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add example

Zhang Xudong 2 years ago
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c48df7e917
39 changed files with 0 additions and 335398 deletions
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      example_data/R_Library/org.My.eg.db/DESCRIPTION
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example_data/R_Library/org.My.eg.db/DESCRIPTION
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@@ -1,16 +0,0 @@
 
-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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example_data/R_Library/org.My.eg.db/INDEX
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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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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
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@@ -1,27 +0,0 @@
 
-#  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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@@ -1,7 +0,0 @@
 
-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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@@ -1,38 +0,0 @@
 
-<!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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@@ -1,97 +0,0 @@
 
-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/Sind.pep.fasta


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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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example_data/go.txt


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example_data/my.emapper.annotations


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example_data/org.My.eg.db/DESCRIPTION
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@@ -1,14 +0,0 @@
 
-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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@@ -1,16 +0,0 @@
 
-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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@@ -1,36 +0,0 @@
 
-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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example_data/org.My.eg.db/man/org.My.egBASE.Rd
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@@ -1,18 +0,0 @@
 
-\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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@@ -1,32 +0,0 @@
 
-\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
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@@ -1,87 +0,0 @@
 
-
 
-\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/org.My.eg.db_1.0.tar.gz
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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

+ 0 - 46
example_data/pathway_stat.txt
View File 

@@ -1,46 +0,0 @@
 
-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%