Bioinformatics Resources - MUSC ProteoGenomics Facility

Bioinformatics Resources

GeneMesh™

GeneMesh™ is a new DNA microarray data analysis tool, GeneMesh, which can accelerate discovery by identifying significant inter-relationships that exist between differentially expressed genes and MeSH categories. Through the use of a robust set of action link features the user can quickly see how genes associated with a MeSH category relate to biological processes, molecular functions, cellular components and signaling pathways. Through access to heatmaps the user can readily see how the genes in any given MeSH categories or any related ontological category behave in response to the experimental stimuli used to generate the original differentially expressed gene data set. A paper describing GeneMesh is published in BMC Bioinformatics (Jani et al., 2010).

ArrayQuest™

ArrayQuest™ is a web-based program for the analysis of DNA microarray data. ArrayQuest™ is designed to apply various types of analysis scripts including those written in R (i.e., Bioconductor) to microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or data uploaded to the ArrayQuest center-point web server in a password-protected area. A paper describing GeneMesh is published in BMC Bioinformatics (Argraves et al., 2005)

Links to Useful Bioinformatics Tools

Array Genetics Bioinformatics Software

Gene ID Conversion Tool from David Bioinformatics Resources

MeSHer

MeSHer is a Java tool for biological literature mining. The application performs a statistical analyis of MeSH terms related to the specified genes to find over-represented biological themes the given sample of genes as compared with the entire population of genes present on the specified array.