ABSTRACT
Motivation Genome-scale studies using next-generation sequencing technologies generate substantial number of differentially-regulated genes. The gene lists need to be further analyzed to identify overrepresented genes and functions in order to guide downstream analyses. Currently available gene enrichment tools rely on functional classifications based on Gene Ontology (GO) terms. A shortcoming of the GO-based classification system is that the GO terms are broad and often redundant, hence necessitating alternate approaches.
Results We propose a new functional enrichment approach, GenFam, to classify as well as enrich overrepresented gene functions, based on gene family categories. GenFam offers a unique approach to mine valuable, biologically-relevant information, beyond the conventional GO term based enrichment. GenFam is available as a web-based, graphical-user interface, which allows users to readily input gene lists, and export results in both tabular and graphical formats. Additionally, users can customize analysis parameters, by choosing from the different significance tests to conduct advanced statistics. Currently, GenFam supports gene family classification and enrichment analyses for seventy-eight plant genomes and gene identifiers that are available on Phytozome v12.0 database.
Availability and implementation The GenFam application is open-source and accessible through world-wide web at http://mandadilab.webfactional.com/home/
Contact kkmandadi{at}tamu.edu