- WHAT: GEO Data Mining & Pathway Enrichment Analysis w/ Open Access Tools
- WHEN: December 9th, 10am-12pm & 1-4pm
- WHERE: Online; instructions upon registration
- WHO: Ansuman Chattopahyay & Sri Chaparala
- HOW: Register here
Workshop Objective:
This is a 5 hour workshop. The morning session (10 am – 12 pm) teaches how to retrieve a list of differentially expressed genes (DEG) associated with a gene expression study by searching GEO using BioJupies (RNA-Seq), GREIN (RNA-Seq) and Geo2R (Microarray).
The afternoon session (1 pm – 4 pm) focuses on uncovering 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.
One week after the workshop, a follow up session (1 pm – 3 pm) will review the hands-on exercise questions distributed during the workshop. We will not be addressing questions on data analysis for personal research projects—researchers are encouraged to request a one-on-one consultation with MBIS for this type of discussion. Registration is not required for the hands-on follow up session. To attend, use the same Zoom link you receive upon registration for this workshop.
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 the 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 Fall 2020 MolBio Info Service Training Workshops schedule
Contact the HSLS Molecular Biology Information Service with any questions.
(Photo by Fabio Bracht on Unsplash)