Microarray Data Analysis

The Bioinformatics Core at the University of Southern Mississippi provides the following expertise to serve your bioinformatics needs:

Statistical analysis and management as well as metabolic path and genetic network modeling of microarray data: We are employing commercial software and other statistics software such as SAS, R and S-plus in addition to computer programming (for some data mining, as necessary) to analyze both cDNA and oligo-microarray data. We are comparing different methods including probe level data extraction, linear and non-linear algorithms, clustering algorithms and expression statistics difference finding algorithms. Our analysis is not dependent on a single software program, instead we try to optimize and update our applications and make sure they are the best that are currently available. We not only perform a statistical analysis, but also try to infer the scientific significance of your data. For example, we consider how to use the right method to find the right marker genes, how to find the most similar patterns, how to interpret gene function, how to compare your data with published data in a meaningful way and how to map your to existing pathways as well as model new pathways. We can also help you organize your micrioarray data, format them as a MIAME standard and store them in a web-accessible database.

Data analysis of genomic, proteomic and metabolomic studies for any model organism: By using linux, unix and windows based software in addition to our own programs, we can handle sequence cleaning and assembly, automatic gene annotation, genetics map making, comparative genomics and phylogenetic analysis, literature and experimental data integration and curation. If you are sequencing genomic or EST sequences, we can easily process the sequences, find the gene sequences or unique genes, and assign the gene name and function on a large scale. We are also very interested in applying our statistical and data mining skills to proteomic and metabolomic studies.

Web accessible database design for storage and management of any biological data: Biologists are generating large amounts of data everyday. If you find that you have huge data sets that your spreadsheet cannot handle, or you want to search something that is not available in the current database, or you have some novel ideas to combine some scientific resources to benefit your scientific colleagues and so on, please let us know. We have strong capabilities in database development and web applications for complex biological data retrieval and publication. We are willing to work on any data sources such as genomics, proteomics and metabolomics data.

Routine bioinformatics applications: Are you doing basic DNA or protein sequence alignment, gene and protein structure prediction, protein domain and motif finding etc? We host and plan to have several software options to meet your basic bioinformatics needs.

Custom programming: Is computation programming necessary in biology science? The answer is yes. Do you want to know the difference between your two groups of gene sequences? Do you want to identify sequence patterns in your DNA, RNA and protein sequences? Do you want to remove the sequences whose length is less than 100? Do you want to rename all the gene names in your sequences? Customized programs easily resolve these problems. If you need programming help, our facility can help you.

Bioinformatics tools development: Besides our independent work, we are happy to collaborate with mathematics, statistics and computer scientists to develop new tools to resolve any biological problems that the existing software fails to address. If you would like to contribute your expertise to the bioinformatics area, please let us know.

Support for grant proposals: We are willing to consult and assist in development of bioinformatics content and needs for grant proposals and ongoing research. Whether you are planning collaborative or independent bioinformatics components to your research, our expertise is most beneficial if we are consulted during the design phase.

For more information about these services contact:
Dr. Youping Deng
Associate Bioinformatics Director
The University of Southern Mississippi
Phone: 601.266.6678
FAX: 601.266.5797
Email: youping.deng@usm.edu