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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  

Registration is required. There are 4 seats available.

Event Organizer

Profile photo of Sofia Fertuzinhos
Sofia Fertuzinhos
Profile photo of Rolando Garcia-Milian
Rolando Garcia-Milian