GEO Data Mining & Pathway Enrichment Analysis w/ Open Access Tools

Workshop Objective:

This is a 4½ 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 - 3:30 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. 

Every Wednesday after a 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:

Class Type

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