SEAS: A System for SEED-Based Pathway Enrichment Analysis

被引：8
|
作者：
Mao, Xizeng [1 ]
Zhang, Yu [3 ,4 ]
Xu, Ying [1 ,2 ,3 ]
机构：
[1] Univ Georgia, Computat Syst Biol Lab, Dept Biochem & Mol Biol, Inst Bioinformat, Athens, GA 30602 USA
[2] Univ Georgia, BioEnergy Sci Ctr BESC, Athens, GA 30602 USA
[3] Jilin Univ, Coll Comp Sci & Technol, Changchun 130023, Peoples R China
[4] Jilin Univ, Key Lab Symbol Computat & Knowledge Engn, Minist Educ, Changchun 130023, Peoples R China
来源：
PLOS ONE | 2011年 / 6卷 / 07期
基金：
美国国家科学基金会;
关键词：
GENE-EXPRESSION DATA; GENOME ANNOTATION; RESOURCES; SERVER;
D O I：
10.1371/journal.pone.0022556
中图分类号：
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
Pathway enrichment analysis represents a key technique for analyzing high-throughput omic data, and it can help to link individual genes or proteins found to be differentially expressed under specific conditions to well-understood biological pathways. We present here a computational tool, SEAS, for pathway enrichment analysis over a given set of genes in a specified organism against the pathways (or subsystems) in the SEED database, a popular pathway database for bacteria. SEAS maps a given set of genes of a bacterium to pathway genes covered by SEED through gene ID and/or orthology mapping, and then calculates the statistical significance of the enrichment of each relevant SEED pathway by the mapped genes. Our evaluation of SEAS indicates that the program provides highly reliable pathway mapping results and identifies more organism-specific pathways than similar existing programs. SEAS is publicly released under the GPL license agreement and freely available at http://csbl.bmb.uga.edu/similar to xizeng/research/seas/.
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收藏
页数：6
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