Enrichment analysis of rice genes

The GO terms and assignments for rice genes were downloaded from Gramene database (http://www.gramene.org/) (Jaiswal[2011 (link)]) and KO from KEGG database (http://www.genome.jp/kegg/) (Kanehisa et al.[2010 (link)]). The RAP rice gene locus IDs in KEGG database were converted to RGAP IDs using RAP-DB ID converter tool (http://rapdb.dna.affrc.go.jp/tools/converter) (Tanaka et al.[2008 (link)]). Then hypergeometric distribution was used to calculate the p value for GO and KO enrichment analyses.

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Cao P., Jung K.H., Choi D., Hwang D., Zhu J, & Ronald P.C. (2012). The Rice Oligonucleotide Array Database: an atlas of rice gene expression. Rice, 5, 17.

Publication 2012

Genes Genome Rap gene Rgap Rice

Corresponding Organization : University of California, Davis

Other organizations : Zhejiang University, Kyung Hee University, Pohang University of Science and Technology

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Protocol cited in 12 other protocols

Variable analysis

independent variables

GO terms and assignments for rice genes
KO from KEGG database

dependent variables

P value for GO and KO enrichment analyses

control variables

RAP rice gene locus IDs in KEGG database were converted to RGAP IDs using RAP-DB ID converter tool

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