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add example

Zhang Xudong 2 years ago
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+ 32 - 1
README.md

@@ -1 +1,32 @@
-# emcp
+# 安装
+
+## 安装依赖
+1. R        
+2. R 包:argparser, tidyverse, formattable, AnnotationForge, seqinr, clusterProfiler       
+
+## 安装 emcp
+
+```
+git clone http://git.genek.cn:3333/zhxd2/emcp.git
+```
+
+# 使用
+
+## 准备输入文件
+
+输入文件为蛋白序列, 参考 example_data 目录下的 proteins.fa        
+
+## 第一步:在线注释
+登录 http://eggnog-mapper.embl.de/ 上传蛋白序列, 在线进行蛋白注释.          
+完成后下载 out.emapper.annotations     
+
+
+## 第二步:运行 emapperx.R
+
+```
+Rscript ../emapperx.R out.emapper.annotations proteins.fa
+```
+
+这一步两个功能:    
+1. 对 emapper 注释结果进行统计绘图      
+2. 构建 OrgDB 用于富集分析等     

+ 16 - 0
example_data/R_Library/org.My.eg.db/DESCRIPTION

@@ -0,0 +1,16 @@
+Package: org.My.eg.db
+Title: Genome wide annotation for M y
+Description: Genome wide annotation for M y, primarily based on mapping using Entrez Gene identifiers.
+Version: 1.0
+Author: zhangsan
+Maintainer: zhangsan <zhangsan@genek.cn>
+Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.52.0)
+Suggests: DBI, annotate, RUnit
+Imports: methods, AnnotationDbi
+License: Artistic-2.0
+organism: M y
+species: M y
+biocViews: OrgDb, annotation
+NeedsCompilation: no
+Packaged: 2021-12-28 06:53:59 UTC; zhxd2
+Built: R 4.0.5; ; 2021-12-28 06:56:34 UTC; unix

+ 4 - 0
example_data/R_Library/org.My.eg.db/INDEX

@@ -0,0 +1,4 @@
+org.My.eg.db            Bioconductor annotation data package
+org.My.egORGANISM       The Organism for org.My.eg
+org.My.eg_dbconn        Collect information about the package
+                        annotation DB

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example_data/R_Library/org.My.eg.db/NAMESPACE

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+import(methods)
+import(AnnotationDbi)
+
+### Only put what is statically exported here. All the AnnObj instances
+### created at load time are dynamically exported (refer to R/zzz.R for
+### the details).
+export(
+    org.My.eg,
+    org.My.eg_dbconn,
+    org.My.eg_dbfile,
+    org.My.eg_dbschema,
+    org.My.eg_dbInfo,
+
+    org.My.egORGANISM
+)
+

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example_data/R_Library/org.My.eg.db/R/org.My.eg.db

@@ -0,0 +1,27 @@
+#  File share/R/nspackloader.R
+#  Part of the R package, https://www.R-project.org
+#
+#  Copyright (C) 1995-2012 The R Core Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  https://www.r-project.org/Licenses/
+
+local({
+    info <- loadingNamespaceInfo()
+    pkg <- info$pkgname
+    ns <- .getNamespace(as.name(pkg))
+    if (is.null(ns))
+        stop("cannot find namespace environment for ", pkg, domain = NA);
+    dbbase <- file.path(info$libname, pkg, "R", pkg)
+    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})

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example_data/R_Library/org.My.eg.db/help/AnIndex

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+org.My.eg	org.My.egBASE
+org.My.eg.db	org.My.egBASE
+org.My.egORGANISM	org.My.egORGANISM
+org.My.eg_dbconn	org.My.eg_dbconn
+org.My.eg_dbfile	org.My.eg_dbconn
+org.My.eg_dbInfo	org.My.eg_dbconn
+org.My.eg_dbschema	org.My.eg_dbconn

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example_data/R_Library/org.My.eg.db/html/00Index.html

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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head><title>R: Genome wide annotation for M y</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<link rel="stylesheet" type="text/css" href="R.css" />
+</head><body>
+<h1> Genome wide annotation for M y
+<img class="toplogo" src="../../../doc/html/Rlogo.svg" alt="[R logo]" />
+</h1>
+<hr/>
+<div style="text-align: center;">
+<a href="../../../doc/html/packages.html"><img class="arrow" src="../../../doc/html/left.jpg" alt="[Up]" /></a>
+<a href="../../../doc/html/index.html"><img class="arrow" src="../../../doc/html/up.jpg" alt="[Top]" /></a>
+</div><h2>Documentation for package &lsquo;org.My.eg.db&rsquo; version 1.0</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td style="width: 25%;"><a href="org.My.egBASE.html">org.My.eg</a></td>
+<td>Bioconductor annotation data package</td></tr>
+<tr><td style="width: 25%;"><a href="org.My.egBASE.html">org.My.eg.db</a></td>
+<td>Bioconductor annotation data package</td></tr>
+<tr><td style="width: 25%;"><a href="org.My.egORGANISM.html">org.My.egORGANISM</a></td>
+<td>The Organism for org.My.eg</td></tr>
+<tr><td style="width: 25%;"><a href="org.My.eg_dbconn.html">org.My.eg_dbconn</a></td>
+<td>Collect information about the package annotation DB</td></tr>
+<tr><td style="width: 25%;"><a href="org.My.eg_dbconn.html">org.My.eg_dbfile</a></td>
+<td>Collect information about the package annotation DB</td></tr>
+<tr><td style="width: 25%;"><a href="org.My.eg_dbconn.html">org.My.eg_dbInfo</a></td>
+<td>Collect information about the package annotation DB</td></tr>
+<tr><td style="width: 25%;"><a href="org.My.eg_dbconn.html">org.My.eg_dbschema</a></td>
+<td>Collect information about the package annotation DB</td></tr>
+</table>
+</body></html>

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example_data/R_Library/org.My.eg.db/html/R.css

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+body {
+    background: white;
+    color: black;
+}
+
+a:link {
+    background: white;
+    color: blue;
+}
+
+a:visited {
+    background: white;
+    color: rgb(50%, 0%, 50%);
+}
+
+h1 {
+    background: white;
+    color: rgb(55%, 55%, 55%);
+    font-family: monospace;
+    font-size: x-large;
+    text-align: center;
+}
+
+h2 {
+    background: white;
+    color: rgb(40%, 40%, 40%);
+    font-family: monospace;
+    font-size: large;
+    text-align: center;
+}
+
+h3 {
+    background: white;
+    color: rgb(40%, 40%, 40%);
+    font-family: monospace;
+    font-size: large;
+}
+
+h4 {
+    background: white;
+    color: rgb(40%, 40%, 40%);
+    font-family: monospace;
+    font-style: italic;
+    font-size: large;
+}
+
+h5 {
+    background: white;
+    color: rgb(40%, 40%, 40%);
+    font-family: monospace;
+}
+
+h6 {
+    background: white;
+    color: rgb(40%, 40%, 40%);
+    font-family: monospace;
+    font-style: italic;
+}
+		
+img.toplogo {
+    width: 4em;
+    vertical-align: middle;
+}
+
+img.arrow {
+    width: 30px;
+    height: 30px;
+    border: 0;
+}
+
+span.acronym {
+    font-size: small;
+}
+
+span.env {
+    font-family: monospace;
+}
+
+span.file {
+    font-family: monospace;
+}
+
+span.option{
+    font-family: monospace;
+}
+
+span.pkg {
+    font-weight: bold;
+}
+
+span.samp{
+    font-family: monospace;
+}
+
+div.vignettes a:hover {
+    background: rgb(85%, 85%, 85%);
+}

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example_data/anno_stat.txt

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+database	number	percentage
+EggNOG	27,161	79.71%
+GO	13,634	40.01%
+COG/KOG	27,161	79.71%
+KEGG Pathway	9,183	26.95%

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+ 14 - 0
example_data/org.My.eg.db/DESCRIPTION

@@ -0,0 +1,14 @@
+Package: org.My.eg.db
+Title: Genome wide annotation for M y
+Description: Genome wide annotation for M y, primarily based on mapping using Entrez Gene identifiers.
+Version: 1.0
+Author: zhangsan
+Maintainer: zhangsan <zhangsan@genek.cn>
+Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.52.0)
+Suggests: DBI, annotate, RUnit
+Imports: methods, AnnotationDbi
+License: Artistic-2.0
+organism: M y
+species: M y
+biocViews: OrgDb, annotation
+

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example_data/org.My.eg.db/NAMESPACE

@@ -0,0 +1,16 @@
+import(methods)
+import(AnnotationDbi)
+
+### Only put what is statically exported here. All the AnnObj instances
+### created at load time are dynamically exported (refer to R/zzz.R for
+### the details).
+export(
+    org.My.eg,
+    org.My.eg_dbconn,
+    org.My.eg_dbfile,
+    org.My.eg_dbschema,
+    org.My.eg_dbInfo,
+
+    org.My.egORGANISM
+)
+

+ 36 - 0
example_data/org.My.eg.db/R/zzz.R

@@ -0,0 +1,36 @@
+datacache <- new.env(hash=TRUE, parent=emptyenv())
+
+org.My.eg <- function() showQCData("org.My.eg", datacache)
+org.My.eg_dbconn <- function() dbconn(datacache)
+org.My.eg_dbfile <- function() dbfile(datacache)
+org.My.eg_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices)
+org.My.eg_dbInfo <- function() dbInfo(datacache)
+
+org.My.egORGANISM <- "M y"
+
+.onLoad <- function(libname, pkgname)
+{
+    ## Connect to the SQLite DB
+    dbfile <- system.file("extdata", "org.My.eg.sqlite", package=pkgname, lib.loc=libname)
+    assign("dbfile", dbfile, envir=datacache)
+    dbconn <- dbFileConnect(dbfile)
+    assign("dbconn", dbconn, envir=datacache)
+
+    ## Create the OrgDb object
+    sPkgname <- sub(".db$","",pkgname)
+    db <- loadDb(system.file("extdata", paste(sPkgname,
+      ".sqlite",sep=""), package=pkgname, lib.loc=libname),
+                   packageName=pkgname)    
+    dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"OrgDb")
+    ns <- asNamespace(pkgname)
+    assign(dbNewname, db, envir=ns)
+    namespaceExport(ns, dbNewname)
+        
+    packageStartupMessage(AnnotationDbi:::annoStartupMessages("org.My.eg.db"))
+}
+
+.onUnload <- function(libpath)
+{
+    dbFileDisconnect(org.My.eg_dbconn())
+}
+

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+\name{org.My.eg.db}
+\alias{org.My.eg.db}
+\alias{org.My.eg}
+\title{Bioconductor annotation data package}
+\description{
+
+  Welcome to the org.My.eg.db annotation Package.  This is an
+  organism specific package. The purpose is to provide detailed
+  information about the species abbreviated in the second part of the
+  package name org.My.eg.db. This package is updated biannually.
+
+  To learn more about this package, users are encouraged to learn about
+  the select, columns, keys and keytypes methods.  These are described
+  in a walkthrough on the bioconductor website as well as in the manual
+  pages and vignettes in the AnnotationDbi package.
+}
+\keyword{datasets}
+

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@@ -0,0 +1,32 @@
+\name{org.My.egORGANISM}
+\alias{org.My.egORGANISM}
+\title{The Organism for org.My.eg}
+\description{
+  org.My.egORGANISM is an R object that contains a single item: a
+  character string that names the organism for which org.My.eg was built.
+}
+
+\details{
+  Although the package name is suggestive of the organism for which it
+  was built, org.My.egORGANISM provides a simple way to programmatically
+  extract the organism name.
+}
+
+\seealso{
+  \itemize{
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
+          the \code{select()} interface.
+  }
+}
+
+\examples{
+## select() interface:
+## Objects in this package can be accessed using the select() interface
+## from the AnnotationDbi package. See ?select for details.
+
+## Bimap interface:
+org.My.egORGANISM
+}
+
+\keyword{datasets}
+

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example_data/org.My.eg.db/man/org.My.eg_dbconn.Rd

@@ -0,0 +1,87 @@
+
+\name{org.My.eg_dbconn}
+
+\alias{org.My.eg_dbconn}
+\alias{org.My.eg_dbfile}
+\alias{org.My.eg_dbschema}
+\alias{org.My.eg_dbInfo}
+
+
+\title{Collect information about the package annotation DB}
+
+\description{
+  Some convenience functions for getting a connection object to (or collecting
+  information about) the package annotation DB.
+}
+
+\usage{
+  org.My.eg_dbconn()
+  org.My.eg_dbfile()
+  org.My.eg_dbschema(file="", show.indices=FALSE)
+  org.My.eg_dbInfo()
+}
+
+\arguments{
+  \item{file}{
+    A connection, or a character string naming the file to print to (see
+    the \code{file} argument of the \code{\link[base]{cat}} function for
+    the details).
+  }
+  \item{show.indices}{
+    The CREATE INDEX statements are not shown by default.
+    Use \code{show.indices=TRUE} to get them.
+  }
+}
+
+\details{
+  \code{org.My.eg_dbconn} returns a connection object to the
+  package annotation DB.  IMPORTANT: Don't call
+  \code{\link[DBI:dbConnect]{dbDisconnect}} on the connection object
+  returned by \code{org.My.eg_dbconn} or you will break all the
+  \code{\link[AnnotationDbi:AnnDbObj-class]{AnnDbObj}} objects defined
+  in this package!
+
+  \code{org.My.eg_dbfile} returns the path (character string) to the
+  package annotation DB (this is an SQLite file).
+
+  \code{org.My.eg_dbschema} prints the schema definition of the
+  package annotation DB.
+
+  \code{org.My.eg_dbInfo} prints other information about the package
+  annotation DB.
+}
+
+\value{
+  \code{org.My.eg_dbconn}: a DBIConnection object representing an
+  open connection to the package annotation DB.
+
+  \code{org.My.eg_dbfile}: a character string with the path to the
+  package annotation DB.
+
+  \code{org.My.eg_dbschema}: none (invisible \code{NULL}).
+
+  \code{org.My.eg_dbInfo}: none (invisible \code{NULL}).
+}
+
+\seealso{
+  \code{\link[DBI:dbSendQuery]{dbGetQuery}},
+  \code{\link[DBI:dbConnect]{dbConnect}},
+  \code{\link[AnnotationDbi:AnnDbObj-class]{dbconn}},
+  \code{\link[AnnotationDbi:AnnDbObj-class]{dbfile}},
+  \code{\link[AnnotationDbi:AnnDbObj-class]{dbschema}},
+  \code{\link[AnnotationDbi:AnnDbObj-class]{dbInfo}}
+}
+
+\examples{
+  library(DBI)
+  ## Count the number of rows in the "genes" table:
+  dbGetQuery(org.My.eg_dbconn(), "SELECT COUNT(*) FROM genes")
+
+  org.My.eg_dbschema()
+
+  org.My.eg_dbInfo()
+}
+
+\keyword{utilities}
+\keyword{datasets}
+

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example_data/pathway.txt


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example_data/pathway_name.txt

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+Pathway	Pathway_Name	Pathway_Class	Pathway_Subclass
+1	ko00010	Glycolysis / Gluconeogenesis	Metabolism	Carbohydrate metabolism
+2	ko00020	Citrate cycle (TCA cycle)	Metabolism	Carbohydrate metabolism
+3	ko00030	Pentose phosphate pathway	Metabolism	Carbohydrate metabolism
+4	ko00040	Pentose and glucuronate interconversions	Metabolism	Carbohydrate metabolism
+5	ko00051	Fructose and mannose metabolism	Metabolism	Carbohydrate metabolism
+6	ko00052	Galactose metabolism	Metabolism	Carbohydrate metabolism
+7	ko00053	Ascorbate and aldarate metabolism	Metabolism	Carbohydrate metabolism
+8	ko00500	Starch and sucrose metabolism	Metabolism	Carbohydrate metabolism
+9	ko00520	Amino sugar and nucleotide sugar metabolism	Metabolism	Carbohydrate metabolism
+10	ko00620	Pyruvate metabolism	Metabolism	Carbohydrate metabolism
+11	ko00630	Glyoxylate and dicarboxylate metabolism	Metabolism	Carbohydrate metabolism
+12	ko00640	Propanoate metabolism	Metabolism	Carbohydrate metabolism
+13	ko00650	Butanoate metabolism	Metabolism	Carbohydrate metabolism
+14	ko00660	C5-Branched dibasic acid metabolism	Metabolism	Carbohydrate metabolism
+15	ko00562	Inositol phosphate metabolism	Metabolism	Carbohydrate metabolism
+16	ko00190	Oxidative phosphorylation	Metabolism	Energy metabolism
+17	ko00195	Photosynthesis	Metabolism	Energy metabolism
+18	ko00196	Photosynthesis - antenna proteins	Metabolism	Energy metabolism
+19	ko00710	Carbon fixation in photosynthetic organisms	Metabolism	Energy metabolism
+20	ko00720	Carbon fixation pathways in prokaryotes	Metabolism	Energy metabolism
+21	ko00680	Methane metabolism	Metabolism	Energy metabolism
+22	ko00910	Nitrogen metabolism	Metabolism	Energy metabolism
+23	ko00920	Sulfur metabolism	Metabolism	Energy metabolism
+24	ko00061	Fatty acid biosynthesis	Metabolism	Lipid metabolism
+25	ko00062	Fatty acid elongation	Metabolism	Lipid metabolism
+26	ko00071	Fatty acid degradation	Metabolism	Lipid metabolism
+27	ko00072	Synthesis and degradation of ketone bodies	Metabolism	Lipid metabolism
+28	ko00073	Cutin, suberine and wax biosynthesis	Metabolism	Lipid metabolism
+29	ko00100	Steroid biosynthesis	Metabolism	Lipid metabolism
+30	ko00120	Primary bile acid biosynthesis	Metabolism	Lipid metabolism
+31	ko00121	Secondary bile acid biosynthesis	Metabolism	Lipid metabolism
+32	ko00140	Steroid hormone biosynthesis	Metabolism	Lipid metabolism
+33	ko00561	Glycerolipid metabolism	Metabolism	Lipid metabolism
+34	ko00564	Glycerophospholipid metabolism	Metabolism	Lipid metabolism
+35	ko00565	Ether lipid metabolism	Metabolism	Lipid metabolism
+36	ko00600	Sphingolipid metabolism	Metabolism	Lipid metabolism
+37	ko00590	Arachidonic acid metabolism	Metabolism	Lipid metabolism
+38	ko00591	Linoleic acid metabolism	Metabolism	Lipid metabolism
+39	ko00592	alpha-Linolenic acid metabolism	Metabolism	Lipid metabolism
+40	ko01040	Biosynthesis of unsaturated fatty acids	Metabolism	Lipid metabolism
+41	ko00230	Purine metabolism	Metabolism	Nucleotide metabolism
+42	ko00240	Pyrimidine metabolism	Metabolism	Nucleotide metabolism
+43	ko00250	Alanine, aspartate and glutamate metabolism	Metabolism	Amino acid metabolism
+44	ko00260	Glycine, serine and threonine metabolism	Metabolism	Amino acid metabolism
+45	ko00270	Cysteine and methionine metabolism	Metabolism	Amino acid metabolism
+46	ko00280	Valine, leucine and isoleucine degradation	Metabolism	Amino acid metabolism
+47	ko00290	Valine, leucine and isoleucine biosynthesis	Metabolism	Amino acid metabolism
+48	ko00300	Lysine biosynthesis	Metabolism	Amino acid metabolism
+49	ko00310	Lysine degradation	Metabolism	Amino acid metabolism
+50	ko00220	Arginine biosynthesis	Metabolism	Amino acid metabolism
+51	ko00330	Arginine and proline metabolism	Metabolism	Amino acid metabolism
+52	ko00340	Histidine metabolism	Metabolism	Amino acid metabolism
+53	ko00350	Tyrosine metabolism	Metabolism	Amino acid metabolism
+54	ko00360	Phenylalanine metabolism	Metabolism	Amino acid metabolism
+55	ko00380	Tryptophan metabolism	Metabolism	Amino acid metabolism
+56	ko00400	Phenylalanine, tyrosine and tryptophan biosynthesis	Metabolism	Amino acid metabolism
+57	ko00410	beta-Alanine metabolism	Metabolism	Metabolism of other amino acids
+58	ko00430	Taurine and hypotaurine metabolism	Metabolism	Metabolism of other amino acids
+59	ko00440	Phosphonate and phosphinate metabolism	Metabolism	Metabolism of other amino acids
+60	ko00450	Selenocompound metabolism	Metabolism	Metabolism of other amino acids
+61	ko00460	Cyanoamino acid metabolism	Metabolism	Metabolism of other amino acids
+62	ko00471	D-Glutamine and D-glutamate metabolism	Metabolism	Metabolism of other amino acids
+63	ko00472	D-Arginine and D-ornithine metabolism	Metabolism	Metabolism of other amino acids
+64	ko00473	D-Alanine metabolism	Metabolism	Metabolism of other amino acids
+65	ko00480	Glutathione metabolism	Metabolism	Metabolism of other amino acids
+66	ko00510	N-Glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+67	ko00513	Various types of N-glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+68	ko00512	Mucin type O-glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+69	ko00515	Mannose type O-glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+70	ko00514	Other types of O-glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+71	ko00532	Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate	Metabolism	Glycan biosynthesis and metabolism
+72	ko00534	Glycosaminoglycan biosynthesis - heparan sulfate / heparin	Metabolism	Glycan biosynthesis and metabolism
+73	ko00533	Glycosaminoglycan biosynthesis - keratan sulfate	Metabolism	Glycan biosynthesis and metabolism
+74	ko00531	Glycosaminoglycan degradation	Metabolism	Glycan biosynthesis and metabolism
+75	ko00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+76	ko00601	Glycosphingolipid biosynthesis - lacto and neolacto series	Metabolism	Glycan biosynthesis and metabolism
+77	ko00603	Glycosphingolipid biosynthesis - globo and isoglobo series	Metabolism	Glycan biosynthesis and metabolism
+78	ko00604	Glycosphingolipid biosynthesis - ganglio series	Metabolism	Glycan biosynthesis and metabolism
+79	ko00540	Lipopolysaccharide biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+80	ko00550	Peptidoglycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+81	ko00511	Other glycan degradation	Metabolism	Glycan biosynthesis and metabolism
+82	ko00571	Lipoarabinomannan (LAM) biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+83	ko00572	Arabinogalactan biosynthesis - Mycobacterium	Metabolism	Glycan biosynthesis and metabolism
+84	ko00730	Thiamine metabolism	Metabolism	Metabolism of cofactors and vitamins
+85	ko00740	Riboflavin metabolism	Metabolism	Metabolism of cofactors and vitamins
+86	ko00750	Vitamin B6 metabolism	Metabolism	Metabolism of cofactors and vitamins
+87	ko00760	Nicotinate and nicotinamide metabolism	Metabolism	Metabolism of cofactors and vitamins
+88	ko00770	Pantothenate and CoA biosynthesis	Metabolism	Metabolism of cofactors and vitamins
+89	ko00780	Biotin metabolism	Metabolism	Metabolism of cofactors and vitamins
+90	ko00785	Lipoic acid metabolism	Metabolism	Metabolism of cofactors and vitamins
+91	ko00790	Folate biosynthesis	Metabolism	Metabolism of cofactors and vitamins
+92	ko00670	One carbon pool by folate	Metabolism	Metabolism of cofactors and vitamins
+93	ko00830	Retinol metabolism	Metabolism	Metabolism of cofactors and vitamins
+94	ko00860	Porphyrin and chlorophyll metabolism	Metabolism	Metabolism of cofactors and vitamins
+95	ko00130	Ubiquinone and other terpenoid-quinone biosynthesis	Metabolism	Metabolism of cofactors and vitamins
+96	ko00900	Terpenoid backbone biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+97	ko00902	Monoterpenoid biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+98	ko00909	Sesquiterpenoid and triterpenoid biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+99	ko00904	Diterpenoid biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+100	ko00906	Carotenoid biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+101	ko00905	Brassinosteroid biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+102	ko00981	Insect hormone biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+103	ko00908	Zeatin biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+104	ko00903	Limonene and pinene degradation	Metabolism	Metabolism of terpenoids and polyketides
+105	ko00281	Geraniol degradation	Metabolism	Metabolism of terpenoids and polyketides
+106	ko01052	Type I polyketide structures	Metabolism	Metabolism of terpenoids and polyketides
+107	ko00522	Biosynthesis of 12-, 14- and 16-membered macrolides	Metabolism	Metabolism of terpenoids and polyketides
+108	ko01051	Biosynthesis of ansamycins	Metabolism	Metabolism of terpenoids and polyketides
+109	ko01059	Biosynthesis of enediyne antibiotics	Metabolism	Metabolism of terpenoids and polyketides
+110	ko01056	Biosynthesis of type II polyketide backbone	Metabolism	Metabolism of terpenoids and polyketides
+111	ko01057	Biosynthesis of type II polyketide products	Metabolism	Metabolism of terpenoids and polyketides
+112	ko00253	Tetracycline biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+113	ko00523	Polyketide sugar unit biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+114	ko01054	Nonribosomal peptide structures	Metabolism	Metabolism of terpenoids and polyketides
+115	ko01053	Biosynthesis of siderophore group nonribosomal peptides	Metabolism	Metabolism of terpenoids and polyketides
+116	ko01055	Biosynthesis of vancomycin group antibiotics	Metabolism	Metabolism of terpenoids and polyketides
+117	ko00940	Phenylpropanoid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+118	ko00945	Stilbenoid, diarylheptanoid and gingerol biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+119	ko00941	Flavonoid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+120	ko00944	Flavone and flavonol biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+121	ko00942	Anthocyanin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+122	ko00943	Isoflavonoid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+123	ko00901	Indole alkaloid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+124	ko00403	Indole diterpene alkaloid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+125	ko00950	Isoquinoline alkaloid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+126	ko00960	Tropane, piperidine and pyridine alkaloid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+127	ko01058	Acridone alkaloid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+128	ko00232	Caffeine metabolism	Metabolism	Biosynthesis of other secondary metabolites
+129	ko00965	Betalain biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+130	ko00966	Glucosinolate biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+131	ko00402	Benzoxazinoid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+132	ko00311	Penicillin and cephalosporin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+133	ko00332	Carbapenem biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+134	ko00261	Monobactam biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+135	ko00331	Clavulanic acid biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+136	ko00521	Streptomycin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+137	ko00524	Neomycin, kanamycin and gentamicin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+138	ko00525	Acarbose and validamycin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+139	ko00231	Puromycin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+140	ko00401	Novobiocin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+141	ko00404	Staurosporine biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+142	ko00405	Phenazine biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+143	ko00333	Prodigiosin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+144	ko00254	Aflatoxin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+145	ko00999	Biosynthesis of secondary metabolites - unclassified	Metabolism	Biosynthesis of other secondary metabolites
+146	ko00362	Benzoate degradation	Metabolism	Xenobiotics biodegradation and metabolism
+147	ko00627	Aminobenzoate degradation	Metabolism	Xenobiotics biodegradation and metabolism
+148	ko00364	Fluorobenzoate degradation	Metabolism	Xenobiotics biodegradation and metabolism
+149	ko00625	Chloroalkane and chloroalkene degradation	Metabolism	Xenobiotics biodegradation and metabolism
+150	ko00361	Chlorocyclohexane and chlorobenzene degradation	Metabolism	Xenobiotics biodegradation and metabolism
+151	ko00623	Toluene degradation	Metabolism	Xenobiotics biodegradation and metabolism
+152	ko00622	Xylene degradation	Metabolism	Xenobiotics biodegradation and metabolism
+153	ko00633	Nitrotoluene degradation	Metabolism	Xenobiotics biodegradation and metabolism
+154	ko00642	Ethylbenzene degradation	Metabolism	Xenobiotics biodegradation and metabolism
+155	ko00643	Styrene degradation	Metabolism	Xenobiotics biodegradation and metabolism
+156	ko00791	Atrazine degradation	Metabolism	Xenobiotics biodegradation and metabolism
+157	ko00930	Caprolactam degradation	Metabolism	Xenobiotics biodegradation and metabolism
+158	ko00363	Bisphenol degradation	Metabolism	Xenobiotics biodegradation and metabolism
+159	ko00621	Dioxin degradation	Metabolism	Xenobiotics biodegradation and metabolism
+160	ko00626	Naphthalene degradation	Metabolism	Xenobiotics biodegradation and metabolism
+161	ko00624	Polycyclic aromatic hydrocarbon degradation	Metabolism	Xenobiotics biodegradation and metabolism
+162	ko00365	Furfural degradation	Metabolism	Xenobiotics biodegradation and metabolism
+163	ko00984	Steroid degradation	Metabolism	Xenobiotics biodegradation and metabolism
+164	ko00980	Metabolism of xenobiotics by cytochrome P450	Metabolism	Xenobiotics biodegradation and metabolism
+165	ko00982	Drug metabolism - cytochrome P450	Metabolism	Xenobiotics biodegradation and metabolism
+166	ko00983	Drug metabolism - other enzymes	Metabolism	Xenobiotics biodegradation and metabolism
+167	ko03020	RNA polymerase	Genetic Information Processing	Transcription
+168	ko03022	Basal transcription factors	Genetic Information Processing	Transcription
+169	ko03040	Spliceosome	Genetic Information Processing	Transcription
+170	ko03010	Ribosome	Genetic Information Processing	Translation
+171	ko00970	Aminoacyl-tRNA biosynthesis	Genetic Information Processing	Translation
+172	ko03013	RNA transport	Genetic Information Processing	Translation
+173	ko03015	mRNA surveillance pathway	Genetic Information Processing	Translation
+174	ko03008	Ribosome biogenesis in eukaryotes	Genetic Information Processing	Translation
+175	ko03060	Protein export	Genetic Information Processing	Folding, sorting and degradation
+176	ko04141	Protein processing in endoplasmic reticulum	Genetic Information Processing	Folding, sorting and degradation
+177	ko04130	SNARE interactions in vesicular transport	Genetic Information Processing	Folding, sorting and degradation
+178	ko04120	Ubiquitin mediated proteolysis	Genetic Information Processing	Folding, sorting and degradation
+179	ko04122	Sulfur relay system	Genetic Information Processing	Folding, sorting and degradation
+180	ko03050	Proteasome	Genetic Information Processing	Folding, sorting and degradation
+181	ko03018	RNA degradation	Genetic Information Processing	Folding, sorting and degradation
+182	ko03030	DNA replication	Genetic Information Processing	Replication and repair
+183	ko03410	Base excision repair	Genetic Information Processing	Replication and repair
+184	ko03420	Nucleotide excision repair	Genetic Information Processing	Replication and repair
+185	ko03430	Mismatch repair	Genetic Information Processing	Replication and repair
+186	ko03440	Homologous recombination	Genetic Information Processing	Replication and repair
+187	ko03450	Non-homologous end-joining	Genetic Information Processing	Replication and repair
+188	ko03460	Fanconi anemia pathway	Genetic Information Processing	Replication and repair
+189	ko02010	ABC transporters	Environmental Information Processing	Membrane transport
+190	ko02060	Phosphotransferase system (PTS)	Environmental Information Processing	Membrane transport
+191	ko03070	Bacterial secretion system	Environmental Information Processing	Membrane transport
+192	ko02020	Two-component system	Environmental Information Processing	Signal transduction
+193	ko04014	Ras signaling pathway	Environmental Information Processing	Signal transduction
+194	ko04015	Rap1 signaling pathway	Environmental Information Processing	Signal transduction
+195	ko04010	MAPK signaling pathway	Environmental Information Processing	Signal transduction
+196	ko04013	MAPK signaling pathway - fly	Environmental Information Processing	Signal transduction
+197	ko04016	MAPK signaling pathway - plant	Environmental Information Processing	Signal transduction
+198	ko04011	MAPK signaling pathway - yeast	Environmental Information Processing	Signal transduction
+199	ko04012	ErbB signaling pathway	Environmental Information Processing	Signal transduction
+200	ko04310	Wnt signaling pathway	Environmental Information Processing	Signal transduction
+201	ko04330	Notch signaling pathway	Environmental Information Processing	Signal transduction
+202	ko04340	Hedgehog signaling pathway	Environmental Information Processing	Signal transduction
+203	ko04341	Hedgehog signaling pathway - fly	Environmental Information Processing	Signal transduction
+204	ko04350	TGF-beta signaling pathway	Environmental Information Processing	Signal transduction
+205	ko04390	Hippo signaling pathway	Environmental Information Processing	Signal transduction
+206	ko04391	Hippo signaling pathway - fly	Environmental Information Processing	Signal transduction
+207	ko04392	Hippo signaling pathway - multiple species	Environmental Information Processing	Signal transduction
+208	ko04370	VEGF signaling pathway	Environmental Information Processing	Signal transduction
+209	ko04371	Apelin signaling pathway	Environmental Information Processing	Signal transduction
+210	ko04630	Jak-STAT signaling pathway	Environmental Information Processing	Signal transduction
+211	ko04064	NF-kappa B signaling pathway	Environmental Information Processing	Signal transduction
+212	ko04668	TNF signaling pathway	Environmental Information Processing	Signal transduction
+213	ko04066	HIF-1 signaling pathway	Environmental Information Processing	Signal transduction
+214	ko04068	FoxO signaling pathway	Environmental Information Processing	Signal transduction
+215	ko04020	Calcium signaling pathway	Environmental Information Processing	Signal transduction
+216	ko04070	Phosphatidylinositol signaling system	Environmental Information Processing	Signal transduction
+217	ko04072	Phospholipase D signaling pathway	Environmental Information Processing	Signal transduction
+218	ko04071	Sphingolipid signaling pathway	Environmental Information Processing	Signal transduction
+219	ko04024	cAMP signaling pathway	Environmental Information Processing	Signal transduction
+220	ko04022	cGMP-PKG signaling pathway	Environmental Information Processing	Signal transduction
+221	ko04151	PI3K-Akt signaling pathway	Environmental Information Processing	Signal transduction
+222	ko04152	AMPK signaling pathway	Environmental Information Processing	Signal transduction
+223	ko04150	mTOR signaling pathway	Environmental Information Processing	Signal transduction
+224	ko04075	Plant hormone signal transduction	Environmental Information Processing	Signal transduction
+225	ko04080	Neuroactive ligand-receptor interaction	Environmental Information Processing	Signaling molecules and interaction
+226	ko04060	Cytokine-cytokine receptor interaction	Environmental Information Processing	Signaling molecules and interaction
+227	ko04512	ECM-receptor interaction	Environmental Information Processing	Signaling molecules and interaction
+228	ko04514	Cell adhesion molecules (CAMs)	Environmental Information Processing	Signaling molecules and interaction
+229	ko04144	Endocytosis	Cellular Processes	Transport and catabolism
+230	ko04145	Phagosome	Cellular Processes	Transport and catabolism
+231	ko04142	Lysosome	Cellular Processes	Transport and catabolism
+232	ko04146	Peroxisome	Cellular Processes	Transport and catabolism
+233	ko04140	Autophagy - animal	Cellular Processes	Transport and catabolism
+234	ko04138	Autophagy - yeast	Cellular Processes	Transport and catabolism
+235	ko04136	Autophagy - other	Cellular Processes	Transport and catabolism
+236	ko04137	Mitophagy - animal	Cellular Processes	Transport and catabolism
+237	ko04139	Mitophagy - yeast	Cellular Processes	Transport and catabolism
+238	ko04110	Cell cycle	Cellular Processes	Cell growth and death
+239	ko04111	Cell cycle - yeast	Cellular Processes	Cell growth and death
+240	ko04112	Cell cycle - Caulobacter	Cellular Processes	Cell growth and death
+241	ko04113	Meiosis - yeast	Cellular Processes	Cell growth and death
+242	ko04114	Oocyte meiosis	Cellular Processes	Cell growth and death
+243	ko04210	Apoptosis	Cellular Processes	Cell growth and death
+244	ko04214	Apoptosis - fly	Cellular Processes	Cell growth and death
+245	ko04215	Apoptosis - multiple species	Cellular Processes	Cell growth and death
+246	ko04216	Ferroptosis	Cellular Processes	Cell growth and death
+247	ko04217	Necroptosis	Cellular Processes	Cell growth and death
+248	ko04115	p53 signaling pathway	Cellular Processes	Cell growth and death
+249	ko04218	Cellular senescence	Cellular Processes	Cell growth and death
+250	ko04510	Focal adhesion	Cellular Processes	Cellular community - eukaryotes
+251	ko04520	Adherens junction	Cellular Processes	Cellular community - eukaryotes
+252	ko04530	Tight junction	Cellular Processes	Cellular community - eukaryotes
+253	ko04540	Gap junction	Cellular Processes	Cellular community - eukaryotes
+254	ko04550	Signaling pathways regulating pluripotency of stem cells	Cellular Processes	Cellular community - eukaryotes
+255	ko02024	Quorum sensing	Cellular Processes	Cellular community - prokaryotes
+256	ko05111	Biofilm formation - Vibrio cholerae	Cellular Processes	Cellular community - prokaryotes
+257	ko02025	Biofilm formation - Pseudomonas aeruginosa	Cellular Processes	Cellular community - prokaryotes
+258	ko02026	Biofilm formation - Escherichia coli	Cellular Processes	Cellular community - prokaryotes
+259	ko02030	Bacterial chemotaxis	Cellular Processes	Cell motility
+260	ko02040	Flagellar assembly	Cellular Processes	Cell motility
+261	ko04810	Regulation of actin cytoskeleton	Cellular Processes	Cell motility
+262	ko04640	Hematopoietic cell lineage	Organismal Systems	Immune system
+263	ko04610	Complement and coagulation cascades	Organismal Systems	Immune system
+264	ko04611	Platelet activation	Organismal Systems	Immune system
+265	ko04620	Toll-like receptor signaling pathway	Organismal Systems	Immune system
+266	ko04624	Toll and Imd signaling pathway	Organismal Systems	Immune system
+267	ko04621	NOD-like receptor signaling pathway	Organismal Systems	Immune system
+268	ko04622	RIG-I-like receptor signaling pathway	Organismal Systems	Immune system
+269	ko04623	Cytosolic DNA-sensing pathway	Organismal Systems	Immune system
+270	ko04625	C-type lectin receptor signaling pathway	Organismal Systems	Immune system
+271	ko04650	Natural killer cell mediated cytotoxicity	Organismal Systems	Immune system
+272	ko04612	Antigen processing and presentation	Organismal Systems	Immune system
+273	ko04660	T cell receptor signaling pathway	Organismal Systems	Immune system
+274	ko04658	Th1 and Th2 cell differentiation	Organismal Systems	Immune system
+275	ko04659	Th17 cell differentiation	Organismal Systems	Immune system
+276	ko04657	IL-17 signaling pathway	Organismal Systems	Immune system
+277	ko04662	B cell receptor signaling pathway	Organismal Systems	Immune system
+278	ko04664	Fc epsilon RI signaling pathway	Organismal Systems	Immune system
+279	ko04666	Fc gamma R-mediated phagocytosis	Organismal Systems	Immune system
+280	ko04670	Leukocyte transendothelial migration	Organismal Systems	Immune system
+281	ko04672	Intestinal immune network for IgA production	Organismal Systems	Immune system
+282	ko04062	Chemokine signaling pathway	Organismal Systems	Immune system
+283	ko04911	Insulin secretion	Organismal Systems	Endocrine system
+284	ko04910	Insulin signaling pathway	Organismal Systems	Endocrine system
+285	ko04922	Glucagon signaling pathway	Organismal Systems	Endocrine system
+286	ko04923	Regulation of lipolysis in adipocytes	Organismal Systems	Endocrine system
+287	ko04920	Adipocytokine signaling pathway	Organismal Systems	Endocrine system
+288	ko03320	PPAR signaling pathway	Organismal Systems	Endocrine system
+289	ko04912	GnRH signaling pathway	Organismal Systems	Endocrine system
+290	ko04913	Ovarian steroidogenesis	Organismal Systems	Endocrine system
+291	ko04915	Estrogen signaling pathway	Organismal Systems	Endocrine system
+292	ko04914	Progesterone-mediated oocyte maturation	Organismal Systems	Endocrine system
+293	ko04917	Prolactin signaling pathway	Organismal Systems	Endocrine system
+294	ko04921	Oxytocin signaling pathway	Organismal Systems	Endocrine system
+295	ko04926	Relaxin signaling pathway	Organismal Systems	Endocrine system
+296	ko04918	Thyroid hormone synthesis	Organismal Systems	Endocrine system
+297	ko04919	Thyroid hormone signaling pathway	Organismal Systems	Endocrine system
+298	ko04928	Parathyroid hormone synthesis, secretion and action	Organismal Systems	Endocrine system
+299	ko04916	Melanogenesis	Organismal Systems	Endocrine system
+300	ko04924	Renin secretion	Organismal Systems	Endocrine system
+301	ko04614	Renin-angiotensin system	Organismal Systems	Endocrine system
+302	ko04925	Aldosterone synthesis and secretion	Organismal Systems	Endocrine system
+303	ko04927	Cortisol synthesis and secretion	Organismal Systems	Endocrine system
+304	ko04260	Cardiac muscle contraction	Organismal Systems	Circulatory system
+305	ko04261	Adrenergic signaling in cardiomyocytes	Organismal Systems	Circulatory system
+306	ko04270	Vascular smooth muscle contraction	Organismal Systems	Circulatory system
+307	ko04970	Salivary secretion	Organismal Systems	Digestive system
+308	ko04971	Gastric acid secretion	Organismal Systems	Digestive system
+309	ko04972	Pancreatic secretion	Organismal Systems	Digestive system
+310	ko04976	Bile secretion	Organismal Systems	Digestive system
+311	ko04973	Carbohydrate digestion and absorption	Organismal Systems	Digestive system
+312	ko04974	Protein digestion and absorption	Organismal Systems	Digestive system
+313	ko04975	Fat digestion and absorption	Organismal Systems	Digestive system
+314	ko04979	Cholesterol metabolism	Organismal Systems	Digestive system
+315	ko04977	Vitamin digestion and absorption	Organismal Systems	Digestive system
+316	ko04978	Mineral absorption	Organismal Systems	Digestive system
+317	ko04962	Vasopressin-regulated water reabsorption	Organismal Systems	Excretory system
+318	ko04960	Aldosterone-regulated sodium reabsorption	Organismal Systems	Excretory system
+319	ko04961	Endocrine and other factor-regulated calcium reabsorption	Organismal Systems	Excretory system
+320	ko04964	Proximal tubule bicarbonate reclamation	Organismal Systems	Excretory system
+321	ko04966	Collecting duct acid secretion	Organismal Systems	Excretory system
+322	ko04724	Glutamatergic synapse	Organismal Systems	Nervous system
+323	ko04727	GABAergic synapse	Organismal Systems	Nervous system
+324	ko04725	Cholinergic synapse	Organismal Systems	Nervous system
+325	ko04728	Dopaminergic synapse	Organismal Systems	Nervous system
+326	ko04726	Serotonergic synapse	Organismal Systems	Nervous system
+327	ko04720	Long-term potentiation	Organismal Systems	Nervous system
+328	ko04730	Long-term depression	Organismal Systems	Nervous system
+329	ko04723	Retrograde endocannabinoid signaling	Organismal Systems	Nervous system
+330	ko04721	Synaptic vesicle cycle	Organismal Systems	Nervous system
+331	ko04722	Neurotrophin signaling pathway	Organismal Systems	Nervous system
+332	ko04744	Phototransduction	Organismal Systems	Sensory system
+333	ko04745	Phototransduction - fly	Organismal Systems	Sensory system
+334	ko04740	Olfactory transduction	Organismal Systems	Sensory system
+335	ko04742	Taste transduction	Organismal Systems	Sensory system
+336	ko04750	Inflammatory mediator regulation of TRP channels	Organismal Systems	Sensory system
+337	ko04320	Dorso-ventral axis formation	Organismal Systems	Development
+338	ko04360	Axon guidance	Organismal Systems	Development
+339	ko04380	Osteoclast differentiation	Organismal Systems	Development
+340	ko04211	Longevity regulating pathway	Organismal Systems	Aging
+341	ko04212	Longevity regulating pathway - worm	Organismal Systems	Aging
+342	ko04213	Longevity regulating pathway - multiple species	Organismal Systems	Aging
+343	ko04710	Circadian rhythm	Organismal Systems	Environmental adaptation
+344	ko04713	Circadian entrainment	Organismal Systems	Environmental adaptation
+345	ko04711	Circadian rhythm - fly	Organismal Systems	Environmental adaptation
+346	ko04712	Circadian rhythm - plant	Organismal Systems	Environmental adaptation
+347	ko04714	Thermogenesis	Organismal Systems	Environmental adaptation
+348	ko04626	Plant-pathogen interaction	Organismal Systems	Environmental adaptation
+349	ko05200	Pathways in cancer	Human Diseases	Cancers: Overview
+350	ko05230	Central carbon metabolism in cancer	Human Diseases	Cancers: Overview
+351	ko05231	Choline metabolism in cancer	Human Diseases	Cancers: Overview
+352	ko05202	Transcriptional misregulation in cancer	Human Diseases	Cancers: Overview
+353	ko05206	MicroRNAs in cancer	Human Diseases	Cancers: Overview
+354	ko05205	Proteoglycans in cancer	Human Diseases	Cancers: Overview
+355	ko05204	Chemical carcinogenesis	Human Diseases	Cancers: Overview
+356	ko05203	Viral carcinogenesis	Human Diseases	Cancers: Overview
+357	ko05210	Colorectal cancer	Human Diseases	Cancers: Specific types
+358	ko05212	Pancreatic cancer	Human Diseases	Cancers: Specific types
+359	ko05225	Hepatocellular carcinoma	Human Diseases	Cancers: Specific types
+360	ko05226	Gastric cancer	Human Diseases	Cancers: Specific types
+361	ko05214	Glioma	Human Diseases	Cancers: Specific types
+362	ko05216	Thyroid cancer	Human Diseases	Cancers: Specific types
+363	ko05221	Acute myeloid leukemia	Human Diseases	Cancers: Specific types
+364	ko05220	Chronic myeloid leukemia	Human Diseases	Cancers: Specific types
+365	ko05217	Basal cell carcinoma	Human Diseases	Cancers: Specific types
+366	ko05218	Melanoma	Human Diseases	Cancers: Specific types
+367	ko05211	Renal cell carcinoma	Human Diseases	Cancers: Specific types
+368	ko05219	Bladder cancer	Human Diseases	Cancers: Specific types
+369	ko05215	Prostate cancer	Human Diseases	Cancers: Specific types
+370	ko05213	Endometrial cancer	Human Diseases	Cancers: Specific types
+371	ko05224	Breast cancer	Human Diseases	Cancers: Specific types
+372	ko05222	Small cell lung cancer	Human Diseases	Cancers: Specific types
+373	ko05223	Non-small cell lung cancer	Human Diseases	Cancers: Specific types
+374	ko05310	Asthma	Human Diseases	Immune diseases
+375	ko05322	Systemic lupus erythematosus	Human Diseases	Immune diseases
+376	ko05323	Rheumatoid arthritis	Human Diseases	Immune diseases
+377	ko05320	Autoimmune thyroid disease	Human Diseases	Immune diseases
+378	ko05321	Inflammatory bowel disease (IBD)	Human Diseases	Immune diseases
+379	ko05330	Allograft rejection	Human Diseases	Immune diseases
+380	ko05332	Graft-versus-host disease	Human Diseases	Immune diseases
+381	ko05340	Primary immunodeficiency	Human Diseases	Immune diseases
+382	ko05010	Alzheimer disease	Human Diseases	Neurodegenerative diseases
+383	ko05012	Parkinson disease	Human Diseases	Neurodegenerative diseases
+384	ko05014	Amyotrophic lateral sclerosis (ALS)	Human Diseases	Neurodegenerative diseases
+385	ko05016	Huntington disease	Human Diseases	Neurodegenerative diseases
+386	ko05020	Prion diseases	Human Diseases	Neurodegenerative diseases
+387	ko05030	Cocaine addiction	Human Diseases	Substance dependence
+388	ko05031	Amphetamine addiction	Human Diseases	Substance dependence
+389	ko05032	Morphine addiction	Human Diseases	Substance dependence
+390	ko05033	Nicotine addiction	Human Diseases	Substance dependence
+391	ko05034	Alcoholism	Human Diseases	Substance dependence
+392	ko05418	Fluid shear stress and atherosclerosis	Human Diseases	Cardiovascular diseases
+393	ko05410	Hypertrophic cardiomyopathy (HCM)	Human Diseases	Cardiovascular diseases
+394	ko05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	Human Diseases	Cardiovascular diseases
+395	ko05414	Dilated cardiomyopathy (DCM)	Human Diseases	Cardiovascular diseases
+396	ko05416	Viral myocarditis	Human Diseases	Cardiovascular diseases
+397	ko04930	Type II diabetes mellitus	Human Diseases	Endocrine and metabolic diseases
+398	ko04940	Type I diabetes mellitus	Human Diseases	Endocrine and metabolic diseases
+399	ko04950	Maturity onset diabetes of the young	Human Diseases	Endocrine and metabolic diseases
+400	ko04932	Non-alcoholic fatty liver disease (NAFLD)	Human Diseases	Endocrine and metabolic diseases
+401	ko04931	Insulin resistance	Human Diseases	Endocrine and metabolic diseases
+402	ko04933	AGE-RAGE signaling pathway in diabetic complications	Human Diseases	Endocrine and metabolic diseases
+403	ko04934	Cushing syndrome	Human Diseases	Endocrine and metabolic diseases
+404	ko05110	Vibrio cholerae infection	Human Diseases	Infectious diseases: Bacterial
+405	ko05120	Epithelial cell signaling in Helicobacter pylori infection	Human Diseases	Infectious diseases: Bacterial
+406	ko05130	Pathogenic Escherichia coli infection	Human Diseases	Infectious diseases: Bacterial
+407	ko05132	Salmonella infection	Human Diseases	Infectious diseases: Bacterial
+408	ko05131	Shigellosis	Human Diseases	Infectious diseases: Bacterial
+409	ko05133	Pertussis	Human Diseases	Infectious diseases: Bacterial
+410	ko05134	Legionellosis	Human Diseases	Infectious diseases: Bacterial
+411	ko05150	Staphylococcus aureus infection	Human Diseases	Infectious diseases: Bacterial
+412	ko05152	Tuberculosis	Human Diseases	Infectious diseases: Bacterial
+413	ko05100	Bacterial invasion of epithelial cells	Human Diseases	Infectious diseases: Bacterial
+414	ko05166	Human T-cell leukemia virus 1 infection	Human Diseases	Infectious diseases: Viral
+415	ko05170	Human immunodeficiency virus 1 infection	Human Diseases	Infectious diseases: Viral
+416	ko05162	Measles	Human Diseases	Infectious diseases: Viral
+417	ko05164	Influenza A	Human Diseases	Infectious diseases: Viral
+418	ko05161	Hepatitis B	Human Diseases	Infectious diseases: Viral
+419	ko05160	Hepatitis C	Human Diseases	Infectious diseases: Viral
+420	ko05168	Herpes simplex infection	Human Diseases	Infectious diseases: Viral
+421	ko05163	Human cytomegalovirus infection	Human Diseases	Infectious diseases: Viral
+422	ko05167	Kaposi sarcoma-associated herpesvirus infection	Human Diseases	Infectious diseases: Viral
+423	ko05169	Epstein-Barr virus infection	Human Diseases	Infectious diseases: Viral
+424	ko05165	Human papillomavirus infection	Human Diseases	Infectious diseases: Viral
+425	ko05146	Amoebiasis	Human Diseases	Infectious diseases: Parasitic
+426	ko05144	Malaria	Human Diseases	Infectious diseases: Parasitic
+427	ko05145	Toxoplasmosis	Human Diseases	Infectious diseases: Parasitic
+428	ko05140	Leishmaniasis	Human Diseases	Infectious diseases: Parasitic
+429	ko05142	Chagas disease (American trypanosomiasis)	Human Diseases	Infectious diseases: Parasitic
+430	ko05143	African trypanosomiasis	Human Diseases	Infectious diseases: Parasitic
+431	ko01501	beta-Lactam resistance	Human Diseases	Drug resistance: Antimicrobial
+432	ko01502	Vancomycin resistance	Human Diseases	Drug resistance: Antimicrobial
+433	ko01503	Cationic antimicrobial peptide (CAMP) resistance	Human Diseases	Drug resistance: Antimicrobial
+434	ko01521	EGFR tyrosine kinase inhibitor resistance	Human Diseases	Drug resistance: Antineoplastic
+435	ko01524	Platinum drug resistance	Human Diseases	Drug resistance: Antineoplastic
+436	ko01523	Antifolate resistance	Human Diseases	Drug resistance: Antineoplastic
+437	ko01522	Endocrine resistance	Human Diseases	Drug resistance: Antineoplastic

+ 46 - 0
example_data/pathway_stat.txt

@@ -0,0 +1,46 @@
+Pathway_Class	Pathway_Subclass	Count	Percentage
+Cellular Processes	Cell growth and death	643	7.00%
+Cellular Processes	Cell motility	105	1.14%
+Cellular Processes	Cellular community - eukaryotes	203	2.21%
+Cellular Processes	Cellular community - prokaryotes	104	1.13%
+Cellular Processes	Transport and catabolism	853	9.29%
+Environmental Information Processing	Membrane transport	88	0.96%
+Environmental Information Processing	Signal transduction	1836	19.99%
+Environmental Information Processing	Signaling molecules and interaction	1	0.01%
+Genetic Information Processing	Folding, sorting and degradation	752	8.19%
+Genetic Information Processing	Replication and repair	307	3.34%
+Genetic Information Processing	Transcription	407	4.43%
+Genetic Information Processing	Translation	1002	10.91%
+Human Diseases	Cancers: Overview	721	7.85%
+Human Diseases	Cancers: Specific types	236	2.57%
+Human Diseases	Cardiovascular diseases	263	2.86%
+Human Diseases	Drug resistance: Antimicrobial	3	0.03%
+Human Diseases	Drug resistance: Antineoplastic	188	2.05%
+Human Diseases	Endocrine and metabolic diseases	371	4.04%
+Human Diseases	Immune diseases	139	1.51%
+Human Diseases	Infectious diseases: Bacterial	570	6.21%
+Human Diseases	Infectious diseases: Parasitic	326	3.55%
+Human Diseases	Infectious diseases: Viral	836	9.10%
+Human Diseases	Neurodegenerative diseases	423	4.61%
+Human Diseases	Substance dependence	161	1.75%
+Metabolism	Amino acid metabolism	744	8.10%
+Metabolism	Biosynthesis of other secondary metabolites	582	6.34%
+Metabolism	Carbohydrate metabolism	1125	12.25%
+Metabolism	Energy metabolism	831	9.05%
+Metabolism	Glycan biosynthesis and metabolism	163	1.78%
+Metabolism	Lipid metabolism	661	7.20%
+Metabolism	Metabolism of cofactors and vitamins	414	4.51%
+Metabolism	Metabolism of other amino acids	300	3.27%
+Metabolism	Metabolism of terpenoids and polyketides	471	5.13%
+Metabolism	Nucleotide metabolism	317	3.45%
+Metabolism	Xenobiotics biodegradation and metabolism	242	2.64%
+Organismal Systems	Aging	249	2.71%
+Organismal Systems	Circulatory system	134	1.46%
+Organismal Systems	Development	85	0.93%
+Organismal Systems	Digestive system	212	2.31%
+Organismal Systems	Endocrine system	592	6.45%
+Organismal Systems	Environmental adaptation	846	9.21%
+Organismal Systems	Excretory system	118	1.28%
+Organismal Systems	Immune system	629	6.85%
+Organismal Systems	Nervous system	680	7.40%
+Organismal Systems	Sensory system	99	1.08%

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+ 68150 - 0
example_data/proteins.fa