HSLS MolBio Workshops

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.

Powerpoints

• Licensed Tools - Partek flow   
• Open Access tools - Cytoscape

Lecture Videos 

• Gene expression visualization using Partek flow

HSLS Self Learning Module on Cytoscape :

Are you interested in using Cytoscape, a powerful network visualization and analysis tool, to explore your gene or protein expression data on your own pace? Please check this self learning module on Gene expression Data and Network visualization using Cytoscape 

Data Download

Partek flow :

• DexAlbvsUnt_Matrix (practice) - hands on practice
• DexAlb Vs.Unt_metadata - Metadata for samples
• Human_allpathways_Bader - a GMT file available from Badder lab comprising pathway Genesets from various databases

Cytoscape : 

• Protein Interaction Network - a list of data sets for creating a protein interaction map
• Human_allpathways_Bader - a GMT file available from Badder lab comprising pathway Genesets from various databases
• AI_vs_DMSO_GSEA_pos - GSEA result for pos that is ready to upload to Cytoscape
• AI_vs_DMSO_GSEA_neg - GSEA result for pos that is ready to upload to Cytoscape
• hands_on_GSEA_pos_sars-Cov2_vs_mock_calu3 - GSEA result for pos that is ready to upload to Cytoscape 
• hands_on_GSEA_neg_sars-Cov2_vs_mock_calu3 - GSEA result for neg that is ready to upload to Cytoscape 

Software

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

• Overview of Partek flow  - Partek flow tutorials

Selected Tutorials

• Partek flow documentation - Webpage for Partekflow documentation
• Visualizations in Partekflow - Webpage for Partekflow visualizations
• Integrated analysis - Integrated analysis of RNASeq and CHIP/ATAC Seq in Partekflow
• A Web Tool for Generating High Quality Machine-readable Biological Pathways - A publication on JoVE journal 
• Cytoscape documentation - Cytoscape Manual

• BioGRID - A database for Protein interactions
• Reactome - A database for pathways
• Venn Diagram Creator
• BioRender - Scientific illustrations creating tool
• PCA Explained (video)
• Hierarchical Clustering (video) 
• Bader group gene datasets 

• RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells 
• Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 13 (2016). 
• PBMC fixation and processing for Chromium single-cell RNA sequencing 

• Protein-protein interaction databases: keeping up with growing interactomes

• NDEx: Accessing Network Models and Streamlining Network Biology Workflows

Feedback

• Class Evaluation

Attribution

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.