Bioinformatics Workshop Series - Session 8: Gene Set Enrichment Analysis (GSEA)
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Bioinformatics Workshop Series - Session 8: Gene Set Enrichment Analysis (GSEA) In-Person
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.
Details:
Target audience: These classes are meant to novices in bulk RNAseq analysis, with none to minimal knowledge in R programming.
Seating – in person classes are limited to 16 places.
Registrations - open to all interested. However, seating will be on “first come, first served” basis.
Recording – we will record the sessions so you can follow asynchronously.
Session 8. 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.
Series Program:
|
Date |
Session |
Mode |
Presenter |
|
9/14/23 |
Session 1 - Intro to annotation of gene expression data |
In-person |
Rolando Milian |
|
9/21/23 |
Session 2 - Find, Download and Transform public bulk RNA seq data to analyze with DESeq2 in RStudio |
In-person |
Sofia Fertuzinhos |
|
9/28/23 |
Session 3 - Upload bulk RNAseq data tables into RStudio and setup a DESeq2 analysis |
In-person |
Sofia Fertuzinhos |
|
10/5/23 |
Session 4 - Manipulate DESeq2’s results() and plot functions |
In-person |
Sofia Fertuzinhos |
|
10/12/23 |
Session 5 – DEMO - Analyzing and Visualizing RNAseq public dataset using Qlucore Omics Explorer |
Online |
Yana Stackpole - Qlucore |
|
10/19/23 |
Session 6 – DEMO - Transcription factors analysis with TRANSFAC |
Online |
Volker – Transfac |
|
10/24/23 |
Session 7 - Functional analysis of omics data: Overrepresentation Analysis ORA |
In-person |
Rolando Milian |
|
10/26/23 |
Session 8 - Gene Set Enrichment Analysis GSEA |
In-person |
Rolando Milian |
- Date:
- Thursday, October 26, 2023
- Time:
- 10:00am - 12:00pm
- Time Zone:
- Eastern Time - US & Canada (change)
- Location:
- SHM L 111, Cushing/Whitney Medical Library, 333 Cedar Street
- Campus:
- Medical School
- Categories:
- Bioinformatics
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