Gene Expression Visualization: Licensed Tools
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
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.
Please include the following statement in the acknowledgments section for all publications, posters, and presentations:
[Name of the software] licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh was used for data analysis.