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Bioinformatics Core

Overview

The Bioinformatics Core is dedicated to providing computational support to the NIMH IRP research community in the areas of microarray data management and analysis, signal transduction pathway modeling, and data mining. A collection of tools for genomic and Microarray analysis could be found here.

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Core Support Areas

Bioinformatics Core provides support for the data analysis of microarray experiments carried out for gene expression (transcription profiling) as well as for microRNA profiling. Both one color (Affymetrix) and two color (Agilent and cDNA) microarray platforms are supported. In addition to the standard analysis, gene set enrichment is also carried out on request. Data retrieval from image files, normalization, statistical analysis, are carried out for the investigators.

The downstream support work for the characterization of interesting genes is also carried out. It includes Ingenuity pathways analysis, promoter characterization for co-regulation, primer design for real time PCR, gene ontology categorization, literature text mining, and much more.

One of the major goals of the facility is to characterize novel genes of interest which are found to be significantly regulated in a microarray experiment but does not have enough biological information available for further research. Using different sequence analysis and system biology tools, these genes are further annotated to recommend possible wet lab experiments.

As technology evolves and new tools become available online or as standby, those are acquired and put to immediate usage for the benefit of the investigators.

Proteomics research is also supported by analyzing data for statistical significance and pathways involvement etc using various bioinformatics tools.

The aforesaid analysis is supported inside mAdb microarray data management system and beyond. Our efforts include coordinating software feature enhancements and modifications requested by the NIMH IRP research community. In addition, we continue to identify and recommend supplementary software analysis tools to augment the capabilities of the mAdb system.

The Bioinformatics Core develops pathway analysis tools to assist with hypothesis generation for signal transduction research. As part of this effort, we are beta testing several cell signaling software platforms that may be of value to NIMH IRP scientists. In addition, we are revamping the pathFinder pathway analysis tool to provide an enhanced platform for the exchange and modeling of cell signaling data so that pathFinder will serve as a knowledge environment for researchers with mutual/converging interests to interact to accelerate translational research activities.

Data mining support is also available upon request. This includes common bioinformatics tools and development of small-scale customized software programs.

Core Organization

Bioinformatics Specialist Dr. Babru B. Samal
Bldg. 49 Rm. 5A68 samalb@mail.nih.gov

The Bioinformatics User´s Group meets periodically to update P.I.´s on the current status and capabilities of the Bioinformatics Core as well as the Microarray Core Facility, to discuss resource needs in bioinformatics related to genomics, cDNA/oligo microarray, proteomics and signal transduction pathway analysis.

Lee E. Eiden Acting Chair
Bioinformatics Users’ Group Bldg 49, 5A38, 496-4110
eidenl@mail.nih.gov