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add example

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

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+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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+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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+#  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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+<!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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+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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+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
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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/org.My.eg.db/R/zzz.R
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+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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example_data/org.My.eg.db/man/org.My.egORGANISM.Rd
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+\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}
 
+

+ 87 - 0
example_data/org.My.eg.db/man/org.My.eg_dbconn.Rd
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+
 
+\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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+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
View File 

@@ -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