- WHAT: GEO Data Mining & Pathway Enrichment Analysis w/ Open Access Tools
- WHEN: February 26th, 10am-12pm & 1-3pm
- WHERE: Scaife Hall, Falk Library, Classroom 2
- WHO: Ansuman Chattopahyay & Sri Chaparala
- HOW: Register here
Workshop Objective:
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, and g:Profiler.
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
Target Audience:
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.
Workshop Guide:
Suggested Reading:
- 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
Attribution:
Please include the following statement in the acknowledgments section for all publications, posters, and presentations: Data analysis was performed using {name of software} software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh.
HSLS Winter/Spring 2020 MolBio Info Service Training Workshops schedule
Contact the HSLS Molecular Biology Information Service with any questions.