modPhEA：真核基因集的模式生物表型富集分析。

modPhEA: model organism Phenotype Enrichment Analysis of eukaryotic gene sets.

机构信息

Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan, ROC.

出版信息

Bioinformatics. 2017 Nov 1;33(21):3505-3507. doi: 10.1093/bioinformatics/btx426.

DOI:10.1093/bioinformatics/btx426

PMID:28666356

Abstract

MOTIVATION

Genome-scale phenotypic data are available for many model organisms, yet existing tools to functionally interpret gene sets from these phenotypic data are largely based on mutagenesis-derived phenotypes observed in mouse or human.

RESULTS

Data from both mutagenesis and knockdown experiments are incorporated into modPhEA to allow users to perform enrichment analyses based on phenotypes observed in budding yeast (Saccharomyces cerevisiae), roundworm (Caenorhabditis elegans), fruit fly (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus) and humans (Homo sapiens). The phenotypes analysed can be customized to investigate complex traits and gene sets from any fully sequenced animal or fungal genome are also supported by modPhEA.

AVAILABILITY AND IMPLEMENTATION

Freely available on the web at http://evol.nhri.org.tw/modPhEA/.

CONTACT

liaoby@nhri.org.tw.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

许多模式生物都有全基因组表型数据，但目前用于从这些表型数据中对基因集进行功能解释的工具在很大程度上是基于在小鼠或人类中观察到的诱变表型。

结果

诱变和敲低实验的数据都被整合到 modPhEA 中，允许用户基于酿酒酵母（Saccharomyces cerevisiae）、秀丽隐杆线虫（Caenorhabditis elegans）、黑腹果蝇（Drosophila melanogaster）、斑马鱼（Danio rerio）、小鼠（Mus musculus）和人类（Homo sapiens）中观察到的表型进行富集分析。通过 modPhEA 还可以分析自定义的复杂性状，并支持来自任何全序列动物或真菌基因组的基因集。