# HG changeset patch
# User proteore
# Date 1541758306 18000
# Node ID 9fe4a861601bd4f708944e16e48d463895111e5c
# Parent 6d5c0ff2b0bd10c08788365d600132b095a71a93
planemo upload commit 7e2bd28d27e13c402acd46500f64d5c117797aa7-dirty
diff -r 6d5c0ff2b0bd -r 9fe4a861601b PathView.R
--- a/PathView.R Fri Sep 14 09:52:28 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,231 +0,0 @@
-#!/usr/bin/Rscript
-#Rscript made for mapping genesID on KEGG pathway with Pathview package
-#input : csv file containing ids (uniprot or geneID) to map, plus parameters
-#output : KEGG pathway : jpeg or pdf file.
-
-suppressMessages(library("pathview"))
-
-read_file <- function(path,header){
- file <- try(read.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote=""),silent=TRUE)
- if (inherits(file,"try-error")){
- stop("File not found !")
- }else{
- return(file)
- }
-}
-
-##### fuction to clean and concatenate pathway name (allow more flexibility for user input)
-concat_string <- function(x){
- x <- gsub(" - .*","",x)
- x <- gsub(" ","",x)
- x <- gsub("-","",x)
- x <- gsub("_","",x)
- x <- gsub(",","",x)
- x <- gsub("\\'","",x)
- x <- gsub("\\(.*)","",x)
- x <- gsub("\\/","",x)
- x <- tolower(x)
- return(x)
-}
-
-
-get_args <- function(){
-
- ## Collect arguments
- args <- commandArgs(TRUE)
-
- ## Default setting when no arguments passed
- if(length(args) < 1) {
- args <- c("--help")
- }
-
- ## Help section
- if("--help" %in% args) {
- cat("Pathview R script
- Arguments:
- --help Print this test
- --input path of the input file (must contains a colum of uniprot and/or geneID accession number)
- --id_list list of ids to use, ',' separated
- --pathways_id Id(s) of pathway(s) to use, if several, semicolon separated list : hsa00010;hsa05412
- --id_type Type of accession number ('uniprotID' or 'geneID')
- --id_column Column containing accesion number of interest (ex : 'c1')
- --header Boolean, TRUE if header FALSE if not
- --ouput Output filename
- --expression_values1 Column containing expression values (first condition)
- --expression_values2 Column containing expression values (second condition)
- --expression_values3 Column containing expression values (third condition)
- --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph
- --species KEGG species (hsa, mmu, ...)
- --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
-
- 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)
-}
-
-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)
-}
-
-clean_bad_character <- function(string) {
- string <- gsub("X","",string)
- string <- gsub(" ","",string)
- return(string)
-}
-
-args <- get_args()
-
-###setting variables
-if (!is.null(args$pathways_id)) {
- ids <- sapply(rapply(strsplit(clean_bad_character(args$pathways_id),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
-}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)
-}
-#if (!is.null(args$pathways_name)) {names <- as.vector(sapply(strsplit(args$pathways_name,","), function(x) concat_string(x),USE.NAMES = FALSE))}
-if (!is.null(args$id_list)) {id_list <- as.vector(strsplit(clean_bad_character(args$id_list),","))}
-id_type <- tolower(args$id_type)
-ncol <- as.numeric(gsub("c", "" ,args$id_column))
-header <- str2bool(args$header)
-#output <- args$output
-native_kegg <- str2bool(args$native_kegg)
-species=args$species
-#org list used in mapped2geneID
-org <- c('Hs','Mm')
-names(org) <- c('hsa','mmu')
-
-
-
-#read input file or list
-if (!is.null(args$input)){
- tab <- read_file(args$input,header)
- tab <- data.frame(tab[which(tab[ncol]!=""),])
-} else {
- tab <- data.frame(id_list)
- ncol=1
-}
-
-e1 <- as.numeric(gsub("c", "" ,args$expression_values1))
-if (!is.null(args$expression_values1)) { colnames(tab)[e1] <- "e1" }
-e2 <- as.numeric(gsub("c", "" ,args$expression_values2))
-if (!is.null(args$expression_values2)) { colnames(tab)[e2] <- "e2" }
-e3 <- as.numeric(gsub("c", "" ,args$expression_values3))
-if (!is.null(args$expression_values3)) { colnames(tab)[e3] <- "e3" }
-
-
-##### map uniprotID to entrez geneID
-if (id_type == "uniprotid") {
-
- uniprotID = tab[,ncol]
- mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL)
- geneID = mapped2geneID[,2]
- tab = cbind(tab,geneID)
-
-}else if (id_type == "geneid"){
-
- colnames(tab)[ncol] <- "geneID"
-
-}
-
-geneID = tab$geneID[which(tab$geneID !="NA")]
-geneID = gsub(" ","",geneID)
-geneID = unlist(strsplit(geneID,"[;]"))
-
-
-#### get hsa pathways list
-#download.file(url = "http://rest.kegg.jp/link/pathway/hsa", destfile = "/home/dchristiany/proteore_project/ProteoRE/tools/pathview/geneID_to_hsa_pathways.csv")
-#geneid_hsa_pathways <- read_file(path = "/home/dchristiany/proteore_project/ProteoRE/tools/pathview/geneID_to_hsa_pathways.csv",FALSE)
-#names(geneid_hsa_pathways) <- c("geneID","pathway")
-
-##### build matrix to map on KEGG pathway (kgml : KEGG xml)
-if (!is.null(args$expression_values1)&is.null(args$expression_values2)&is.null(args$expression_values3)){
- mat <- as.data.frame(cbind(tab$e1)[which(!is.na(tab$geneID)),])
- row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))]
-} else if (!is.null(args$expression_values1)&!is.null(args$expression_values2)&is.null(args$expression_values3)){
- mat <- as.data.frame(cbind(tab$e1,tab$e2)[which(!is.na(tab$geneID)),])
- row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))]
-}else if (!is.null(args$expression_values1)&!is.null(args$expression_values2)&!is.null(args$expression_values3)){
- mat <- as.data.frame(cbind(tab$e1,tab$e2,tab$e3)[which(!is.na(tab$geneID)),])
- row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))]
-} else {
- mat <- geneID
-}
-
-
-#### simulation data test
-#exp1 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=100)
-#exp2 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=50)
-#exp3 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=10)
-#tab <- cbind(tab,exp1,exp2,exp3)
-
-#write.table(tab, file='/home/dchristiany/proteore_project/ProteoRE/tools/pathview/Lacombe_sim_expression_data.tsv', quote=FALSE, sep='\t',row.names = FALSE)
-
-#mat <- exp1[1:nrow(tab)]
-#names(mat) <- geneID
-
-
-#####mapping geneID (with or without expression values) on KEGG pathway
-plot.col.key= TRUE
-low_color = "green"
-mid_color = "#F3F781" #yellow
-high_color = "red"
-if (is.null(tab$e1)) {
- plot.col.key= FALSE #if there's no exrepession data, we don't show the color key
- high_color = "#81BEF7" #blue
-}
-
-for (id in ids) {
- pathview(gene.data = mat,
- pathway.id = id,
- species = species,
- kegg.dir = ".",
- gene.idtype = "entrez",
- 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))
-}
-
-########using keggview.native
-
-#xml.file=system.file("extdata", "hsa00010.xml", package = "pathview")
-#node.data=node.info("/home/dchristiany/hsa00010.xml")
-#plot.data.gene=node.map(mol.data=test, node.data, node.types="gene")
-#colors =node.color(plot.data = plot.data.gene[,1:9])
\ No newline at end of file
diff -r 6d5c0ff2b0bd -r 9fe4a861601b Pathview.xml
--- a/Pathview.xml Fri Sep 14 09:52:28 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,250 +0,0 @@
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- 10.1093/nar/gkx372
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-@misc{renameTODO,
- author = {Weijun Luo},
- year = {2013},
- title = {pathview},
- url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
-}
-
-
diff -r 6d5c0ff2b0bd -r 9fe4a861601b README.rst
--- a/README.rst Fri Sep 14 09:52:28 2018 -0400
+++ b/README.rst Fri Nov 09 05:11:46 2018 -0500
@@ -15,18 +15,52 @@
This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
-Select your identifier type : UniprotAC or Entrez gene ID
+You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat.
-Select an input file containing ids in a column, set header and column number or copy/paste your ids.
+If your input have another type of IDs, please use the ID_Converter tool.
+
+**Input:**
+
-You can import 1 to 3 column(s) of expression values if you are importing ids from a file.
+- 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)
-Select a species of interest.
+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"
-Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) or import it from a file.
+|
-Select the graph format : KEGG (jpg) or graphviz (pdf)
+**Output:**
-Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways.
+- a **collection dataset** named 'KEGG pathways map from ', 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
-Output : One file (png or pdf) for each selected pathway.
\ No newline at end of file
+-----
+
+.. 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
diff -r 6d5c0ff2b0bd -r 9fe4a861601b hsa_pathways.loc.sample
--- a/hsa_pathways.loc.sample Fri Sep 14 09:52:28 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,330 +0,0 @@
-#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
diff -r 6d5c0ff2b0bd -r 9fe4a861601b kegg_pathways.loc.sample
--- a/kegg_pathways.loc.sample Fri Sep 14 09:52:28 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-hsa_pathways Human (hsa) hsa tool-data/hsa_pathways.tsv
-mmu_pathways Mouse (mmu) mmu tool-data/mmu_pathways.tsv
\ No newline at end of file
diff -r 6d5c0ff2b0bd -r 9fe4a861601b kegg_pathways_list_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kegg_pathways_list_index.loc.sample Fri Nov 09 05:11:46 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
diff -r 6d5c0ff2b0bd -r 9fe4a861601b kegg_pathways_visualization.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kegg_pathways_visualization.R Fri Nov 09 05:11:46 2018 -0500
@@ -0,0 +1,275 @@
+#!/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"))
+
+read_file <- function(path,header){
+ file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),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)
+}
+
+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)
+}
+
+#return a summary from the mapping with pathview in a vector
+mapping_summary <- function(pv.out,species,id,id_type){
+
+ mapped <- pv.out$plot.data.gene$kegg.names[which(pv.out$plot.data.gene$all.mapped!='')]
+ nb_mapped <- length(mapped)
+ nb_kegg_id <- length(unique(pv.out$plot.data.gene$kegg.names))
+ ratio = round((nb_mapped/nb_kegg_id)*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"){
+ row <- c(pathway_id,pathway_name,length(unique(geneID)),nb_kegg_id,nb_mapped,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_kegg_id,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)
+}
+
+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$V1
+
+ return(args)
+}
+
+args <- get_args()
+
+#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_visualization/args.Rda")
+#load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_visualization/args.Rda")
+
+###setting variables
+if (!is.null(args$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]!=""),])
+} else {
+ tab <- data.frame(id_list,stringsAsFactors = F)
+ ncol=1
+}
+
+#fold change columns
+#make sure its double and name expression value columns
+if (fold_change_data){
+ fold_change <- as.integer(unlist(strsplit(gsub("c","",args$fold_change_col),",")))
+ if (length(fold_change) > 3) { fold_change= fold_change[1:3] }
+ for (i in 1:length(fold_change)) {
+ fc_col = fold_change[i]
+ colnames(tab)[fc_col] <- paste("e",i,sep='')
+ tab[,fc_col] <- as.double(gsub(",",".",as.character(tab[,fc_col]) ))
+ }
+}
+
+##### map uniprotID to entrez geneID
+if (id_type == "uniprotid") {
+ uniprotID = tab[,ncol]
+ mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL)
+ geneID = mapped2geneID[,2]
+ tab = cbind(tab,geneID)
+}else if (id_type == "geneid"){
+ colnames(tab)[ncol] <- "geneID"
+}
+
+geneID = as.character(tab$geneID[which(!is.na(tab$geneID))])
+geneID = gsub(" ","",geneID)
+geneID = unlist(strsplit(geneID,"[;]"))
+
+##### build matrix to map on KEGG pathway (kgml : KEGG xml)
+if (fold_change_data) {
+ geneID_indices = which(!duplicated(geneID))
+ if (length(fold_change) == 3){
+ mat <- as.data.frame(cbind(tab$e1,tab$e2,tab$e3)[which(!is.na(tab$geneID)),])
+ mat = mat[geneID_indices,]
+ row.names(mat) <- geneID[geneID_indices]
+ } else if (length(fold_change) == 2){
+ mat <- as.data.frame(cbind(tab$e1,tab$e2)[which(!is.na(tab$geneID)),])
+ mat = mat[geneID_indices,]
+ row.names(mat) <- geneID[geneID_indices]
+ } else {
+ mat <- as.data.frame(cbind(tab$e1)[which(!is.na(tab$geneID)),])
+ mat = mat[geneID_indices,]
+ names(mat) <- geneID[geneID_indices]
+ }
+} else {
+ mat <- geneID
+}
+
+#####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 (is.null(tab$e1)) {
+ plot.col.key= FALSE #if there's no exrepession data, we don't show the color key
+ high_color = "#81BEF7" #blue
+}
+
+#create graph(s) and text output
+for (id in ids) {
+ suffix= get_suffix(pathways_list,species,id)
+ pv.out <- suppressMessages(pathview(gene.data = mat,
+ gene.idtype = "entrez",
+ pathway.id = id,
+ species = species,
+ kegg.dir = ".",
+ out.suffix=suffix,
+ kegg.native = native_kegg,
+ low = list(gene = low_color, cpd = "blue"),
+ mid = list(gene = mid_color, cpd = "transparent"),
+ high = list(gene = high_color, cpd = "yellow"),
+ na.col="#D8D8D8", #gray
+ cpd.data=NULL,
+ plot.col.key = plot.col.key,
+ pdf.size=c(9,9)))
+
+ if (is.list(pv.out)){
+
+ #creating text file
+ if (!exists("DF")) {
+ DF <- data.frame(t(mapping_summary(pv.out,species,id,id_type)),stringsAsFactors = F,check.names = F)
+ } else {
+ #print (mapping_summary(pv.out,species,id))
+ DF <- rbind(DF,data.frame(t(mapping_summary(pv.out,species,id,id_type)),stringsAsFactors = F,check.names = F))
+ }
+ }
+
+}
+
+DF <- as.data.frame(apply(DF, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
+
+#text file output
+write.table(DF,file=args$output,quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
diff -r 6d5c0ff2b0bd -r 9fe4a861601b kegg_pathways_visualization.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kegg_pathways_visualization.xml Fri Nov 09 05:11:46 2018 -0500
@@ -0,0 +1,305 @@
+
+ map visualisation (PathView)
+
+ bioconductor-pathview
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
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+
+
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+
+
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+
+
+
+
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+
+
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+
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+
+
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+
+
+
+
+
+
+
+ native=="false" and input["ids"] == "file"
+
+
+
+ native=="true" and input["ids"] == "file"
+
+
+
+ native=="false" and input["ids"] == "text"
+
+
+
+ native=="true" and input["ids"] == "text"
+
+
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+
+
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+
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+
+
+
+
+
+
+
+
+
+
+ ', 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.
+ ]]>
+
+ 10.1093/nar/gkx372
+
+@misc{renameTODO,
+ author = {Weijun Luo},
+ year = {2013},
+ title = {pathview},
+ url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
+}
+
+
diff -r 6d5c0ff2b0bd -r 9fe4a861601b mmu_pathways.loc.sample
--- a/mmu_pathways.loc.sample Fri Sep 14 09:52:28 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,326 +0,0 @@
-#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
diff -r 6d5c0ff2b0bd -r 9fe4a861601b tool-data/rno_pathways.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rno_pathways.loc Fri Nov 09 05:11:46 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
diff -r 6d5c0ff2b0bd -r 9fe4a861601b tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Fri Sep 14 09:52:28 2018 -0400
+++ b/tool_data_table_conf.xml.sample Fri Nov 09 05:11:46 2018 -0500
@@ -1,5 +1,9 @@
+
value,name
@@ -8,4 +12,8 @@
value,name
+