GeneIntegrator: An integrated microarray data management and analysis system

Monday, October 24, 2011 — Poster Session I
Noon – 2:00 p.m.	Natcher Conference Center	NIAID	BIOINFO-10

Authors

• J Li
• S Varma
• Y Guo
• Y Mohamoud
• Y Zhang
• H Su
• M Lenardo
• Y Huyen

Abstract

As the deluge of data grows with the advent of high throughput technologies, it has become difficult for scientists to find and organize data pertinent to particular fields of research. While much of the data is deposited into major international data marts, the sheer volume that a user needs to comb through becomes overwhelming. This is magnified when one considers that there are multiple kinds of data to mine from multiple species. GeneIntegrator provides a robust Web-based microarray data analysis system for the NIAID Laboratory of Immunology and Laboratory of Host Defenses. Scientists can upload experimental microarray data or import data from NCBI’s Gene Expression Omnibus. Analysis is performed using pre-defined protocols to generate gene lists of interest. GeneIntegrator uses the gene lists to query several online databases (MGI, RefDIC, UCSC gene sorter, OMIM, Gene Ontology, and HGNC) to provide an aggregated annotation and visualization of results, such as gene ontology, function, associated diseases, homologous genes, and data from related gene microarray studies. GeneIntegrator was developed using Grails Web framework and MySQL database. The data analysis backend was developed using R and GenePattern genomic analysis platform. GeneIntegrator relies on a cluster system to schedule jobs and process biological data sets.

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