Registration Required

The Bioinformatics Support Hub has designed this teaching series for researchers interested in learning the basics steps for re-analysis of publicly available bulk-RNAseq data. We will introduce you to basic genomic data annotation concepts, including where to find data to re-analyze, how to perform differential gene analysis, how to add gene annotations, and how to visualize your results. Finally, we'll demonstrate different approaches to gene perform gene pathway analysis. Importantly, we have introduced interspersed coached-practice sessions to which attendees will be invited to participate. In these sessions, you will be able to try things for yourself and get immediate support if needed. (Please see below for overall schedule).    

• Session 1 - Intro to annotation of gene expression data (Tue, August 2^nd)
• Session 2 - Where in the World is the Data You Need? How to Find and Reuse Data (e.g. GREIN) – (Thurs, August 4^th)
• Coached-practice 1 - Exercise sources and genomic information format (annotations and gene ID) of datasets (Tue, August 9^th)

• Session 3 - Re-analyze public dataset with DESeq2 package (Thurs, August 11^th)
• Session 4 - biomaRt using R package (Tue, August 16^th)
• Coached-practice 2 - Differential Gene expression, annotation (Thurs, August 18^th)

• Session 5 - Visualization with Qlucore (Tue, August 23^rd)
• Coached-practice 3 - Visualization with Qlucore (Thurs, August 25^th)

• Session 6 – Functional analysis of omics data: Overrepresentation Analysis (ORA) (Tue, August 30^th)
• Session 7 – Gene Set Enrichment Analysis GSEA (Thurs, September 1^st)
• Coached-practice 4 – Functional Pathway Analysis (Tue, August 6^th)

Gene Set Enrichment Analysis (GSEA)

Attendance: In person

Gene Set Enrichment Analysis (GSEA) (UC San Diego/Broad Institute) determines whether a set of genes shows statistically significant differences between two biological conditions (e.g., phenotypes). From this session/workshop you will learn how to run GSEA on your own datasets using the GSEA desktop application. During the session we will use a tutorial dataset that will be made available to all the registrants.

The goals of the session are:

• To learn how to prepare your data and files for running GSEA.
• To learn about Molecular Signature Database (MSigDB).
• To learn how to run GSEA analysis and the Leadin-edge analysis and results interpretation.
• Send and visualize the results using the Enrichment Map app.

This session is suitable for both beginner and intermediate users of GSEA.

Prerequisites:

Download and install the GSEA desktop version on your laptop.

Download and install Cytoscape software

A tutorial dataset will be made available to all registrants