Gene Expression Visualization

Workshop Objective:

This is a 4½ hour workshop on the visualization of gene expression data. The morning session (10 am - 12 pm) focuses on HSLS-licensed Partek Flow software.  The afternoon session (1 pm - 3:30 pm) focuses on Cytoscape, a powerful open access data visualization tool used to integrate, visualize molecular interaction networks, and analyze and interpret data. We also cover how to generate enrichment maps for GSEA and g:Profiler results in Cytoscape.

Participants will learn how to

  • import RNA-Seq count matrix data into Partek Flow and identify differentially expressed genes 
  • generate publication quality graphics such as PCA, volcano plots, heat maps, and Venn diagrams 
  • upload gene lists into the publicly available protein interaction database StringDB to retrieve relevant interaction networks
  • import interaction networks into Cytoscape and analyze the functional enrichment such as gene ontology terms and pathways

Target Audience:

Experimental biologists seeking to learn how to visualize the data generated through experiments or retrieved from a publication or a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither computer programming experience nor familiarity with command line interface is required.

Workshop Requirements:

Workshop Guide:


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.

Class Type

Upcoming Classes

Gene Expression Visualization

Event Details

Instructor: Srilakshmi Chaparala, Ansuman Chattopadhyay
Time: to
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