This is a 4-hour workshop. The morning session (10am - 12pm) provides a brief overview of bioinformatics concepts and software used for interpreting a gene list using pathway and network information. The afternoon session (1pm - 3pm) focuses on hands-on practice using Open Access (and routinely updated) tools--BioJupies, GEO2R, GSEA - Broad Institute, g:Profiler, and Cytoscape.
Participants will learn how to
- retrieve a list of differentially expressed genes (DEG) associated with a gene expression study by searching GEO using BioJupies (RNA-Seq) and Geo2R (Microarray)
- uncover the biology hidden behind the extracted DEG list by searching publicly available pathway enrichment analysis resources including Gene Ontology (GO), Molecular Signature Database (MsigDB), Reactome, Panther, KEGG, PathwayCommons, and WikiPathways using GSEA and g:Profiler
Experimental biologists seeking to analyze gene lists generated through omics experiments. The software covered in the workshop operates through a user-friendly, point-and-click graphical user Interface, so neither programming experience nor familiarity with command line interface is required.
- Pulikkan, J. A., Hegde, M., Ahmad, H. M., Belaghzal, H., Illendula, A., Yu, J., … Castilla, L. H. (2018). CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell, 174(1), 172–186.e21. doi:10.1016/j.cell.2018.05.048
- Reimand, J., Isserlin, R., Voisin, V., Kucera, M., Tannus-Lopes, C., Rostamianfar, A., … Bader, G. D. (2019). Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap. Nature Protocols, 14(2), 482–517. doi:10.1038/s41596-018-0103-9