Microarray and Genome Informatics

National Institute Of Environmental Health Sciences

Investigators

Linked publications, trials & patents

Abstract

Completed the collaborative support of investigators' research: 1) Developed a tool called goSTAG for utilizing GO Subtrees to Tag and Annotate Genes that are part of a set. Using gene lists from microarray, RNA sequencing (RNA-Seq) or other genomic high-throughput technologies, goSTAG performs GO enrichment analysis and clusters the GO terms based on the p-values from the significance tests. GO subtrees are constructed for each cluster, and the term that has the most paths to the root within the subtree is used to tag and annotate the cluster as the biological theme. 2) Identified gene pathway crosstalk between chemicals with different modes or action (MOAs). Using a weighted network analysis of gene expression data from the livers of male Sprague-Dawley rats exposed to chemicals that elicit their effects through receptor mediated MOAs or non-receptor mediated MOAs, gene regulatory networks were highly preserved and statistically significant in each of the two MOA classes. 3) Developed a database called RATEmiRs for the rat atlas of tissue-specific and enriched miRs to allow users to dynamically determine mature-, iso- and pre-miR expression abundance and specificity in rat tissues and organs. Data-driven pipelines are available to tailor the identification of enriched and specific miRs in a given tissue. Organ-specific pipelines reveal miRs that are expressed exclusively in a given organ comprised of several tissues. A user-driven approach is also available to assess the tissue expression of user-specified miRs.