SC EPSCoR/IDeA

SC INBRE Bioinformatics Core

Bioinformatics Core Mission

The goal off the SC INBRE Bioinformatics Core is to increase the National Institutes of Health research capacity of the state by providing bioinformatics support to faculty, post-doctoral fellows, graduate students, and undergraduate students of the lead and partner institutions.

Bioinformatics Core Services

The SC INBRE Bioinformatics Core offers assistance to any investigators from any of the participating institutions with:

Affymetrix DNA Microarray Data Analysis:
We provide custom Affymetrix DNA microarray data analysis using ArrayQuest and dChip as well as training for independent use of these systems.
Click here for additional information.

Agilent DNA Microarray Data Analysis:
We provide custom Agilent DNA microarray data analysis using limmaGUI (Bioconductor) and CARMAweb as well as training for independent use of these systems.
Click here for additional information.

Training on Genesifter, a commercial tool for analysis of any microarray platform, is also available.

New Bioinformatics Tool Speeds Analysis of Transcriptomic Data
Researchers at the South Carolina INBRE Bioinformatics Core have developed a new web-based program, GeneMesh, for analysis of high throughput gene expression data (see article in BMC Bioinformatics at http://www.biomedcentral.com/1471-2105/11/166/abstract). GeneMesh, can accelerate discovery by identifying significant inter-relationships that exist between differentially expressed genes and information in the Medical Subject Headings (MeSH) hierarchical index. Through the use of a robust set of action link features users can quickly see how genes associated with MeSH categories relate to biological processes, molecular functions, cellular components and signaling pathways. Through heatmap displays users can readily see how the genes in any given MeSH category or any related ontological category behave in response to the experimental stimuli used to generate the original differentially expressed gene data set. GeneMesh operates on data derived from the major commercial microarray platforms, including Affymetrix, Agilent and Illumina and is freely available online at http://proteogenomics.musc.edu/genemesh/. 

Bioinformatics Events

Documentation from past events of the Bioinformatics Core can be found in the EPSCoR/IDeA archive.

Bioinformatics Core Mailing List

To register, please enter your information here.  Registrants will be emailed information on SC INBRE Bioinformatics Core Sponsored events and services.

Bioinformatics Core User Policy

Data analysis services provided by SC INBRE Bioinformatics Core and Core-Affiliated facilities are free of charge for researchers affiliated with the SC INBRE Program. All researchers who receive service at no charge are required to acknowledge the SC INBRE grant (P20 RR-016461) in proposals and publications. Core staff should be considered for co-authorship when they have made significant scientific or intellectual contributions to the work reported or when they share in the responsibility and accountability for the results.