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: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Abstract Summary: DroPhEA is a core module of a web application that facilitates research in insect functional genomics through enrichment analysis on mutant phenotypes of fruit fly (Drosophila melanogaster). The phenotypes investigated in the analyses can be predefined by FlyBase or customized by users. DroPhEA allows users to specify mutation or ortholog types, displays enriched term results in a hierarchical structure and supports analyses on gene sets of all insect species with a fully sequenced genome. Availability: http://evol.nhri.org.tw/phenome/DroPhEA/ Contact: [email protected] Supplementary Information: Supplementary data are available at Bioinformatics online.

Abstract Summary: MamPhEA is a web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes. It allows users to conduct enrichment analysis on predefined or user-defined phenotypes, gives users the option to specify phenotypes derived from null mutations, produces easily comprehensible results and supports analyses on genes of all mammalian species with a fully sequenced genome. Availability: http://evol.nhri.org.tw/MamPhEA/ Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.