HotGene methodology

HotGene is an interactive interface that allows visualization of gene annotations in an user-defined manner. HotGene clusters genes according to Gene Ontology (GO) terms, Swiss-Prot Keywords (SPK) and/or enriched transcriptional factor (TF) binding sites in a nonredundant manner. The users can visualize the functional or pathway compositions of their gene sets of interest in an intuitive and comprehensive manner.

The Gene Ontology (GO) (www.geneontology.org) terms are currently the standard terminology for gene annotations. However, GO terms are redundant among different levels, which may pose a problem for overviewing genomic or proteomic data. PatternGenius addresses the need of life science researchers for an efficient and “relevant” interpretation of their data by incorporating a “GO Redundancy Filter (GRF)” in HotGene. While interrogating the data, the users can apply the GRF algorithm to the visual display interface to avoid repeated representations of GO terms that describe similar biology.

The default settings of HotGene have been optimized for a comprehensive and unbiased functional overview of gene sets in most cases. HotGene further provides a zoomable feature which allows the user to adjust the number of gene clusters or GO term levels to be displayed for different illustrative purposes.

A complete study of complex genomic/proteomic data requires not only an overview of related function or pathway networks but also a detailed understanding of each gene clusters or associations among them. To address this need, HotGene further features an “focused zoom-in” function that allows the users to iteratively zoom in any selected node or link from the present network and interrogate its function or pathway network using a lower level of GO terms or other interrogation options.