D8", #gray + cpd.data=NULL, + plot.col.key = plot.col.key, + pdf.size=c(9,9))) + + if (is.list(pv.out)){ + + #creating text file + if (!exists("DF")) { + DF <- data.frame(t(mapping_summary(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID)),stringsAsFactors = F,check.names = F) + } else { + #print (mapping_summary(pv.out,species,id)) + DF <- rbind(DF,data.frame(t(mapping_summary(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID)),stringsAsFactors = F,check.names = F)) + } + } + } + + DF <- as.data.frame(apply(DF, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA + + #text file output + write.table(DF,file=args$output,quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE) +} + +main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_maps_visualization.xml Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,333 @@ +<tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.06.1"> + <description>of quantified genes/proteins</description> + <requirements> + <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> + <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/kegg_maps_visualization.R + #if $input.ids == "text" + --id_list="$input.txt" + #else + --input="$input.file" + --id_column="$input.ncol" + --header="$input.header" + #end if + #if $species.pathways.pathways_id != "pathways_file" + --pathways_id="$species.pathways.pids" + #else + --pathways_input="$species.pathways.file" + --header2="$species.pathways.header2" + --pathway_col="$species.pathways.ncol2" + #end if + --id_type="$id_type" + --native_kegg="$native" + + + #if $input.ids=="file" and $input.foldchange.fc=="true" + --fold_change_data="$input.foldchange.fc" + --fold_change_col="$input.foldchange.fc_col" + #else + --fold_change_data="false" + #end if + + --species=${species.ref_file} + --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] } + --output="$text_output" + + ]]></command> + <inputs> + <conditional name="species"> + <param name="ref_file" type="select" label="Select species" > + <option value="hsa">Human (H. sapiens)</option> + <option value="mmu">Mouse (M. musculus)</option> + <option value="rno">Rat (R. norvegicus)</option> + </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> + <option value="pathways_file">KEGG pathway id(s) from file</option> + </param> + <when value="pathways_names"> + <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> + <options from_data_table="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 tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + <when value="pathways_file"> + <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> + <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" /> + <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> + </conditional> + </when> + <when value="mmu"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="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> + <option value="pathways_file">KEGG pathway id(s) from file</option> + </param> + <when value="pathways_names"> + <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> + <options from_data_table="mmu_pathways"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="pathways_ids"> + <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "mmu00053 mmu00340"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + <when value="pathways_file"> + <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id " help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" /> + <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> + <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> + </conditional> + </when> + <when value="rno"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="Enter your pathway(s) name/id" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> + <option value="pathways_names">KEGG pathway name(s)</option> + <option value="pathways_ids">KEGG pathway id(s)</option> + <option value="pathways_file">KEGG pathway id(s) from file</option> + </param> + <when value="pathways_names"> + <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> + <options from_data_table="rno_pathways"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="pathways_ids"> + <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + <when value="pathways_file"> + <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> + <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" /> + <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> + </conditional> + </when> + </conditional> + <param name="id_type" type="select" label="Select your identifiers type for the genes to map on the pathway(s):"> + <option value="geneID" selected="true">Entrez gene ID</option> + <option value="keggid">KEGG genes ID</option> + <option value="uniprotID">Uniprot Accession number</option> + </param> + <conditional name="input" > + <param name="ids" type="select" label="Enter your 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 tab, space or carriage return into the form field, for example: P31946 P62258' > + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular" label="Select 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 contains a header?" /> + <param name="ncol" type="text" value="c1" label="The column which contains your IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <conditional name="foldchange" > + <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Do you have fold change values to represent on the graph ?"/> + <when value="true"> + <param name="fc_col" type="text" label="Please enter column(s) number of fold change data separated by ','. 3 columns max" help="For example : c1,c3,c4"/> + </when> + <when value="false"/> + </conditional> + </when> + </conditional> + <param name="native" type="select" label="Choose the output graphical format"> + <option value="true">KEGG map (.png)</option> + <option value="false">Graphviz layout engine (.pdf)</option> + </param> + </inputs> + <outputs> + <data name="text_output" format="tsv" label="KEGG maps visualization text output"/> + <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="graphviz_output_from_file"> + <filter>native=="false" and input["ids"] == "file"</filter> + <discover_datasets pattern="(?P<designation>.+\..*)\.pdf" ext="pdf" /> + </collection> + <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="kegg_graph_output_from_file"> + <filter>native=="true" and input["ids"] == "file"</filter> + <discover_datasets pattern="(?P<designation>.+\..*)\.png" ext="png"/> + </collection> + <collection type="list" label="KEGG maps visualization" name="graphviz_output_from_list"> + <filter>native=="false" and input["ids"] == "text"</filter> + <discover_datasets pattern="(?P<designation>.+\..*)\.pdf" ext="pdf" /> + </collection> + <collection type="list" label="KEGG maps visualization" name="kegg_graph_output_from_list"> + <filter>native=="true" and input["ids"] == "text"</filter> + <discover_datasets pattern="(?P<designation>.+\..*)\.png" ext="png" /> + </collection> + </outputs> + <tests> + <!--test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="Lacombe_et_al_2017_OK.txt"/> + <param name="header" value="true"/> + <param name="ncol" value="c1"/> + </conditional> + <conditional name="pathways"> + <param name="pathways_id" value="pathways_ids"/> + <param name="pids" value="04514,05167,00010"/> + </conditional> + <param name="id_type" value="uniprotID"/> + <param name="species" value="hsa"/> + <param name="native" value="true"/> + <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/> + <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/> + <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/> + </test--> + </tests> + <help><![CDATA[ +This tool map a list identifiers to KEGG pathway with the R package 'pathview'. + +You can map Entrez gene ID, KEGG genes ID or Uniprot accession number from three species : human, mouse and rat. + +If your input have another type of IDs, please use the ID_Converter tool. + +**Input:** + + +- KEGG Pathways IDs to be used for mapping can be set by: + - chosing from the KEGG pathways name list + - giving a list (copy/paste) + - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column) +- Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number or in a column of a file (tabular, tsv, txt). +- Fold change values (up to three columns) from a dataset (same dataset as identifiers to map) can be added. + +You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values. + +.. csv-table:: Simulated data + :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3" + + "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759" + "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064" + "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729" + "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788" + +| + + +.. class:: warningmark + +If there's more than one id per line in the defined column, it will be split to have only one id per line. For example this table: + +.. csv-table:: Simulated data + :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" + + "ENSG00000136881","Q14032","BAAT_HUMAN" + "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000244731","P0C0L4","CO4A_HUMAN" + +| + +will become: + +.. csv-table:: Simulated data + :header: "Ensembl_Gene","UniProt.AC","UniProt.ID" + + "ENSG00000136881","Q14032","BAAT_HUMAN" + "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN" + "ENSG00000244731","P0C0L4","CO4A_HUMAN" + +| + +**Output:** + +- a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway. +- a **summary text file** (.tsv) of the mapping(s) with the following columns + - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids + - **pathway name**: name(s) of KEGG pathway(s) used for mapping + - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs + - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping + - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway + - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway + - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs + - **Entrez gene ID mapped**: list of mapped Entrez gene IDs + - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs + +----- + +.. class:: infomark + +**Database:** + +KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/ + +User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html + + +----- + +.. 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/kegg_pathways_list_index.loc.sample Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,4 @@ +#value name path +hsa Homo sapiens tool-data/hsa_pathways.loc +mmu Mus musculus tool-data/mmu_pathways.loc +rno Rattus norvegicus tool-data/rno_pathways.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Lacombe_et_al_2017_OK.txt Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,165 @@ +Protein accession number (UniProt) Protein name Number of peptides (razor + unique) +P15924 Desmoplakin 69 +P02538 Keratin, type II cytoskeletal 6A 53 +P02768 Serum albumin 44 +P08779 Keratin, type I cytoskeletal 16 29 +Q02413 Desmoglein-1 24 +P07355 "Annexin A2;Putative annexin A2-like protein" 22 +P14923 Junction plakoglobin 22 +P02788 Lactotransferrin 21 +Q9HC84 Mucin-5B 21 +P29508 Serpin B3 20 +P63261 Actin, cytoplasmic 2 19 +Q8N1N4 Keratin, type II cytoskeletal 78 18 +Q04695 Keratin, type I cytoskeletal 17 18 +P01876 Ig alpha-1 chain C region 16 +Q01469 Fatty acid-binding protein 5, epidermal 15 +P31944 Caspase-14 15 +P01833 Polymeric immunoglobulin receptor 15 +P06733 Alpha-enolase 15 +P25311 Zinc-alpha-2-glycoprotein 15 +Q15149 Plectin 15 +P19013 Keratin, type II cytoskeletal 4 13 +Q6KB66 Keratin, type II cytoskeletal 80 13 +Q08188 Protein-glutamine gamma-glutamyltransferase E 12 +P13646 Keratin, type I cytoskeletal 13 11 +Q86YZ3 Hornerin 11 +P04259 Keratin, type II cytoskeletal 6B 10 +P02545 "Prelamin-A/C;Lamin-A/C" 10 +P04083 Annexin A1 10 +P11021 78 kDa glucose-regulated protein 10 +P02787 Serotransferrin 9 +P04040 Catalase 9 +P31151 Protein S100-A7 9 +P31947 14-3-3 protein sigma 9 +Q96P63 Serpin B12 9 +P14618 Pyruvate kinase PKM 9 +P60174 Triosephosphate isomerase 9 +Q06830 Peroxiredoxin-1 9 +P01040 Cystatin-A 8 +P05089 Arginase-1 8 +P01834 Ig kappa chain C region 8 +P04406 Glyceraldehyde-3-phosphate dehydrogenase 8 +P0DMV9 Heat shock 70 kDa protein 1B 8 +P13639 Elongation factor 2 8 +P35579 Myosin-9 8 +P68371 Tubulin beta-4B chain 8 +Q8WVV4 Protein POF1B 8 +O75635 Serpin B7 7 +P01857 Ig gamma-1 chain C region 7 +P61626 Lysozyme C 7 +P68363 Tubulin alpha-1B chain 7 +P01009 "Alpha-1-antitrypsin;Short peptide from AAT" 6 +P07900 Heat shock protein HSP 90-alpha 6 +Q9NZH8 Interleukin-36 gamma 6 +O43707 "Alpha-actinin-4;Alpha-actinin-1" 6 +O75223 Gamma-glutamylcyclotransferase 6 +P00338 L-lactate dehydrogenase A chain 6 +P07339 Cathepsin D 6 +P62987 Ubiquitin-60S ribosomal protein L40 6 +P10599 Thioredoxin 6 +Q9UGM3 Deleted in malignant brain tumors 1 protein 6 +Q9UI42 Carboxypeptidase A4 6 +P47929 Galectin-7 5 +Q13867 Bleomycin hydrolase 5 +Q6P4A8 Phospholipase B-like 1 5 +O75369 Filamin-B 5 +P00441 Superoxide dismutase [Cu-Zn] 5 +P04792 Heat shock protein beta-1 5 +P11142 Heat shock cognate 71 kDa protein 5 +P58107 Epiplakin 5 +P60842 Eukaryotic initiation factor 4A-I 5 +P62937 Peptidyl-prolyl cis-trans isomerase A 5 +P63104 14-3-3 protein zeta/delta 5 +Q92820 Gamma-glutamyl hydrolase 5 +O75342 Arachidonate 12-lipoxygenase, 12R-type 4 +P09211 Glutathione S-transferase P 4 +P31025 Lipocalin-1 4 +P48594 Serpin B4 4 +Q14574 Desmocollin-3 4 +Q5T750 Skin-specific protein 32 4 +Q6UWP8 Suprabasin 4 +O60911 Cathepsin L2 4 +P00558 Phosphoglycerate kinase 1 4 +P04075 Fructose-bisphosphate aldolase A 4 +P07384 Calpain-1 catalytic subunit 4 +P0CG05 Ig lambda-2 chain C regions 4 +P18206 Vinculin 4 +P62258 14-3-3 protein epsilon 4 +P68871 Hemoglobin subunit beta 4 +Q9C075 Keratin, type I cytoskeletal 23 4 +A8K2U0 Alpha-2-macroglobulin-like protein 1 3 +P00738 Haptoglobin 3 +P01011 Alpha-1-antichymotrypsin 3 +P02763 Alpha-1-acid glycoprotein 1 3 +P18510 Interleukin-1 receptor antagonist protein 3 +P22528 Cornifin-B 3 +P30740 Leukocyte elastase inhibitor 3 +P80188 Neutrophil gelatinase-associated lipocalin 3 +Q15828 Cystatin-M 3 +Q9HCY8 Protein S100-A14 3 +P01623 Ig kappa chain V-III region 3 +P01877 Ig alpha-2 chain C region 3 +P06396 Gelsolin 3 +P14735 Insulin-degrading enzyme 3 +P20933 N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase 3 +P25788 Proteasome subunit alpha type-3 3 +P26641 Elongation factor 1-gamma 3 +P36952 Serpin B5 3 +P40926 Malate dehydrogenase, mitochondrial 3 +Q9Y6R7 IgGFc-binding protein 3 +O95274 Ly6/PLAUR domain-containing protein 3 2 +P00491 Purine nucleoside phosphorylase 2 +P04080 Cystatin-B 2 +P09972 Fructose-bisphosphate aldolase C 2 +P19012 Keratin, type I cytoskeletal 15 2 +P20930 Filaggrin 2 +Q96FX8 p53 apoptosis effector related to PMP-22 2 +Q9UIV8 Serpin B13 2 +P01625 Ig kappa chain V-IV region Len 2 +P01765 Ig heavy chain V-III region TIL 2 +P01766 Ig heavy chain V-III region BRO 2 +P01860 Ig gamma-3 chain C region 2 +P01871 Ig mu chain C region 2 +P05090 Apolipoprotein D 2 +P06870 Kallikrein-1 2 +P07858 Cathepsin B 2 +P08865 40S ribosomal protein SA 2 +P11279 Lysosome-associated membrane glycoprotein 1 2 +P13473 Lysosome-associated membrane glycoprotein 2 2 +P19971 Thymidine phosphorylase 2 +P23284 Peptidyl-prolyl cis-trans isomerase B 2 +P23396 40S ribosomal protein S3 2 +P25705 ATP synthase subunit alpha, mitochondrial 2 +P27482 Calmodulin-like protein 3 2 +P31949 Protein S100-A11 2 +P40121 Macrophage-capping protein 2 +P42357 Histidine ammonia-lyase 2 +P47756 F-actin-capping protein subunit beta 2 +P48637 Glutathione synthetase 2 +P49720 Proteasome subunit beta type-3 2 +P50395 Rab GDP dissociation inhibitor beta 2 +P59998 Actin-related protein 2/3 complex subunit 4 2 +P61160 Actin-related protein 2 2 +P61916 Epididymal secretory protein E1 2 +P04745 Alpha-amylase 1 23 +Q9NZT1 Calmodulin-like protein 5 8 +P12273 Prolactin-inducible protein 6 +Q96DA0 Zymogen granule protein 16 homolog B 5 +P01036 Cystatin-S 5 +Q8TAX7 Mucin-7 2 +P01037 Cystatin-SN 2 +P09228 Cystatin-SA 2 +P04264 Keratin, type II cytoskeletal 1 61 +P35908 Keratin, type II cytoskeletal 2 epidermal 40 +P13645 Keratin, type I cytoskeletal 10 40 +Q5D862 Filaggrin-2 14 +Q5T749 Keratinocyte proline-rich protein 13 +Q8IW75 Serpin A12 3 +P81605 Dermcidin 3 +P22531 Small proline-rich protein 2E 3 +P59666 Neutrophil defensin 3 2 +P78386 Keratin, type II cuticular Hb5 2 + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/hsa_pathways.loc Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,330 @@ +#value name +hsa00010 Glycolysis / Gluconeogenesis +hsa00020 Citrate cycle (TCA cycle) +hsa00030 Pentose phosphate pathway +hsa00040 Pentose and glucuronate interconversions +hsa00051 Fructose and mannose metabolism +hsa00052 Galactose metabolism +hsa00053 Ascorbate and aldarate metabolism +hsa00061 Fatty acid biosynthesis +hsa00062 Fatty acid elongation +hsa00071 Fatty acid degradation +hsa00072 Synthesis and degradation of ketone bodies +hsa00100 Steroid biosynthesis +hsa00120 Primary bile acid biosynthesis +hsa00130 Ubiquinone and other terpenoid-quinone biosynthesis +hsa00140 Steroid hormone biosynthesis +hsa00190 Oxidative phosphorylation +hsa00220 Arginine biosynthesis +hsa00230 Purine metabolism +hsa00232 Caffeine metabolism +hsa00240 Pyrimidine metabolism +hsa00250 Alanine, aspartate and glutamate metabolism +hsa00260 Glycine, serine and threonine metabolism +hsa00270 Cysteine and methionine metabolism +hsa00280 Valine, leucine and isoleucine degradation +hsa00290 Valine, leucine and isoleucine biosynthesis +hsa00310 Lysine degradation +hsa00330 Arginine and proline metabolism +hsa00340 Histidine metabolism +hsa00350 Tyrosine metabolism +hsa00360 Phenylalanine metabolism +hsa00380 Tryptophan metabolism +hsa00400 Phenylalanine, tyrosine and tryptophan biosynthesis +hsa00410 beta-Alanine metabolism +hsa00430 Taurine and hypotaurine metabolism +hsa00440 Phosphonate and phosphinate metabolism +hsa00450 Selenocompound metabolism +hsa00471 D-Glutamine and D-glutamate metabolism +hsa00472 D-Arginine and D-ornithine metabolism +hsa00480 Glutathione metabolism +hsa00500 Starch and sucrose metabolism +hsa00510 N-Glycan biosynthesis +hsa00511 Other glycan degradation +hsa00512 Mucin type O-glycan biosynthesis +hsa00514 Other types of O-glycan biosynthesis +hsa00515 Mannose type O-glycan biosynthesis +hsa00520 Amino sugar and nucleotide sugar metabolism +hsa00524 Neomycin, kanamycin and gentamicin biosynthesis +hsa00531 Glycosaminoglycan degradation +hsa00532 Glycosaminoglycan biosynthesis +hsa00533 Glycosaminoglycan biosynthesis +hsa00534 Glycosaminoglycan biosynthesis +hsa00561 Glycerolipid metabolism +hsa00562 Inositol phosphate metabolism +hsa00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +hsa00564 Glycerophospholipid metabolism +hsa00565 Ether lipid metabolism +hsa00590 Arachidonic acid metabolism +hsa00591 Linoleic acid metabolism +hsa00592 alpha-Linolenic acid metabolism +hsa00600 Sphingolipid metabolism +hsa00601 Glycosphingolipid biosynthesis +hsa00603 Glycosphingolipid biosynthesis +hsa00604 Glycosphingolipid biosynthesis +hsa00620 Pyruvate metabolism +hsa00630 Glyoxylate and dicarboxylate metabolism +hsa00640 Propanoate metabolism +hsa00650 Butanoate metabolism +hsa00670 One carbon pool by folate +hsa00730 Thiamine metabolism +hsa00740 Riboflavin metabolism +hsa00750 Vitamin B6 metabolism +hsa00760 Nicotinate and nicotinamide metabolism +hsa00770 Pantothenate and CoA biosynthesis +hsa00780 Biotin metabolism +hsa00785 Lipoic acid metabolism +hsa00790 Folate biosynthesis +hsa00830 Retinol metabolism +hsa00860 Porphyrin and chlorophyll metabolism +hsa00900 Terpenoid backbone biosynthesis +hsa00910 Nitrogen metabolism +hsa00920 Sulfur metabolism +hsa00970 Aminoacyl-tRNA biosynthesis +hsa00980 Metabolism of xenobiotics by cytochrome P450 +hsa00982 Drug metabolism +hsa00983 Drug metabolism +hsa01040 Biosynthesis of unsaturated fatty acids +hsa01100 Metabolic pathways +hsa01200 Carbon metabolism +hsa01210 2-Oxocarboxylic acid metabolism +hsa01212 Fatty acid metabolism +hsa01230 Biosynthesis of amino acids +hsa01521 EGFR tyrosine kinase inhibitor resistance +hsa01522 Endocrine resistance +hsa01523 Antifolate resistance +hsa01524 Platinum drug resistance +hsa02010 ABC transporters +hsa03008 Ribosome biogenesis in eukaryotes +hsa03010 Ribosome +hsa03013 RNA transport +hsa03015 mRNA surveillance pathway +hsa03018 RNA degradation +hsa03020 RNA polymerase +hsa03022 Basal transcription factors +hsa03030 DNA replication +hsa03040 Spliceosome +hsa03050 Proteasome +hsa03060 Protein export +hsa03320 PPAR signaling pathway +hsa03410 Base excision repair +hsa03420 Nucleotide excision repair +hsa03430 Mismatch repair +hsa03440 Homologous recombination +hsa03450 Non-homologous end-joining +hsa03460 Fanconi anemia pathway +hsa04010 MAPK signaling pathway +hsa04012 ErbB signaling pathway +hsa04014 Ras signaling pathway +hsa04015 Rap1 signaling pathway +hsa04020 Calcium signaling pathway +hsa04022 cGMP-PKG signaling pathway +hsa04024 cAMP signaling pathway +hsa04060 Cytokine-cytokine receptor interaction +hsa04062 Chemokine signaling pathway +hsa04064 NF-kappa B signaling pathway +hsa04066 HIF-1 signaling pathway +hsa04068 FoxO signaling pathway +hsa04070 Phosphatidylinositol signaling system +hsa04071 Sphingolipid signaling pathway +hsa04072 Phospholipase D signaling pathway +hsa04080 Neuroactive ligand-receptor interaction +hsa04110 Cell cycle +hsa04114 Oocyte meiosis +hsa04115 p53 signaling pathway +hsa04120 Ubiquitin mediated proteolysis +hsa04122 Sulfur relay system +hsa04130 SNARE interactions in vesicular transport +hsa04136 Autophagy +hsa04137 Mitophagy +hsa04140 Autophagy +hsa04141 Protein processing in endoplasmic reticulum +hsa04142 Lysosome +hsa04144 Endocytosis +hsa04145 Phagosome +hsa04146 Peroxisome +hsa04150 mTOR signaling pathway +hsa04151 PI3K-Akt signaling pathway +hsa04152 AMPK signaling pathway +hsa04210 Apoptosis +hsa04211 Longevity regulating pathway +hsa04213 Longevity regulating pathway +hsa04215 Apoptosis +hsa04216 Ferroptosis +hsa04217 Necroptosis +hsa04218 Cellular senescence +hsa04260 Cardiac muscle contraction +hsa04261 Adrenergic signaling in cardiomyocytes +hsa04270 Vascular smooth muscle contraction +hsa04310 Wnt signaling pathway +hsa04330 Notch signaling pathway +hsa04340 Hedgehog signaling pathway +hsa04350 TGF-beta signaling pathway +hsa04360 Axon guidance +hsa04370 VEGF signaling pathway +hsa04371 Apelin signaling pathway +hsa04380 Osteoclast differentiation +hsa04390 Hippo signaling pathway +hsa04392 Hippo signaling pathway +hsa04510 Focal adhesion +hsa04512 ECM-receptor interaction +hsa04514 Cell adhesion molecules (CAMs) +hsa04520 Adherens junction +hsa04530 Tight junction +hsa04540 Gap junction +hsa04550 Signaling pathways regulating pluripotency of stem cells +hsa04610 Complement and coagulation cascades +hsa04611 Platelet activation +hsa04612 Antigen processing and presentation +hsa04614 Renin-angiotensin system +hsa04620 Toll-like receptor signaling pathway +hsa04621 NOD-like receptor signaling pathway +hsa04622 RIG-I-like receptor signaling pathway +hsa04623 Cytosolic DNA-sensing pathway +hsa04625 C-type lectin receptor signaling pathway +hsa04630 Jak-STAT signaling pathway +hsa04640 Hematopoietic cell lineage +hsa04650 Natural killer cell mediated cytotoxicity +hsa04657 IL-17 signaling pathway +hsa04658 Th1 and Th2 cell differentiation +hsa04659 Th17 cell differentiation +hsa04660 T cell receptor signaling pathway +hsa04662 B cell receptor signaling pathway +hsa04664 Fc epsilon RI signaling pathway +hsa04666 Fc gamma R-mediated phagocytosis +hsa04668 TNF signaling pathway +hsa04670 Leukocyte transendothelial migration +hsa04672 Intestinal immune network for IgA production +hsa04710 Circadian rhythm +hsa04713 Circadian entrainment +hsa04714 Thermogenesis +hsa04720 Long-term potentiation +hsa04721 Synaptic vesicle cycle +hsa04722 Neurotrophin signaling pathway +hsa04723 Retrograde endocannabinoid signaling +hsa04724 Glutamatergic synapse +hsa04725 Cholinergic synapse +hsa04726 Serotonergic synapse +hsa04727 GABAergic synapse +hsa04728 Dopaminergic synapse +hsa04730 Long-term depression +hsa04740 Olfactory transduction +hsa04742 Taste transduction +hsa04744 Phototransduction +hsa04750 Inflammatory mediator regulation of TRP channels +hsa04810 Regulation of actin cytoskeleton +hsa04910 Insulin signaling pathway +hsa04911 Insulin secretion +hsa04912 GnRH signaling pathway +hsa04913 Ovarian steroidogenesis +hsa04914 Progesterone-mediated oocyte maturation +hsa04915 Estrogen signaling pathway +hsa04916 Melanogenesis +hsa04917 Prolactin signaling pathway +hsa04918 Thyroid hormone synthesis +hsa04919 Thyroid hormone signaling pathway +hsa04920 Adipocytokine signaling pathway +hsa04921 Oxytocin signaling pathway +hsa04922 Glucagon signaling pathway +hsa04923 Regulation of lipolysis in adipocytes +hsa04924 Renin secretion +hsa04925 Aldosterone synthesis and secretion +hsa04926 Relaxin signaling pathway +hsa04927 Cortisol synthesis and secretion +hsa04928 Parathyroid hormone synthesis, secretion and action +hsa04930 Type II diabetes mellitus +hsa04931 Insulin resistance +hsa04932 Non-alcoholic fatty liver disease (NAFLD) +hsa04933 AGE-RAGE signaling pathway in diabetic complications +hsa04934 Cushing's syndrome +hsa04940 Type I diabetes mellitus +hsa04950 Maturity onset diabetes of the young +hsa04960 Aldosterone-regulated sodium reabsorption +hsa04961 Endocrine and other factor-regulated calcium reabsorption +hsa04962 Vasopressin-regulated water reabsorption +hsa04964 Proximal tubule bicarbonate reclamation +hsa04966 Collecting duct acid secretion +hsa04970 Salivary secretion +hsa04971 Gastric acid secretion +hsa04972 Pancreatic secretion +hsa04973 Carbohydrate digestion and absorption +hsa04974 Protein digestion and absorption +hsa04975 Fat digestion and absorption +hsa04976 Bile secretion +hsa04977 Vitamin digestion and absorption +hsa04978 Mineral absorption +hsa04979 Cholesterol metabolism +hsa05010 Alzheimer's disease +hsa05012 Parkinson's disease +hsa05014 Amyotrophic lateral sclerosis (ALS) +hsa05016 Huntington's disease +hsa05020 Prion diseases +hsa05030 Cocaine addiction +hsa05031 Amphetamine addiction +hsa05032 Morphine addiction +hsa05033 Nicotine addiction +hsa05034 Alcoholism +hsa05100 Bacterial invasion of epithelial cells +hsa05110 Vibrio cholerae infection +hsa05120 Epithelial cell signaling in Helicobacter pylori infection +hsa05130 Pathogenic Escherichia coli infection +hsa05131 Shigellosis +hsa05132 Salmonella infection +hsa05133 Pertussis +hsa05134 Legionellosis +hsa05140 Leishmaniasis +hsa05142 Chagas disease (American trypanosomiasis) +hsa05143 African trypanosomiasis +hsa05144 Malaria +hsa05145 Toxoplasmosis +hsa05146 Amoebiasis +hsa05150 Staphylococcus aureus infection +hsa05152 Tuberculosis +hsa05160 Hepatitis C +hsa05161 Hepatitis B +hsa05162 Measles +hsa05163 Human cytomegalovirus infection +hsa05164 Influenza A +hsa05165 Human papillomavirus infection +hsa05166 HTLV-I infection +hsa05167 Kaposi's sarcoma-associated herpesvirus infection +hsa05168 Herpes simplex infection +hsa05169 Epstein-Barr virus infection +hsa05200 Pathways in cancer +hsa05202 Transcriptional misregulation in cancer +hsa05203 Viral carcinogenesis +hsa05204 Chemical carcinogenesis +hsa05205 Proteoglycans in cancer +hsa05206 MicroRNAs in cancer +hsa05210 Colorectal cancer +hsa05211 Renal cell carcinoma +hsa05212 Pancreatic cancer +hsa05213 Endometrial cancer +hsa05214 Glioma +hsa05215 Prostate cancer +hsa05216 Thyroid cancer +hsa05217 Basal cell carcinoma +hsa05218 Melanoma +hsa05219 Bladder cancer +hsa05220 Chronic myeloid leukemia +hsa05221 Acute myeloid leukemia +hsa05222 Small cell lung cancer +hsa05223 Non-small cell lung cancer +hsa05224 Breast cancer +hsa05225 Hepatocellular carcinoma +hsa05226 Gastric cancer +hsa05230 Central carbon metabolism in cancer +hsa05231 Choline metabolism in cancer +hsa05310 Asthma +hsa05320 Autoimmune thyroid disease +hsa05321 Inflammatory bowel disease (IBD) +hsa05322 Systemic lupus erythematosus +hsa05323 Rheumatoid arthritis +hsa05330 Allograft rejection +hsa05332 Graft-versus-host disease +hsa05340 Primary immunodeficiency +hsa05410 Hypertrophic cardiomyopathy (HCM) +hsa05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +hsa05414 Dilated cardiomyopathy (DCM) +hsa05416 Viral myocarditis +hsa05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/hsa_pathways.loc.sample Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,330 @@ +#value name +hsa00010 Glycolysis / Gluconeogenesis +hsa00020 Citrate cycle (TCA cycle) +hsa00030 Pentose phosphate pathway +hsa00040 Pentose and glucuronate interconversions +hsa00051 Fructose and mannose metabolism +hsa00052 Galactose metabolism +hsa00053 Ascorbate and aldarate metabolism +hsa00061 Fatty acid biosynthesis +hsa00062 Fatty acid elongation +hsa00071 Fatty acid degradation +hsa00072 Synthesis and degradation of ketone bodies +hsa00100 Steroid biosynthesis +hsa00120 Primary bile acid biosynthesis +hsa00130 Ubiquinone and other terpenoid-quinone biosynthesis +hsa00140 Steroid hormone biosynthesis +hsa00190 Oxidative phosphorylation +hsa00220 Arginine biosynthesis +hsa00230 Purine metabolism +hsa00232 Caffeine metabolism +hsa00240 Pyrimidine metabolism +hsa00250 Alanine, aspartate and glutamate metabolism +hsa00260 Glycine, serine and threonine metabolism +hsa00270 Cysteine and methionine metabolism +hsa00280 Valine, leucine and isoleucine degradation +hsa00290 Valine, leucine and isoleucine biosynthesis +hsa00310 Lysine degradation +hsa00330 Arginine and proline metabolism +hsa00340 Histidine metabolism +hsa00350 Tyrosine metabolism +hsa00360 Phenylalanine metabolism +hsa00380 Tryptophan metabolism +hsa00400 Phenylalanine, tyrosine and tryptophan biosynthesis +hsa00410 beta-Alanine metabolism +hsa00430 Taurine and hypotaurine metabolism +hsa00440 Phosphonate and phosphinate metabolism +hsa00450 Selenocompound metabolism +hsa00471 D-Glutamine and D-glutamate metabolism +hsa00472 D-Arginine and D-ornithine metabolism +hsa00480 Glutathione metabolism +hsa00500 Starch and sucrose metabolism +hsa00510 N-Glycan biosynthesis +hsa00511 Other glycan degradation +hsa00512 Mucin type O-glycan biosynthesis +hsa00514 Other types of O-glycan biosynthesis +hsa00515 Mannose type O-glycan biosynthesis +hsa00520 Amino sugar and nucleotide sugar metabolism +hsa00524 Neomycin, kanamycin and gentamicin biosynthesis +hsa00531 Glycosaminoglycan degradation +hsa00532 Glycosaminoglycan biosynthesis +hsa00533 Glycosaminoglycan biosynthesis +hsa00534 Glycosaminoglycan biosynthesis +hsa00561 Glycerolipid metabolism +hsa00562 Inositol phosphate metabolism +hsa00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +hsa00564 Glycerophospholipid metabolism +hsa00565 Ether lipid metabolism +hsa00590 Arachidonic acid metabolism +hsa00591 Linoleic acid metabolism +hsa00592 alpha-Linolenic acid metabolism +hsa00600 Sphingolipid metabolism +hsa00601 Glycosphingolipid biosynthesis +hsa00603 Glycosphingolipid biosynthesis +hsa00604 Glycosphingolipid biosynthesis +hsa00620 Pyruvate metabolism +hsa00630 Glyoxylate and dicarboxylate metabolism +hsa00640 Propanoate metabolism +hsa00650 Butanoate metabolism +hsa00670 One carbon pool by folate +hsa00730 Thiamine metabolism +hsa00740 Riboflavin metabolism +hsa00750 Vitamin B6 metabolism +hsa00760 Nicotinate and nicotinamide metabolism +hsa00770 Pantothenate and CoA biosynthesis +hsa00780 Biotin metabolism +hsa00785 Lipoic acid metabolism +hsa00790 Folate biosynthesis +hsa00830 Retinol metabolism +hsa00860 Porphyrin and chlorophyll metabolism +hsa00900 Terpenoid backbone biosynthesis +hsa00910 Nitrogen metabolism +hsa00920 Sulfur metabolism +hsa00970 Aminoacyl-tRNA biosynthesis +hsa00980 Metabolism of xenobiotics by cytochrome P450 +hsa00982 Drug metabolism +hsa00983 Drug metabolism +hsa01040 Biosynthesis of unsaturated fatty acids +hsa01100 Metabolic pathways +hsa01200 Carbon metabolism +hsa01210 2-Oxocarboxylic acid metabolism +hsa01212 Fatty acid metabolism +hsa01230 Biosynthesis of amino acids +hsa01521 EGFR tyrosine kinase inhibitor resistance +hsa01522 Endocrine resistance +hsa01523 Antifolate resistance +hsa01524 Platinum drug resistance +hsa02010 ABC transporters +hsa03008 Ribosome biogenesis in eukaryotes +hsa03010 Ribosome +hsa03013 RNA transport +hsa03015 mRNA surveillance pathway +hsa03018 RNA degradation +hsa03020 RNA polymerase +hsa03022 Basal transcription factors +hsa03030 DNA replication +hsa03040 Spliceosome +hsa03050 Proteasome +hsa03060 Protein export +hsa03320 PPAR signaling pathway +hsa03410 Base excision repair +hsa03420 Nucleotide excision repair +hsa03430 Mismatch repair +hsa03440 Homologous recombination +hsa03450 Non-homologous end-joining +hsa03460 Fanconi anemia pathway +hsa04010 MAPK signaling pathway +hsa04012 ErbB signaling pathway +hsa04014 Ras signaling pathway +hsa04015 Rap1 signaling pathway +hsa04020 Calcium signaling pathway +hsa04022 cGMP-PKG signaling pathway +hsa04024 cAMP signaling pathway +hsa04060 Cytokine-cytokine receptor interaction +hsa04062 Chemokine signaling pathway +hsa04064 NF-kappa B signaling pathway +hsa04066 HIF-1 signaling pathway +hsa04068 FoxO signaling pathway +hsa04070 Phosphatidylinositol signaling system +hsa04071 Sphingolipid signaling pathway +hsa04072 Phospholipase D signaling pathway +hsa04080 Neuroactive ligand-receptor interaction +hsa04110 Cell cycle +hsa04114 Oocyte meiosis +hsa04115 p53 signaling pathway +hsa04120 Ubiquitin mediated proteolysis +hsa04122 Sulfur relay system +hsa04130 SNARE interactions in vesicular transport +hsa04136 Autophagy +hsa04137 Mitophagy +hsa04140 Autophagy +hsa04141 Protein processing in endoplasmic reticulum +hsa04142 Lysosome +hsa04144 Endocytosis +hsa04145 Phagosome +hsa04146 Peroxisome +hsa04150 mTOR signaling pathway +hsa04151 PI3K-Akt signaling pathway +hsa04152 AMPK signaling pathway +hsa04210 Apoptosis +hsa04211 Longevity regulating pathway +hsa04213 Longevity regulating pathway +hsa04215 Apoptosis +hsa04216 Ferroptosis +hsa04217 Necroptosis +hsa04218 Cellular senescence +hsa04260 Cardiac muscle contraction +hsa04261 Adrenergic signaling in cardiomyocytes +hsa04270 Vascular smooth muscle contraction +hsa04310 Wnt signaling pathway +hsa04330 Notch signaling pathway +hsa04340 Hedgehog signaling pathway +hsa04350 TGF-beta signaling pathway +hsa04360 Axon guidance +hsa04370 VEGF signaling pathway +hsa04371 Apelin signaling pathway +hsa04380 Osteoclast differentiation +hsa04390 Hippo signaling pathway +hsa04392 Hippo signaling pathway +hsa04510 Focal adhesion +hsa04512 ECM-receptor interaction +hsa04514 Cell adhesion molecules (CAMs) +hsa04520 Adherens junction +hsa04530 Tight junction +hsa04540 Gap junction +hsa04550 Signaling pathways regulating pluripotency of stem cells +hsa04610 Complement and coagulation cascades +hsa04611 Platelet activation +hsa04612 Antigen processing and presentation +hsa04614 Renin-angiotensin system +hsa04620 Toll-like receptor signaling pathway +hsa04621 NOD-like receptor signaling pathway +hsa04622 RIG-I-like receptor signaling pathway +hsa04623 Cytosolic DNA-sensing pathway +hsa04625 C-type lectin receptor signaling pathway +hsa04630 Jak-STAT signaling pathway +hsa04640 Hematopoietic cell lineage +hsa04650 Natural killer cell mediated cytotoxicity +hsa04657 IL-17 signaling pathway +hsa04658 Th1 and Th2 cell differentiation +hsa04659 Th17 cell differentiation +hsa04660 T cell receptor signaling pathway +hsa04662 B cell receptor signaling pathway +hsa04664 Fc epsilon RI signaling pathway +hsa04666 Fc gamma R-mediated phagocytosis +hsa04668 TNF signaling pathway +hsa04670 Leukocyte transendothelial migration +hsa04672 Intestinal immune network for IgA production +hsa04710 Circadian rhythm +hsa04713 Circadian entrainment +hsa04714 Thermogenesis +hsa04720 Long-term potentiation +hsa04721 Synaptic vesicle cycle +hsa04722 Neurotrophin signaling pathway +hsa04723 Retrograde endocannabinoid signaling +hsa04724 Glutamatergic synapse +hsa04725 Cholinergic synapse +hsa04726 Serotonergic synapse +hsa04727 GABAergic synapse +hsa04728 Dopaminergic synapse +hsa04730 Long-term depression +hsa04740 Olfactory transduction +hsa04742 Taste transduction +hsa04744 Phototransduction +hsa04750 Inflammatory mediator regulation of TRP channels +hsa04810 Regulation of actin cytoskeleton +hsa04910 Insulin signaling pathway +hsa04911 Insulin secretion +hsa04912 GnRH signaling pathway +hsa04913 Ovarian steroidogenesis +hsa04914 Progesterone-mediated oocyte maturation +hsa04915 Estrogen signaling pathway +hsa04916 Melanogenesis +hsa04917 Prolactin signaling pathway +hsa04918 Thyroid hormone synthesis +hsa04919 Thyroid hormone signaling pathway +hsa04920 Adipocytokine signaling pathway +hsa04921 Oxytocin signaling pathway +hsa04922 Glucagon signaling pathway +hsa04923 Regulation of lipolysis in adipocytes +hsa04924 Renin secretion +hsa04925 Aldosterone synthesis and secretion +hsa04926 Relaxin signaling pathway +hsa04927 Cortisol synthesis and secretion +hsa04928 Parathyroid hormone synthesis, secretion and action +hsa04930 Type II diabetes mellitus +hsa04931 Insulin resistance +hsa04932 Non-alcoholic fatty liver disease (NAFLD) +hsa04933 AGE-RAGE signaling pathway in diabetic complications +hsa04934 Cushing's syndrome +hsa04940 Type I diabetes mellitus +hsa04950 Maturity onset diabetes of the young +hsa04960 Aldosterone-regulated sodium reabsorption +hsa04961 Endocrine and other factor-regulated calcium reabsorption +hsa04962 Vasopressin-regulated water reabsorption +hsa04964 Proximal tubule bicarbonate reclamation +hsa04966 Collecting duct acid secretion +hsa04970 Salivary secretion +hsa04971 Gastric acid secretion +hsa04972 Pancreatic secretion +hsa04973 Carbohydrate digestion and absorption +hsa04974 Protein digestion and absorption +hsa04975 Fat digestion and absorption +hsa04976 Bile secretion +hsa04977 Vitamin digestion and absorption +hsa04978 Mineral absorption +hsa04979 Cholesterol metabolism +hsa05010 Alzheimer's disease +hsa05012 Parkinson's disease +hsa05014 Amyotrophic lateral sclerosis (ALS) +hsa05016 Huntington's disease +hsa05020 Prion diseases +hsa05030 Cocaine addiction +hsa05031 Amphetamine addiction +hsa05032 Morphine addiction +hsa05033 Nicotine addiction +hsa05034 Alcoholism +hsa05100 Bacterial invasion of epithelial cells +hsa05110 Vibrio cholerae infection +hsa05120 Epithelial cell signaling in Helicobacter pylori infection +hsa05130 Pathogenic Escherichia coli infection +hsa05131 Shigellosis +hsa05132 Salmonella infection +hsa05133 Pertussis +hsa05134 Legionellosis +hsa05140 Leishmaniasis +hsa05142 Chagas disease (American trypanosomiasis) +hsa05143 African trypanosomiasis +hsa05144 Malaria +hsa05145 Toxoplasmosis +hsa05146 Amoebiasis +hsa05150 Staphylococcus aureus infection +hsa05152 Tuberculosis +hsa05160 Hepatitis C +hsa05161 Hepatitis B +hsa05162 Measles +hsa05163 Human cytomegalovirus infection +hsa05164 Influenza A +hsa05165 Human papillomavirus infection +hsa05166 HTLV-I infection +hsa05167 Kaposi's sarcoma-associated herpesvirus infection +hsa05168 Herpes simplex infection +hsa05169 Epstein-Barr virus infection +hsa05200 Pathways in cancer +hsa05202 Transcriptional misregulation in cancer +hsa05203 Viral carcinogenesis +hsa05204 Chemical carcinogenesis +hsa05205 Proteoglycans in cancer +hsa05206 MicroRNAs in cancer +hsa05210 Colorectal cancer +hsa05211 Renal cell carcinoma +hsa05212 Pancreatic cancer +hsa05213 Endometrial cancer +hsa05214 Glioma +hsa05215 Prostate cancer +hsa05216 Thyroid cancer +hsa05217 Basal cell carcinoma +hsa05218 Melanoma +hsa05219 Bladder cancer +hsa05220 Chronic myeloid leukemia +hsa05221 Acute myeloid leukemia +hsa05222 Small cell lung cancer +hsa05223 Non-small cell lung cancer +hsa05224 Breast cancer +hsa05225 Hepatocellular carcinoma +hsa05226 Gastric cancer +hsa05230 Central carbon metabolism in cancer +hsa05231 Choline metabolism in cancer +hsa05310 Asthma +hsa05320 Autoimmune thyroid disease +hsa05321 Inflammatory bowel disease (IBD) +hsa05322 Systemic lupus erythematosus +hsa05323 Rheumatoid arthritis +hsa05330 Allograft rejection +hsa05332 Graft-versus-host disease +hsa05340 Primary immunodeficiency +hsa05410 Hypertrophic cardiomyopathy (HCM) +hsa05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +hsa05414 Dilated cardiomyopathy (DCM) +hsa05416 Viral myocarditis +hsa05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mmu_pathways.loc Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,326 @@ +#value name +mmu00010 Glycolysis / Gluconeogenesis +mmu00020 Citrate cycle (TCA cycle) +mmu00030 Pentose phosphate pathway +mmu00040 Pentose and glucuronate interconversions +mmu00051 Fructose and mannose metabolism +mmu00052 Galactose metabolism +mmu00053 Ascorbate and aldarate metabolism +mmu00061 Fatty acid biosynthesis +mmu00062 Fatty acid elongation +mmu00071 Fatty acid degradation +mmu00072 Synthesis and degradation of ketone bodies +mmu00100 Steroid biosynthesis +mmu00120 Primary bile acid biosynthesis +mmu00130 Ubiquinone and other terpenoid-quinone biosynthesis +mmu00140 Steroid hormone biosynthesis +mmu00190 Oxidative phosphorylation +mmu00220 Arginine biosynthesis +mmu00230 Purine metabolism +mmu00232 Caffeine metabolism +mmu00240 Pyrimidine metabolism +mmu00250 Alanine, aspartate and glutamate metabolism +mmu00260 Glycine, serine and threonine metabolism +mmu00270 Cysteine and methionine metabolism +mmu00280 Valine, leucine and isoleucine degradation +mmu00290 Valine, leucine and isoleucine biosynthesis +mmu00310 Lysine degradation +mmu00330 Arginine and proline metabolism +mmu00340 Histidine metabolism +mmu00350 Tyrosine metabolism +mmu00360 Phenylalanine metabolism +mmu00380 Tryptophan metabolism +mmu00400 Phenylalanine, tyrosine and tryptophan biosynthesis +mmu00410 beta-Alanine metabolism +mmu00430 Taurine and hypotaurine metabolism +mmu00440 Phosphonate and phosphinate metabolism +mmu00450 Selenocompound metabolism +mmu00471 D-Glutamine and D-glutamate metabolism +mmu00472 D-Arginine and D-ornithine metabolism +mmu00480 Glutathione metabolism +mmu00500 Starch and sucrose metabolism +mmu00510 N-Glycan biosynthesis +mmu00511 Other glycan degradation +mmu00512 Mucin type O-glycan biosynthesis +mmu00514 Other types of O-glycan biosynthesis +mmu00515 Mannose type O-glycan biosynthesis +mmu00520 Amino sugar and nucleotide sugar metabolism +mmu00524 Neomycin, kanamycin and gentamicin biosynthesis +mmu00531 Glycosaminoglycan degradation +mmu00532 Glycosaminoglycan biosynthesis +mmu00533 Glycosaminoglycan biosynthesis +mmu00534 Glycosaminoglycan biosynthesis +mmu00561 Glycerolipid metabolism +mmu00562 Inositol phosphate metabolism +mmu00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +mmu00564 Glycerophospholipid metabolism +mmu00565 Ether lipid metabolism +mmu00590 Arachidonic acid metabolism +mmu00591 Linoleic acid metabolism +mmu00592 alpha-Linolenic acid metabolism +mmu00600 Sphingolipid metabolism +mmu00601 Glycosphingolipid biosynthesis +mmu00603 Glycosphingolipid biosynthesis +mmu00604 Glycosphingolipid biosynthesis +mmu00620 Pyruvate metabolism +mmu00630 Glyoxylate and dicarboxylate metabolism +mmu00640 Propanoate metabolism +mmu00650 Butanoate metabolism +mmu00670 One carbon pool by folate +mmu00730 Thiamine metabolism +mmu00740 Riboflavin metabolism +mmu00750 Vitamin B6 metabolism +mmu00760 Nicotinate and nicotinamide metabolism +mmu00770 Pantothenate and CoA biosynthesis +mmu00780 Biotin metabolism +mmu00785 Lipoic acid metabolism +mmu00790 Folate biosynthesis +mmu00830 Retinol metabolism +mmu00860 Porphyrin and chlorophyll metabolism +mmu00900 Terpenoid backbone biosynthesis +mmu00910 Nitrogen metabolism +mmu00920 Sulfur metabolism +mmu00970 Aminoacyl-tRNA biosynthesis +mmu00980 Metabolism of xenobiotics by cytochrome P450 +mmu00982 Drug metabolism +mmu00983 Drug metabolism +mmu01040 Biosynthesis of unsaturated fatty acids +mmu01100 Metabolic pathways +mmu01200 Carbon metabolism +mmu01210 2-Oxocarboxylic acid metabolism +mmu01212 Fatty acid metabolism +mmu01230 Biosynthesis of amino acids +mmu01521 EGFR tyrosine kinase inhibitor resistance +mmu01522 Endocrine resistance +mmu01523 Antifolate resistance +mmu01524 Platinum drug resistance +mmu02010 ABC transporters +mmu03008 Ribosome biogenesis in eukaryotes +mmu03010 Ribosome +mmu03013 RNA transport +mmu03015 mRNA surveillance pathway +mmu03018 RNA degradation +mmu03020 RNA polymerase +mmu03022 Basal transcription factors +mmu03030 DNA replication +mmu03040 Spliceosome +mmu03050 Proteasome +mmu03060 Protein export +mmu03320 PPAR signaling pathway +mmu03410 Base excision repair +mmu03420 Nucleotide excision repair +mmu03430 Mismatch repair +mmu03440 Homologous recombination +mmu03450 Non-homologous end-joining +mmu03460 Fanconi anemia pathway +mmu04010 MAPK signaling pathway +mmu04012 ErbB signaling pathway +mmu04014 Ras signaling pathway +mmu04015 Rap1 signaling pathway +mmu04020 Calcium signaling pathway +mmu04022 cGMP-PKG signaling pathway +mmu04024 cAMP signaling pathway +mmu04060 Cytokine-cytokine receptor interaction +mmu04062 Chemokine signaling pathway +mmu04064 NF-kappa B signaling pathway +mmu04066 HIF-1 signaling pathway +mmu04068 FoxO signaling pathway +mmu04070 Phosphatidylinositol signaling system +mmu04071 Sphingolipid signaling pathway +mmu04072 Phospholipase D signaling pathway +mmu04080 Neuroactive ligand-receptor interaction +mmu04110 Cell cycle +mmu04114 Oocyte meiosis +mmu04115 p53 signaling pathway +mmu04120 Ubiquitin mediated proteolysis +mmu04122 Sulfur relay system +mmu04130 SNARE interactions in vesicular transport +mmu04136 Autophagy +mmu04137 Mitophagy +mmu04140 Autophagy +mmu04141 Protein processing in endoplasmic reticulum +mmu04142 Lysosome +mmu04144 Endocytosis +mmu04145 Phagosome +mmu04146 Peroxisome +mmu04150 mTOR signaling pathway +mmu04151 PI3K-Akt signaling pathway +mmu04152 AMPK signaling pathway +mmu04210 Apoptosis +mmu04211 Longevity regulating pathway +mmu04213 Longevity regulating pathway +mmu04215 Apoptosis +mmu04216 Ferroptosis +mmu04217 Necroptosis +mmu04218 Cellular senescence +mmu04260 Cardiac muscle contraction +mmu04261 Adrenergic signaling in cardiomyocytes +mmu04270 Vascular smooth muscle contraction +mmu04310 Wnt signaling pathway +mmu04330 Notch signaling pathway +mmu04340 Hedgehog signaling pathway +mmu04350 TGF-beta signaling pathway +mmu04360 Axon guidance +mmu04370 VEGF signaling pathway +mmu04371 Apelin signaling pathway +mmu04380 Osteoclast differentiation +mmu04390 Hippo signaling pathway +mmu04392 Hippo signaling pathway +mmu04510 Focal adhesion +mmu04512 ECM-receptor interaction +mmu04514 Cell adhesion molecules (CAMs) +mmu04520 Adherens junction +mmu04530 Tight junction +mmu04540 Gap junction +mmu04550 Signaling pathways regulating pluripotency of stem cells +mmu04610 Complement and coagulation cascades +mmu04611 Platelet activation +mmu04612 Antigen processing and presentation +mmu04614 Renin-angiotensin system +mmu04620 Toll-like receptor signaling pathway +mmu04621 NOD-like receptor signaling pathway +mmu04622 RIG-I-like receptor signaling pathway +mmu04623 Cytosolic DNA-sensing pathway +mmu04625 C-type lectin receptor signaling pathway +mmu04630 Jak-STAT signaling pathway +mmu04640 Hematopoietic cell lineage +mmu04650 Natural killer cell mediated cytotoxicity +mmu04657 IL-17 signaling pathway +mmu04658 Th1 and Th2 cell differentiation +mmu04659 Th17 cell differentiation +mmu04660 T cell receptor signaling pathway +mmu04662 B cell receptor signaling pathway +mmu04664 Fc epsilon RI signaling pathway +mmu04666 Fc gamma R-mediated phagocytosis +mmu04668 TNF signaling pathway +mmu04670 Leukocyte transendothelial migration +mmu04672 Intestinal immune network for IgA production +mmu04710 Circadian rhythm +mmu04713 Circadian entrainment +mmu04714 Thermogenesis +mmu04720 Long-term potentiation +mmu04721 Synaptic vesicle cycle +mmu04722 Neurotrophin signaling pathway +mmu04723 Retrograde endocannabinoid signaling +mmu04724 Glutamatergic synapse +mmu04725 Cholinergic synapse +mmu04726 Serotonergic synapse +mmu04727 GABAergic synapse +mmu04728 Dopaminergic synapse +mmu04730 Long-term depression +mmu04740 Olfactory transduction +mmu04742 Taste transduction +mmu04744 Phototransduction +mmu04750 Inflammatory mediator regulation of TRP channels +mmu04810 Regulation of actin cytoskeleton +mmu04910 Insulin signaling pathway +mmu04911 Insulin secretion +mmu04912 GnRH signaling pathway +mmu04913 Ovarian steroidogenesis +mmu04914 Progesterone-mediated oocyte maturation +mmu04915 Estrogen signaling pathway +mmu04916 Melanogenesis +mmu04917 Prolactin signaling pathway +mmu04918 Thyroid hormone synthesis +mmu04919 Thyroid hormone signaling pathway +mmu04920 Adipocytokine signaling pathway +mmu04921 Oxytocin signaling pathway +mmu04922 Glucagon signaling pathway +mmu04923 Regulation of lipolysis in adipocytes +mmu04924 Renin secretion +mmu04925 Aldosterone synthesis and secretion +mmu04926 Relaxin signaling pathway +mmu04927 Cortisol synthesis and secretion +mmu04928 Parathyroid hormone synthesis, secretion and action +mmu04930 Type II diabetes mellitus +mmu04931 Insulin resistance +mmu04932 Non-alcoholic fatty liver disease (NAFLD) +mmu04933 AGE-RAGE signaling pathway in diabetic complications +mmu04934 Cushing's syndrome +mmu04940 Type I diabetes mellitus +mmu04950 Maturity onset diabetes of the young +mmu04960 Aldosterone-regulated sodium reabsorption +mmu04961 Endocrine and other factor-regulated calcium reabsorption +mmu04962 Vasopressin-regulated water reabsorption +mmu04964 Proximal tubule bicarbonate reclamation +mmu04966 Collecting duct acid secretion +mmu04970 Salivary secretion +mmu04971 Gastric acid secretion +mmu04972 Pancreatic secretion +mmu04973 Carbohydrate digestion and absorption +mmu04974 Protein digestion and absorption +mmu04975 Fat digestion and absorption +mmu04976 Bile secretion +mmu04977 Vitamin digestion and absorption +mmu04978 Mineral absorption +mmu04979 Cholesterol metabolism +mmu05010 Alzheimer's disease +mmu05012 Parkinson's disease +mmu05014 Amyotrophic lateral sclerosis (ALS) +mmu05016 Huntington's disease +mmu05020 Prion diseases +mmu05030 Cocaine addiction +mmu05031 Amphetamine addiction +mmu05032 Morphine addiction +mmu05033 Nicotine addiction +mmu05034 Alcoholism +mmu05100 Bacterial invasion of epithelial cells +mmu05132 Salmonella infection +mmu05133 Pertussis +mmu05134 Legionellosis +mmu05140 Leishmaniasis +mmu05142 Chagas disease (American trypanosomiasis) +mmu05143 African trypanosomiasis +mmu05144 Malaria +mmu05145 Toxoplasmosis +mmu05146 Amoebiasis +mmu05150 Staphylococcus aureus infection +mmu05152 Tuberculosis +mmu05160 Hepatitis C +mmu05161 Hepatitis B +mmu05162 Measles +mmu05163 Human cytomegalovirus infection +mmu05164 Influenza A +mmu05165 Human papillomavirus infection +mmu05166 HTLV-I infection +mmu05167 Kaposi's sarcoma-associated herpesvirus infection +mmu05168 Herpes simplex infection +mmu05169 Epstein-Barr virus infection +mmu05200 Pathways in cancer +mmu05202 Transcriptional misregulation in cancer +mmu05203 Viral carcinogenesis +mmu05204 Chemical carcinogenesis +mmu05205 Proteoglycans in cancer +mmu05206 MicroRNAs in cancer +mmu05210 Colorectal cancer +mmu05211 Renal cell carcinoma +mmu05212 Pancreatic cancer +mmu05213 Endometrial cancer +mmu05214 Glioma +mmu05215 Prostate cancer +mmu05216 Thyroid cancer +mmu05217 Basal cell carcinoma +mmu05218 Melanoma +mmu05219 Bladder cancer +mmu05220 Chronic myeloid leukemia +mmu05221 Acute myeloid leukemia +mmu05222 Small cell lung cancer +mmu05223 Non-small cell lung cancer +mmu05224 Breast cancer +mmu05225 Hepatocellular carcinoma +mmu05226 Gastric cancer +mmu05230 Central carbon metabolism in cancer +mmu05231 Choline metabolism in cancer +mmu05310 Asthma +mmu05320 Autoimmune thyroid disease +mmu05321 Inflammatory bowel disease (IBD) +mmu05322 Systemic lupus erythematosus +mmu05323 Rheumatoid arthritis +mmu05330 Allograft rejection +mmu05332 Graft-versus-host disease +mmu05340 Primary immunodeficiency +mmu05410 Hypertrophic cardiomyopathy (HCM) +mmu05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +mmu05414 Dilated cardiomyopathy (DCM) +mmu05416 Viral myocarditis +mmu05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mmu_pathways.loc.sample Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,326 @@ +#value name +mmu00010 Glycolysis / Gluconeogenesis +mmu00020 Citrate cycle (TCA cycle) +mmu00030 Pentose phosphate pathway +mmu00040 Pentose and glucuronate interconversions +mmu00051 Fructose and mannose metabolism +mmu00052 Galactose metabolism +mmu00053 Ascorbate and aldarate metabolism +mmu00061 Fatty acid biosynthesis +mmu00062 Fatty acid elongation +mmu00071 Fatty acid degradation +mmu00072 Synthesis and degradation of ketone bodies +mmu00100 Steroid biosynthesis +mmu00120 Primary bile acid biosynthesis +mmu00130 Ubiquinone and other terpenoid-quinone biosynthesis +mmu00140 Steroid hormone biosynthesis +mmu00190 Oxidative phosphorylation +mmu00220 Arginine biosynthesis +mmu00230 Purine metabolism +mmu00232 Caffeine metabolism +mmu00240 Pyrimidine metabolism +mmu00250 Alanine, aspartate and glutamate metabolism +mmu00260 Glycine, serine and threonine metabolism +mmu00270 Cysteine and methionine metabolism +mmu00280 Valine, leucine and isoleucine degradation +mmu00290 Valine, leucine and isoleucine biosynthesis +mmu00310 Lysine degradation +mmu00330 Arginine and proline metabolism +mmu00340 Histidine metabolism +mmu00350 Tyrosine metabolism +mmu00360 Phenylalanine metabolism +mmu00380 Tryptophan metabolism +mmu00400 Phenylalanine, tyrosine and tryptophan biosynthesis +mmu00410 beta-Alanine metabolism +mmu00430 Taurine and hypotaurine metabolism +mmu00440 Phosphonate and phosphinate metabolism +mmu00450 Selenocompound metabolism +mmu00471 D-Glutamine and D-glutamate metabolism +mmu00472 D-Arginine and D-ornithine metabolism +mmu00480 Glutathione metabolism +mmu00500 Starch and sucrose metabolism +mmu00510 N-Glycan biosynthesis +mmu00511 Other glycan degradation +mmu00512 Mucin type O-glycan biosynthesis +mmu00514 Other types of O-glycan biosynthesis +mmu00515 Mannose type O-glycan biosynthesis +mmu00520 Amino sugar and nucleotide sugar metabolism +mmu00524 Neomycin, kanamycin and gentamicin biosynthesis +mmu00531 Glycosaminoglycan degradation +mmu00532 Glycosaminoglycan biosynthesis +mmu00533 Glycosaminoglycan biosynthesis +mmu00534 Glycosaminoglycan biosynthesis +mmu00561 Glycerolipid metabolism +mmu00562 Inositol phosphate metabolism +mmu00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +mmu00564 Glycerophospholipid metabolism +mmu00565 Ether lipid metabolism +mmu00590 Arachidonic acid metabolism +mmu00591 Linoleic acid metabolism +mmu00592 alpha-Linolenic acid metabolism +mmu00600 Sphingolipid metabolism +mmu00601 Glycosphingolipid biosynthesis +mmu00603 Glycosphingolipid biosynthesis +mmu00604 Glycosphingolipid biosynthesis +mmu00620 Pyruvate metabolism +mmu00630 Glyoxylate and dicarboxylate metabolism +mmu00640 Propanoate metabolism +mmu00650 Butanoate metabolism +mmu00670 One carbon pool by folate +mmu00730 Thiamine metabolism +mmu00740 Riboflavin metabolism +mmu00750 Vitamin B6 metabolism +mmu00760 Nicotinate and nicotinamide metabolism +mmu00770 Pantothenate and CoA biosynthesis +mmu00780 Biotin metabolism +mmu00785 Lipoic acid metabolism +mmu00790 Folate biosynthesis +mmu00830 Retinol metabolism +mmu00860 Porphyrin and chlorophyll metabolism +mmu00900 Terpenoid backbone biosynthesis +mmu00910 Nitrogen metabolism +mmu00920 Sulfur metabolism +mmu00970 Aminoacyl-tRNA biosynthesis +mmu00980 Metabolism of xenobiotics by cytochrome P450 +mmu00982 Drug metabolism +mmu00983 Drug metabolism +mmu01040 Biosynthesis of unsaturated fatty acids +mmu01100 Metabolic pathways +mmu01200 Carbon metabolism +mmu01210 2-Oxocarboxylic acid metabolism +mmu01212 Fatty acid metabolism +mmu01230 Biosynthesis of amino acids +mmu01521 EGFR tyrosine kinase inhibitor resistance +mmu01522 Endocrine resistance +mmu01523 Antifolate resistance +mmu01524 Platinum drug resistance +mmu02010 ABC transporters +mmu03008 Ribosome biogenesis in eukaryotes +mmu03010 Ribosome +mmu03013 RNA transport +mmu03015 mRNA surveillance pathway +mmu03018 RNA degradation +mmu03020 RNA polymerase +mmu03022 Basal transcription factors +mmu03030 DNA replication +mmu03040 Spliceosome +mmu03050 Proteasome +mmu03060 Protein export +mmu03320 PPAR signaling pathway +mmu03410 Base excision repair +mmu03420 Nucleotide excision repair +mmu03430 Mismatch repair +mmu03440 Homologous recombination +mmu03450 Non-homologous end-joining +mmu03460 Fanconi anemia pathway +mmu04010 MAPK signaling pathway +mmu04012 ErbB signaling pathway +mmu04014 Ras signaling pathway +mmu04015 Rap1 signaling pathway +mmu04020 Calcium signaling pathway +mmu04022 cGMP-PKG signaling pathway +mmu04024 cAMP signaling pathway +mmu04060 Cytokine-cytokine receptor interaction +mmu04062 Chemokine signaling pathway +mmu04064 NF-kappa B signaling pathway +mmu04066 HIF-1 signaling pathway +mmu04068 FoxO signaling pathway +mmu04070 Phosphatidylinositol signaling system +mmu04071 Sphingolipid signaling pathway +mmu04072 Phospholipase D signaling pathway +mmu04080 Neuroactive ligand-receptor interaction +mmu04110 Cell cycle +mmu04114 Oocyte meiosis +mmu04115 p53 signaling pathway +mmu04120 Ubiquitin mediated proteolysis +mmu04122 Sulfur relay system +mmu04130 SNARE interactions in vesicular transport +mmu04136 Autophagy +mmu04137 Mitophagy +mmu04140 Autophagy +mmu04141 Protein processing in endoplasmic reticulum +mmu04142 Lysosome +mmu04144 Endocytosis +mmu04145 Phagosome +mmu04146 Peroxisome +mmu04150 mTOR signaling pathway +mmu04151 PI3K-Akt signaling pathway +mmu04152 AMPK signaling pathway +mmu04210 Apoptosis +mmu04211 Longevity regulating pathway +mmu04213 Longevity regulating pathway +mmu04215 Apoptosis +mmu04216 Ferroptosis +mmu04217 Necroptosis +mmu04218 Cellular senescence +mmu04260 Cardiac muscle contraction +mmu04261 Adrenergic signaling in cardiomyocytes +mmu04270 Vascular smooth muscle contraction +mmu04310 Wnt signaling pathway +mmu04330 Notch signaling pathway +mmu04340 Hedgehog signaling pathway +mmu04350 TGF-beta signaling pathway +mmu04360 Axon guidance +mmu04370 VEGF signaling pathway +mmu04371 Apelin signaling pathway +mmu04380 Osteoclast differentiation +mmu04390 Hippo signaling pathway +mmu04392 Hippo signaling pathway +mmu04510 Focal adhesion +mmu04512 ECM-receptor interaction +mmu04514 Cell adhesion molecules (CAMs) +mmu04520 Adherens junction +mmu04530 Tight junction +mmu04540 Gap junction +mmu04550 Signaling pathways regulating pluripotency of stem cells +mmu04610 Complement and coagulation cascades +mmu04611 Platelet activation +mmu04612 Antigen processing and presentation +mmu04614 Renin-angiotensin system +mmu04620 Toll-like receptor signaling pathway +mmu04621 NOD-like receptor signaling pathway +mmu04622 RIG-I-like receptor signaling pathway +mmu04623 Cytosolic DNA-sensing pathway +mmu04625 C-type lectin receptor signaling pathway +mmu04630 Jak-STAT signaling pathway +mmu04640 Hematopoietic cell lineage +mmu04650 Natural killer cell mediated cytotoxicity +mmu04657 IL-17 signaling pathway +mmu04658 Th1 and Th2 cell differentiation +mmu04659 Th17 cell differentiation +mmu04660 T cell receptor signaling pathway +mmu04662 B cell receptor signaling pathway +mmu04664 Fc epsilon RI signaling pathway +mmu04666 Fc gamma R-mediated phagocytosis +mmu04668 TNF signaling pathway +mmu04670 Leukocyte transendothelial migration +mmu04672 Intestinal immune network for IgA production +mmu04710 Circadian rhythm +mmu04713 Circadian entrainment +mmu04714 Thermogenesis +mmu04720 Long-term potentiation +mmu04721 Synaptic vesicle cycle +mmu04722 Neurotrophin signaling pathway +mmu04723 Retrograde endocannabinoid signaling +mmu04724 Glutamatergic synapse +mmu04725 Cholinergic synapse +mmu04726 Serotonergic synapse +mmu04727 GABAergic synapse +mmu04728 Dopaminergic synapse +mmu04730 Long-term depression +mmu04740 Olfactory transduction +mmu04742 Taste transduction +mmu04744 Phototransduction +mmu04750 Inflammatory mediator regulation of TRP channels +mmu04810 Regulation of actin cytoskeleton +mmu04910 Insulin signaling pathway +mmu04911 Insulin secretion +mmu04912 GnRH signaling pathway +mmu04913 Ovarian steroidogenesis +mmu04914 Progesterone-mediated oocyte maturation +mmu04915 Estrogen signaling pathway +mmu04916 Melanogenesis +mmu04917 Prolactin signaling pathway +mmu04918 Thyroid hormone synthesis +mmu04919 Thyroid hormone signaling pathway +mmu04920 Adipocytokine signaling pathway +mmu04921 Oxytocin signaling pathway +mmu04922 Glucagon signaling pathway +mmu04923 Regulation of lipolysis in adipocytes +mmu04924 Renin secretion +mmu04925 Aldosterone synthesis and secretion +mmu04926 Relaxin signaling pathway +mmu04927 Cortisol synthesis and secretion +mmu04928 Parathyroid hormone synthesis, secretion and action +mmu04930 Type II diabetes mellitus +mmu04931 Insulin resistance +mmu04932 Non-alcoholic fatty liver disease (NAFLD) +mmu04933 AGE-RAGE signaling pathway in diabetic complications +mmu04934 Cushing's syndrome +mmu04940 Type I diabetes mellitus +mmu04950 Maturity onset diabetes of the young +mmu04960 Aldosterone-regulated sodium reabsorption +mmu04961 Endocrine and other factor-regulated calcium reabsorption +mmu04962 Vasopressin-regulated water reabsorption +mmu04964 Proximal tubule bicarbonate reclamation +mmu04966 Collecting duct acid secretion +mmu04970 Salivary secretion +mmu04971 Gastric acid secretion +mmu04972 Pancreatic secretion +mmu04973 Carbohydrate digestion and absorption +mmu04974 Protein digestion and absorption +mmu04975 Fat digestion and absorption +mmu04976 Bile secretion +mmu04977 Vitamin digestion and absorption +mmu04978 Mineral absorption +mmu04979 Cholesterol metabolism +mmu05010 Alzheimer's disease +mmu05012 Parkinson's disease +mmu05014 Amyotrophic lateral sclerosis (ALS) +mmu05016 Huntington's disease +mmu05020 Prion diseases +mmu05030 Cocaine addiction +mmu05031 Amphetamine addiction +mmu05032 Morphine addiction +mmu05033 Nicotine addiction +mmu05034 Alcoholism +mmu05100 Bacterial invasion of epithelial cells +mmu05132 Salmonella infection +mmu05133 Pertussis +mmu05134 Legionellosis +mmu05140 Leishmaniasis +mmu05142 Chagas disease (American trypanosomiasis) +mmu05143 African trypanosomiasis +mmu05144 Malaria +mmu05145 Toxoplasmosis +mmu05146 Amoebiasis +mmu05150 Staphylococcus aureus infection +mmu05152 Tuberculosis +mmu05160 Hepatitis C +mmu05161 Hepatitis B +mmu05162 Measles +mmu05163 Human cytomegalovirus infection +mmu05164 Influenza A +mmu05165 Human papillomavirus infection +mmu05166 HTLV-I infection +mmu05167 Kaposi's sarcoma-associated herpesvirus infection +mmu05168 Herpes simplex infection +mmu05169 Epstein-Barr virus infection +mmu05200 Pathways in cancer +mmu05202 Transcriptional misregulation in cancer +mmu05203 Viral carcinogenesis +mmu05204 Chemical carcinogenesis +mmu05205 Proteoglycans in cancer +mmu05206 MicroRNAs in cancer +mmu05210 Colorectal cancer +mmu05211 Renal cell carcinoma +mmu05212 Pancreatic cancer +mmu05213 Endometrial cancer +mmu05214 Glioma +mmu05215 Prostate cancer +mmu05216 Thyroid cancer +mmu05217 Basal cell carcinoma +mmu05218 Melanoma +mmu05219 Bladder cancer +mmu05220 Chronic myeloid leukemia +mmu05221 Acute myeloid leukemia +mmu05222 Small cell lung cancer +mmu05223 Non-small cell lung cancer +mmu05224 Breast cancer +mmu05225 Hepatocellular carcinoma +mmu05226 Gastric cancer +mmu05230 Central carbon metabolism in cancer +mmu05231 Choline metabolism in cancer +mmu05310 Asthma +mmu05320 Autoimmune thyroid disease +mmu05321 Inflammatory bowel disease (IBD) +mmu05322 Systemic lupus erythematosus +mmu05323 Rheumatoid arthritis +mmu05330 Allograft rejection +mmu05332 Graft-versus-host disease +mmu05340 Primary immunodeficiency +mmu05410 Hypertrophic cardiomyopathy (HCM) +mmu05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +mmu05414 Dilated cardiomyopathy (DCM) +mmu05416 Viral myocarditis +mmu05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rno_pathways.loc Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,326 @@ +rno00010 Glycolysis / Gluconeogenesis +rno00020 Citrate cycle (TCA cycle) +rno00030 Pentose phosphate pathway +rno00040 Pentose and glucuronate interconversions +rno00051 Fructose and mannose metabolism +rno00052 Galactose metabolism +rno00053 Ascorbate and aldarate metabolism +rno00061 Fatty acid biosynthesis +rno00062 Fatty acid elongation +rno00071 Fatty acid degradation +rno00072 Synthesis and degradation of ketone bodies +rno00100 Steroid biosynthesis +rno00120 Primary bile acid biosynthesis +rno00130 Ubiquinone and other terpenoid-quinone biosynthesis +rno00140 Steroid hormone biosynthesis +rno00190 Oxidative phosphorylation +rno00220 Arginine biosynthesis +rno00230 Purine metabolism +rno00232 Caffeine metabolism +rno00240 Pyrimidine metabolism +rno00250 Alanine, aspartate and glutamate metabolism +rno00260 Glycine, serine and threonine metabolism +rno00270 Cysteine and methionine metabolism +rno00280 Valine, leucine and isoleucine degradation +rno00290 Valine, leucine and isoleucine biosynthesis +rno00310 Lysine degradation +rno00330 Arginine and proline metabolism +rno00340 Histidine metabolism +rno00350 Tyrosine metabolism +rno00360 Phenylalanine metabolism +rno00380 Tryptophan metabolism +rno00400 Phenylalanine, tyrosine and tryptophan biosynthesis +rno00410 beta-Alanine metabolism +rno00430 Taurine and hypotaurine metabolism +rno00440 Phosphonate and phosphinate metabolism +rno00450 Selenocompound metabolism +rno00471 D-Glutamine and D-glutamate metabolism +rno00472 D-Arginine and D-ornithine metabolism +rno00480 Glutathione metabolism +rno00500 Starch and sucrose metabolism +rno00510 N-Glycan biosynthesis +rno00511 Other glycan degradation +rno00512 Mucin type O-glycan biosynthesis +rno00514 Other types of O-glycan biosynthesis +rno00515 Mannose type O-glycan biosynthesis +rno00520 Amino sugar and nucleotide sugar metabolism +rno00524 Neomycin, kanamycin and gentamicin biosynthesis +rno00531 Glycosaminoglycan degradation +rno00532 Glycosaminoglycan biosynthesis +rno00533 Glycosaminoglycan biosynthesis +rno00534 Glycosaminoglycan biosynthesis +rno00561 Glycerolipid metabolism +rno00562 Inositol phosphate metabolism +rno00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +rno00564 Glycerophospholipid metabolism +rno00565 Ether lipid metabolism +rno00590 Arachidonic acid metabolism +rno00591 Linoleic acid metabolism +rno00592 alpha-Linolenic acid metabolism +rno00600 Sphingolipid metabolism +rno00601 Glycosphingolipid biosynthesis +rno00603 Glycosphingolipid biosynthesis +rno00604 Glycosphingolipid biosynthesis +rno00620 Pyruvate metabolism +rno00630 Glyoxylate and dicarboxylate metabolism +rno00640 Propanoate metabolism +rno00650 Butanoate metabolism +rno00670 One carbon pool by folate +rno00730 Thiamine metabolism +rno00740 Riboflavin metabolism +rno00750 Vitamin B6 metabolism +rno00760 Nicotinate and nicotinamide metabolism +rno00770 Pantothenate and CoA biosynthesis +rno00780 Biotin metabolism +rno00785 Lipoic acid metabolism +rno00790 Folate biosynthesis +rno00830 Retinol metabolism +rno00860 Porphyrin and chlorophyll metabolism +rno00900 Terpenoid backbone biosynthesis +rno00910 Nitrogen metabolism +rno00920 Sulfur metabolism +rno00970 Aminoacyl-tRNA biosynthesis +rno00980 Metabolism of xenobiotics by cytochrome P450 +rno00982 Drug metabolism +rno00983 Drug metabolism +rno01040 Biosynthesis of unsaturated fatty acids +rno01100 Metabolic pathways +rno01200 Carbon metabolism +rno01210 2-Oxocarboxylic acid metabolism +rno01212 Fatty acid metabolism +rno01230 Biosynthesis of amino acids +rno01521 EGFR tyrosine kinase inhibitor resistance +rno01522 Endocrine resistance +rno01523 Antifolate resistance +rno01524 Platinum drug resistance +rno02010 ABC transporters +rno03008 Ribosome biogenesis in eukaryotes +rno03010 Ribosome +rno03013 RNA transport +rno03015 mRNA surveillance pathway +rno03018 RNA degradation +rno03020 RNA polymerase +rno03022 Basal transcription factors +rno03030 DNA replication +rno03040 Spliceosome +rno03050 Proteasome +rno03060 Protein export +rno03320 PPAR signaling pathway +rno03410 Base excision repair +rno03420 Nucleotide excision repair +rno03430 Mismatch repair +rno03440 Homologous recombination +rno03450 Non-homologous end-joining +rno03460 Fanconi anemia pathway +rno04010 MAPK signaling pathway +rno04012 ErbB signaling pathway +rno04014 Ras signaling pathway +rno04015 Rap1 signaling pathway +rno04020 Calcium signaling pathway +rno04022 cGMP-PKG signaling pathway +rno04024 cAMP signaling pathway +rno04060 Cytokine-cytokine receptor interaction +rno04062 Chemokine signaling pathway +rno04064 NF-kappa B signaling pathway +rno04066 HIF-1 signaling pathway +rno04068 FoxO signaling pathway +rno04070 Phosphatidylinositol signaling system +rno04071 Sphingolipid signaling pathway +rno04072 Phospholipase D signaling pathway +rno04080 Neuroactive ligand-receptor interaction +rno04110 Cell cycle +rno04114 Oocyte meiosis +rno04115 p53 signaling pathway +rno04120 Ubiquitin mediated proteolysis +rno04122 Sulfur relay system +rno04130 SNARE interactions in vesicular transport +rno04136 Autophagy +rno04137 Mitophagy +rno04140 Autophagy +rno04141 Protein processing in endoplasmic reticulum +rno04142 Lysosome +rno04144 Endocytosis +rno04145 Phagosome +rno04146 Peroxisome +rno04150 mTOR signaling pathway +rno04151 PI3K-Akt signaling pathway +rno04152 AMPK signaling pathway +rno04210 Apoptosis +rno04211 Longevity regulating pathway +rno04213 Longevity regulating pathway +rno04215 Apoptosis +rno04216 Ferroptosis +rno04217 Necroptosis +rno04218 Cellular senescence +rno04260 Cardiac muscle contraction +rno04261 Adrenergic signaling in cardiomyocytes +rno04270 Vascular smooth muscle contraction +rno04310 Wnt signaling pathway +rno04330 Notch signaling pathway +rno04340 Hedgehog signaling pathway +rno04350 TGF-beta signaling pathway +rno04360 Axon guidance +rno04370 VEGF signaling pathway +rno04371 Apelin signaling pathway +rno04380 Osteoclast differentiation +rno04390 Hippo signaling pathway +rno04392 Hippo signaling pathway +rno04510 Focal adhesion +rno04512 ECM-receptor interaction +rno04514 Cell adhesion molecules (CAMs) +rno04520 Adherens junction +rno04530 Tight junction +rno04540 Gap junction +rno04550 Signaling pathways regulating pluripotency of stem cells +rno04610 Complement and coagulation cascades +rno04611 Platelet activation +rno04612 Antigen processing and presentation +rno04614 Renin-angiotensin system +rno04620 Toll-like receptor signaling pathway +rno04621 NOD-like receptor signaling pathway +rno04622 RIG-I-like receptor signaling pathway +rno04623 Cytosolic DNA-sensing pathway +rno04625 C-type lectin receptor signaling pathway +rno04630 JAK-STAT signaling pathway +rno04640 Hematopoietic cell lineage +rno04650 Natural killer cell mediated cytotoxicity +rno04657 IL-17 signaling pathway +rno04658 Th1 and Th2 cell differentiation +rno04659 Th17 cell differentiation +rno04660 T cell receptor signaling pathway +rno04662 B cell receptor signaling pathway +rno04664 Fc epsilon RI signaling pathway +rno04666 Fc gamma R-mediated phagocytosis +rno04668 TNF signaling pathway +rno04670 Leukocyte transendothelial migration +rno04672 Intestinal immune network for IgA production +rno04710 Circadian rhythm +rno04713 Circadian entrainment +rno04714 Thermogenesis +rno04720 Long-term potentiation +rno04721 Synaptic vesicle cycle +rno04722 Neurotrophin signaling pathway +rno04723 Retrograde endocannabinoid signaling +rno04724 Glutamatergic synapse +rno04725 Cholinergic synapse +rno04726 Serotonergic synapse +rno04727 GABAergic synapse +rno04728 Dopaminergic synapse +rno04730 Long-term depression +rno04740 Olfactory transduction +rno04742 Taste transduction +rno04744 Phototransduction +rno04750 Inflammatory mediator regulation of TRP channels +rno04810 Regulation of actin cytoskeleton +rno04910 Insulin signaling pathway +rno04911 Insulin secretion +rno04912 GnRH signaling pathway +rno04913 Ovarian steroidogenesis +rno04914 Progesterone-mediated oocyte maturation +rno04915 Estrogen signaling pathway +rno04916 Melanogenesis +rno04917 Prolactin signaling pathway +rno04918 Thyroid hormone synthesis +rno04919 Thyroid hormone signaling pathway +rno04920 Adipocytokine signaling pathway +rno04921 Oxytocin signaling pathway +rno04922 Glucagon signaling pathway +rno04923 Regulation of lipolysis in adipocytes +rno04924 Renin secretion +rno04925 Aldosterone synthesis and secretion +rno04926 Relaxin signaling pathway +rno04927 Cortisol synthesis and secretion +rno04928 Parathyroid hormone synthesis, secretion and action +rno04930 Type II diabetes mellitus +rno04931 Insulin resistance +rno04932 Non-alcoholic fatty liver disease (NAFLD) +rno04933 AGE-RAGE signaling pathway in diabetic complications +rno04934 Cushing syndrome +rno04940 Type I diabetes mellitus +rno04950 Maturity onset diabetes of the young +rno04960 Aldosterone-regulated sodium reabsorption +rno04961 Endocrine and other factor-regulated calcium reabsorption +rno04962 Vasopressin-regulated water reabsorption +rno04964 Proximal tubule bicarbonate reclamation +rno04966 Collecting duct acid secretion +rno04970 Salivary secretion +rno04971 Gastric acid secretion +rno04972 Pancreatic secretion +rno04973 Carbohydrate digestion and absorption +rno04974 Protein digestion and absorption +rno04975 Fat digestion and absorption +rno04976 Bile secretion +rno04977 Vitamin digestion and absorption +rno04978 Mineral absorption +rno04979 Cholesterol metabolism +rno05010 Alzheimer disease +rno05012 Parkinson disease +rno05014 Amyotrophic lateral sclerosis (ALS) +rno05016 Huntington disease +rno05020 Prion diseases +rno05030 Cocaine addiction +rno05031 Amphetamine addiction +rno05032 Morphine addiction +rno05033 Nicotine addiction +rno05034 Alcoholism +rno05100 Bacterial invasion of epithelial cells +rno05132 Salmonella infection +rno05133 Pertussis +rno05134 Legionellosis +rno05140 Leishmaniasis +rno05142 Chagas disease (American trypanosomiasis) +rno05143 African trypanosomiasis +rno05144 Malaria +rno05145 Toxoplasmosis +rno05146 Amoebiasis +rno05150 Staphylococcus aureus infection +rno05152 Tuberculosis +rno05160 Hepatitis C +rno05161 Hepatitis B +rno05162 Measles +rno05163 Human cytomegalovirus infection +rno05164 Influenza A +rno05165 Human papillomavirus infection +rno05166 Human T-cell leukemia virus 1 infection +rno05167 Kaposi sarcoma-associated herpesvirus infection +rno05168 Herpes simplex infection +rno05169 Epstein-Barr virus infection +rno05170 Human immunodeficiency virus 1 infection +rno05200 Pathways in cancer +rno05202 Transcriptional misregulation in cancer +rno05203 Viral carcinogenesis +rno05204 Chemical carcinogenesis +rno05205 Proteoglycans in cancer +rno05206 MicroRNAs in cancer +rno05210 Colorectal cancer +rno05211 Renal cell carcinoma +rno05212 Pancreatic cancer +rno05213 Endometrial cancer +rno05214 Glioma +rno05215 Prostate cancer +rno05216 Thyroid cancer +rno05217 Basal cell carcinoma +rno05218 Melanoma +rno05219 Bladder cancer +rno05220 Chronic myeloid leukemia +rno05221 Acute myeloid leukemia +rno05222 Small cell lung cancer +rno05223 Non-small cell lung cancer +rno05224 Breast cancer +rno05225 Hepatocellular carcinoma +rno05226 Gastric cancer +rno05230 Central carbon metabolism in cancer +rno05231 Choline metabolism in cancer +rno05310 Asthma +rno05320 Autoimmune thyroid disease +rno05321 Inflammatory bowel disease (IBD) +rno05322 Systemic lupus erythematosus +rno05323 Rheumatoid arthritis +rno05330 Allograft rejection +rno05332 Graft-versus-host disease +rno05340 Primary immunodeficiency +rno05410 Hypertrophic cardiomyopathy (HCM) +rno05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +rno05414 Dilated cardiomyopathy (DCM) +rno05416 Viral myocarditis +rno05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rno_pathways.loc.sample Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,326 @@ +rno00010 Glycolysis / Gluconeogenesis +rno00020 Citrate cycle (TCA cycle) +rno00030 Pentose phosphate pathway +rno00040 Pentose and glucuronate interconversions +rno00051 Fructose and mannose metabolism +rno00052 Galactose metabolism +rno00053 Ascorbate and aldarate metabolism +rno00061 Fatty acid biosynthesis +rno00062 Fatty acid elongation +rno00071 Fatty acid degradation +rno00072 Synthesis and degradation of ketone bodies +rno00100 Steroid biosynthesis +rno00120 Primary bile acid biosynthesis +rno00130 Ubiquinone and other terpenoid-quinone biosynthesis +rno00140 Steroid hormone biosynthesis +rno00190 Oxidative phosphorylation +rno00220 Arginine biosynthesis +rno00230 Purine metabolism +rno00232 Caffeine metabolism +rno00240 Pyrimidine metabolism +rno00250 Alanine, aspartate and glutamate metabolism +rno00260 Glycine, serine and threonine metabolism +rno00270 Cysteine and methionine metabolism +rno00280 Valine, leucine and isoleucine degradation +rno00290 Valine, leucine and isoleucine biosynthesis +rno00310 Lysine degradation +rno00330 Arginine and proline metabolism +rno00340 Histidine metabolism +rno00350 Tyrosine metabolism +rno00360 Phenylalanine metabolism +rno00380 Tryptophan metabolism +rno00400 Phenylalanine, tyrosine and tryptophan biosynthesis +rno00410 beta-Alanine metabolism +rno00430 Taurine and hypotaurine metabolism +rno00440 Phosphonate and phosphinate metabolism +rno00450 Selenocompound metabolism +rno00471 D-Glutamine and D-glutamate metabolism +rno00472 D-Arginine and D-ornithine metabolism +rno00480 Glutathione metabolism +rno00500 Starch and sucrose metabolism +rno00510 N-Glycan biosynthesis +rno00511 Other glycan degradation +rno00512 Mucin type O-glycan biosynthesis +rno00514 Other types of O-glycan biosynthesis +rno00515 Mannose type O-glycan biosynthesis +rno00520 Amino sugar and nucleotide sugar metabolism +rno00524 Neomycin, kanamycin and gentamicin biosynthesis +rno00531 Glycosaminoglycan degradation +rno00532 Glycosaminoglycan biosynthesis +rno00533 Glycosaminoglycan biosynthesis +rno00534 Glycosaminoglycan biosynthesis +rno00561 Glycerolipid metabolism +rno00562 Inositol phosphate metabolism +rno00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis +rno00564 Glycerophospholipid metabolism +rno00565 Ether lipid metabolism +rno00590 Arachidonic acid metabolism +rno00591 Linoleic acid metabolism +rno00592 alpha-Linolenic acid metabolism +rno00600 Sphingolipid metabolism +rno00601 Glycosphingolipid biosynthesis +rno00603 Glycosphingolipid biosynthesis +rno00604 Glycosphingolipid biosynthesis +rno00620 Pyruvate metabolism +rno00630 Glyoxylate and dicarboxylate metabolism +rno00640 Propanoate metabolism +rno00650 Butanoate metabolism +rno00670 One carbon pool by folate +rno00730 Thiamine metabolism +rno00740 Riboflavin metabolism +rno00750 Vitamin B6 metabolism +rno00760 Nicotinate and nicotinamide metabolism +rno00770 Pantothenate and CoA biosynthesis +rno00780 Biotin metabolism +rno00785 Lipoic acid metabolism +rno00790 Folate biosynthesis +rno00830 Retinol metabolism +rno00860 Porphyrin and chlorophyll metabolism +rno00900 Terpenoid backbone biosynthesis +rno00910 Nitrogen metabolism +rno00920 Sulfur metabolism +rno00970 Aminoacyl-tRNA biosynthesis +rno00980 Metabolism of xenobiotics by cytochrome P450 +rno00982 Drug metabolism +rno00983 Drug metabolism +rno01040 Biosynthesis of unsaturated fatty acids +rno01100 Metabolic pathways +rno01200 Carbon metabolism +rno01210 2-Oxocarboxylic acid metabolism +rno01212 Fatty acid metabolism +rno01230 Biosynthesis of amino acids +rno01521 EGFR tyrosine kinase inhibitor resistance +rno01522 Endocrine resistance +rno01523 Antifolate resistance +rno01524 Platinum drug resistance +rno02010 ABC transporters +rno03008 Ribosome biogenesis in eukaryotes +rno03010 Ribosome +rno03013 RNA transport +rno03015 mRNA surveillance pathway +rno03018 RNA degradation +rno03020 RNA polymerase +rno03022 Basal transcription factors +rno03030 DNA replication +rno03040 Spliceosome +rno03050 Proteasome +rno03060 Protein export +rno03320 PPAR signaling pathway +rno03410 Base excision repair +rno03420 Nucleotide excision repair +rno03430 Mismatch repair +rno03440 Homologous recombination +rno03450 Non-homologous end-joining +rno03460 Fanconi anemia pathway +rno04010 MAPK signaling pathway +rno04012 ErbB signaling pathway +rno04014 Ras signaling pathway +rno04015 Rap1 signaling pathway +rno04020 Calcium signaling pathway +rno04022 cGMP-PKG signaling pathway +rno04024 cAMP signaling pathway +rno04060 Cytokine-cytokine receptor interaction +rno04062 Chemokine signaling pathway +rno04064 NF-kappa B signaling pathway +rno04066 HIF-1 signaling pathway +rno04068 FoxO signaling pathway +rno04070 Phosphatidylinositol signaling system +rno04071 Sphingolipid signaling pathway +rno04072 Phospholipase D signaling pathway +rno04080 Neuroactive ligand-receptor interaction +rno04110 Cell cycle +rno04114 Oocyte meiosis +rno04115 p53 signaling pathway +rno04120 Ubiquitin mediated proteolysis +rno04122 Sulfur relay system +rno04130 SNARE interactions in vesicular transport +rno04136 Autophagy +rno04137 Mitophagy +rno04140 Autophagy +rno04141 Protein processing in endoplasmic reticulum +rno04142 Lysosome +rno04144 Endocytosis +rno04145 Phagosome +rno04146 Peroxisome +rno04150 mTOR signaling pathway +rno04151 PI3K-Akt signaling pathway +rno04152 AMPK signaling pathway +rno04210 Apoptosis +rno04211 Longevity regulating pathway +rno04213 Longevity regulating pathway +rno04215 Apoptosis +rno04216 Ferroptosis +rno04217 Necroptosis +rno04218 Cellular senescence +rno04260 Cardiac muscle contraction +rno04261 Adrenergic signaling in cardiomyocytes +rno04270 Vascular smooth muscle contraction +rno04310 Wnt signaling pathway +rno04330 Notch signaling pathway +rno04340 Hedgehog signaling pathway +rno04350 TGF-beta signaling pathway +rno04360 Axon guidance +rno04370 VEGF signaling pathway +rno04371 Apelin signaling pathway +rno04380 Osteoclast differentiation +rno04390 Hippo signaling pathway +rno04392 Hippo signaling pathway +rno04510 Focal adhesion +rno04512 ECM-receptor interaction +rno04514 Cell adhesion molecules (CAMs) +rno04520 Adherens junction +rno04530 Tight junction +rno04540 Gap junction +rno04550 Signaling pathways regulating pluripotency of stem cells +rno04610 Complement and coagulation cascades +rno04611 Platelet activation +rno04612 Antigen processing and presentation +rno04614 Renin-angiotensin system +rno04620 Toll-like receptor signaling pathway +rno04621 NOD-like receptor signaling pathway +rno04622 RIG-I-like receptor signaling pathway +rno04623 Cytosolic DNA-sensing pathway +rno04625 C-type lectin receptor signaling pathway +rno04630 JAK-STAT signaling pathway +rno04640 Hematopoietic cell lineage +rno04650 Natural killer cell mediated cytotoxicity +rno04657 IL-17 signaling pathway +rno04658 Th1 and Th2 cell differentiation +rno04659 Th17 cell differentiation +rno04660 T cell receptor signaling pathway +rno04662 B cell receptor signaling pathway +rno04664 Fc epsilon RI signaling pathway +rno04666 Fc gamma R-mediated phagocytosis +rno04668 TNF signaling pathway +rno04670 Leukocyte transendothelial migration +rno04672 Intestinal immune network for IgA production +rno04710 Circadian rhythm +rno04713 Circadian entrainment +rno04714 Thermogenesis +rno04720 Long-term potentiation +rno04721 Synaptic vesicle cycle +rno04722 Neurotrophin signaling pathway +rno04723 Retrograde endocannabinoid signaling +rno04724 Glutamatergic synapse +rno04725 Cholinergic synapse +rno04726 Serotonergic synapse +rno04727 GABAergic synapse +rno04728 Dopaminergic synapse +rno04730 Long-term depression +rno04740 Olfactory transduction +rno04742 Taste transduction +rno04744 Phototransduction +rno04750 Inflammatory mediator regulation of TRP channels +rno04810 Regulation of actin cytoskeleton +rno04910 Insulin signaling pathway +rno04911 Insulin secretion +rno04912 GnRH signaling pathway +rno04913 Ovarian steroidogenesis +rno04914 Progesterone-mediated oocyte maturation +rno04915 Estrogen signaling pathway +rno04916 Melanogenesis +rno04917 Prolactin signaling pathway +rno04918 Thyroid hormone synthesis +rno04919 Thyroid hormone signaling pathway +rno04920 Adipocytokine signaling pathway +rno04921 Oxytocin signaling pathway +rno04922 Glucagon signaling pathway +rno04923 Regulation of lipolysis in adipocytes +rno04924 Renin secretion +rno04925 Aldosterone synthesis and secretion +rno04926 Relaxin signaling pathway +rno04927 Cortisol synthesis and secretion +rno04928 Parathyroid hormone synthesis, secretion and action +rno04930 Type II diabetes mellitus +rno04931 Insulin resistance +rno04932 Non-alcoholic fatty liver disease (NAFLD) +rno04933 AGE-RAGE signaling pathway in diabetic complications +rno04934 Cushing syndrome +rno04940 Type I diabetes mellitus +rno04950 Maturity onset diabetes of the young +rno04960 Aldosterone-regulated sodium reabsorption +rno04961 Endocrine and other factor-regulated calcium reabsorption +rno04962 Vasopressin-regulated water reabsorption +rno04964 Proximal tubule bicarbonate reclamation +rno04966 Collecting duct acid secretion +rno04970 Salivary secretion +rno04971 Gastric acid secretion +rno04972 Pancreatic secretion +rno04973 Carbohydrate digestion and absorption +rno04974 Protein digestion and absorption +rno04975 Fat digestion and absorption +rno04976 Bile secretion +rno04977 Vitamin digestion and absorption +rno04978 Mineral absorption +rno04979 Cholesterol metabolism +rno05010 Alzheimer disease +rno05012 Parkinson disease +rno05014 Amyotrophic lateral sclerosis (ALS) +rno05016 Huntington disease +rno05020 Prion diseases +rno05030 Cocaine addiction +rno05031 Amphetamine addiction +rno05032 Morphine addiction +rno05033 Nicotine addiction +rno05034 Alcoholism +rno05100 Bacterial invasion of epithelial cells +rno05132 Salmonella infection +rno05133 Pertussis +rno05134 Legionellosis +rno05140 Leishmaniasis +rno05142 Chagas disease (American trypanosomiasis) +rno05143 African trypanosomiasis +rno05144 Malaria +rno05145 Toxoplasmosis +rno05146 Amoebiasis +rno05150 Staphylococcus aureus infection +rno05152 Tuberculosis +rno05160 Hepatitis C +rno05161 Hepatitis B +rno05162 Measles +rno05163 Human cytomegalovirus infection +rno05164 Influenza A +rno05165 Human papillomavirus infection +rno05166 Human T-cell leukemia virus 1 infection +rno05167 Kaposi sarcoma-associated herpesvirus infection +rno05168 Herpes simplex infection +rno05169 Epstein-Barr virus infection +rno05170 Human immunodeficiency virus 1 infection +rno05200 Pathways in cancer +rno05202 Transcriptional misregulation in cancer +rno05203 Viral carcinogenesis +rno05204 Chemical carcinogenesis +rno05205 Proteoglycans in cancer +rno05206 MicroRNAs in cancer +rno05210 Colorectal cancer +rno05211 Renal cell carcinoma +rno05212 Pancreatic cancer +rno05213 Endometrial cancer +rno05214 Glioma +rno05215 Prostate cancer +rno05216 Thyroid cancer +rno05217 Basal cell carcinoma +rno05218 Melanoma +rno05219 Bladder cancer +rno05220 Chronic myeloid leukemia +rno05221 Acute myeloid leukemia +rno05222 Small cell lung cancer +rno05223 Non-small cell lung cancer +rno05224 Breast cancer +rno05225 Hepatocellular carcinoma +rno05226 Gastric cancer +rno05230 Central carbon metabolism in cancer +rno05231 Choline metabolism in cancer +rno05310 Asthma +rno05320 Autoimmune thyroid disease +rno05321 Inflammatory bowel disease (IBD) +rno05322 Systemic lupus erythematosus +rno05323 Rheumatoid arthritis +rno05330 Allograft rejection +rno05332 Graft-versus-host disease +rno05340 Primary immunodeficiency +rno05410 Hypertrophic cardiomyopathy (HCM) +rno05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) +rno05414 Dilated cardiomyopathy (DCM) +rno05416 Viral myocarditis +rno05418 Fluid shear stress and atherosclerosis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Dec 06 08:27:31 2018 -0500 @@ -0,0 +1,19 @@ +<tables> + <!-- Location kegg_pathways file for pathview tool --> + <table name="kegg_pathways_list_index" comment_char="#"> + <columns>value,name,path</columns> + <file path="tool-data/kegg_pathways_list_index.loc"/> + </table> + <table name="hsa_pathways" comment_char="#"> + <columns>value,name</columns> + <file path="tool-data/hsa_pathways.loc" /> + </table> + <table name="mmu_pathways" comment_char="#"> + <columns>value,name</columns> + <file path="tool-data/mmu_pathways.loc" /> + </table> + <table name="rno_pathways" comment_char="#"> + <columns>value,name</columns> + <file path="tool-data/rno_pathways.loc" /> + </table> +</tables>