Bioinformatics Tool Development
Members of the Argraves laboratory are involved with development of bioinformatics computational resources including web-based tools for analyzing and archiving DNA microarray data and performing functional categorization of proteins. Several efforts are being conducted in collaboration with Array Genetics, Inc. Please visit their website to access a number of freely available web-based bioinformatics tools.
MUSC DNA Microarray Database
MUSC DNA Microarray Database: Through a grant from the National Institutes of health (CA95841) we have developed a web-based relational database system for archiving DNA microarray hybridization data (raw and normalized) derived experimentation performed through our DNA Microarray Facility. The database was designed using microArrayDB and uses MySQL server to store microarray hybridization data and metadata such as project information (i.e., investigator contact information, experimental design), cRNA target information and process controlling information.
The MUSC DNA Microarray Database has been described in an article published in the journal Bioinformatics (Argraves et al., 2003) An important aspect of the database is that it allows users to schedule the release of their microarray data into the public domain. Click here to access publically available DNA microarray data. Use the 'At-a-glance' feature to view a summary of DNA microarray data stored in the database.
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 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. ArrayQuest has been described in an article published in the journal BMC Bioinformatics (Argraves et al., 2005).
GeneMesh™
GeneMesh™ is a web-based program that uses a database of genes associated with Medical Subject Heading (MeSH) terms to help investigators mine DNA microarray data to find associations between genes and major MeSH terms hiearchical descriptors (i.e., Anatomy, Biological Sciences, Disease etc.) as well as descriptor subheadings (i.e., Cardiovascular System, Genetic Processes, Immune System Diseases etc.).
The NASA EPSCoR Archive of DNA Microarray Data
NASA EPSCoR Archive of DNA Microarray Data - The NASA EPSCoR Archive of DNA Microarray Data is an archive for centralized storage and dissemination of transcriptomic data collected from STS-108 and ground control mouse tissues. The database contains raw DNA microarray data as well as associated experimental annotations. All data is stored using the DNA Microarray Information Management System (DMIMS) called uArrayDB. uArrayDB is operated through a web-accessible interface that facilitates the deposition of DNA microarray data as well as allowing public access to data in the database.
Support for the implimentation of these resources comes from a a grant from the National Cancer Institute (CA 095841) and the National Heart Lung and Blood Institute (P20RR016434).