Data Analysis Services Offered
- Next Generation Sequence Analysis
- Gene Expression, Methylation and mRNA Analysis
- System Biology Analysis
Now that you have your raw data (whether it is gene expression, genotyping, methylation, microRNA, Next Generation Sequencing, etc...), the big question arises. What type of analyses needs to be performed to make sense of it? We offer a variety of tools necessary to answer your questions.
Please contact David Crossman for all of your data analysis needs. Dr. Crossman provides expertise in both the data analysis and the downstream applications of Systems Biology. He is proficient with a variety of data analysis tools such as Agilent's GeneSpring, Illumina's GenomeStudio, the tools found in Galaxy (Bowtie, Tophat, Cufflinks, etc...), as well as the NGS tools via command line. He is also proficient in a variety of Systems Biology tools such as Ingenuity's IPA, ThomsonReuters' Metacore (previously GeneGo) and Cytoscape. He performs systems analyses on various "-omics" datasets obtained from the various "-omics" platforms available to the UAB investigator.
Next Generation Sequencing Analysis
For Next Generation Sequencing analysis, the HCGS along with UAB's CCTS-BMI group and UAB IT's Research Computing group has installed a local instance of Galaxy, which will allow for easier access to this suite of tools.
Galaxy: "Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more..."
***If you would like access to UAB's local install of Galaxy, please contact David Crossman, or you can use PennState's version.
Gene Expression, Methylation and microRNA Analysis
For gene expression, genotyping, methylation and microRNA, the Heflin Center for Genomic Science (HCGS) uses a couple of commercially available software packages, Agilent's GeneSpring and Illumina's GenomeStudio.
GeneSpring: "Agilent's GeneSpring GX software provides powerful, accessible statistical tools for fast visualization and analysis of transcriptomics, genomics, proteomics and metabolomics data. Designed specifically for the needs of biologists, GeneSpring GX offers an interactive desktop computing environment that promotes investigation and enables understanding of microarray data within a biological context."
***We no longer have a multi-seat license which allows any UAB investigator to have access to this powerful software analysis program. However, we do have a single license of GeneSpring installed on one of our local machines. Please contact David Crossman if you would like to have access to GeneSpring.
GenomeStudio: "Visualize and analyze data generated by all of Illumina's platforms with GenomeStudio Data Analysis Software. This powerful informatics solution supports the primary analysis of sequence-based data produced by the Genome AnalyzerIIx and microarray-based data generated by the iScan System and BeadXpress Reader. Performance optimized tools and a user-friendly graphical interface allow you to quickly and easily convert data into meaningful results for your genome analysis and research."
Systems Biology Analysis (Downstream)
Now that you have a gene list, some sort of biological context of what that lists represents would be extremely useful to you for any further analysis. One of the several Systems Biology tools we use is Ingenuity Pathway Analysis.
Ingenuity IPA: "IPA is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research. IPA has been broadly adopted by the life science research community and is cited in thousands of peer-reviewed journal articles."
"IPA helps you understand biology at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. Even if you don’t have experimental data, you can use IPA to intelligently search the Ingenuity® Knowledge Base for information on genes, proteins, chemicals, drugs, and molecular relationships to build biological models or get up to speed in a relevant area of research. IPA provides the right biological context to facilitate informed decision-making, advance research project design, and generate new testable hypotheses."