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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.


Gene expression Visualization

This workshop focuses on the visualization of gene expression data using HSLS-licensed Partek Flow software and also open access tool Cytoscape.

Partek flow :  We cover the overview of Partek flow software, how to transfer/import gene expression data into Partek flow, run differential expression tools and interpret the results with PCA, heatmap, dot plot, and volcano plots.

Cytoscape :  We cover how to upload gene lists into the publicly available protein interaction databases such as StringDB to retrieve relevant interaction networks and import them into Cytoscape and analyze gene ontology terms and pathways. We also cover how to generate enrichment maps using GSEA/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
  • how to analyze protein interaction networks and also gene enrichment maps in Cytoscape 

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 Materials

Data Download

Partek flow :

Cytoscape : 


  • Partek flow - Software registration page on HSLS website (Registration Required)
  • Cytoscape - network data integration, analysis, and visualization tool (No Registration)


Selected Tutorials

Databases and Tools




Partek Flow

Partek Flow software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh (RRID:SCR_011975) was used for data analysis.