Pathway Enrichment Analysis: Licensed Tools
This is a 4½ hour workshop. The morning session (10 am - 12 pm) provides a brief overview of bioinformatics concepts and software used for interpreting a gene list using pathway and network information. The afternoon session (1 pm - 3:30 pm) focuses on software demonstration using 3 HSLS-licensed tools: Correlation Engine, Ingenuity Pathway Analysis (IPA), and MetaCore.
Participants will learn how to
- retrieve a list of differentially expressed genes (DEG) associated with a genome-scale experiment such as an RNA-Seq gene expression study ("treatment vs. control," "tumor vs. normal" or "infected vs. Mock") by searching gene expression data repositories (NCBI GEO)
- glean mechanistic insights by finding statistically overrepresented terms (biological functions, molecular processes, diseases, etc.) and pathways present in that DEG list
- predict upstream causal regulators (transcription factors, miRNA, etc.)
- retrieve datasets from GEO that show similar or opposite gene expression profiles
Experimental biologists working with human, mouse, or rat tissues and seeking to interpret gene lists generated through omics experiments such as gene expression, protein interactions, and SNP arrays. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.
Software Registration and Download
Publications from Pitt Showing Software Applications
Software Documentations / Tutorials
Featured Publication Showing CLC Genomics, IPA and Metacore Application
Please include the following statement in the acknowledgments section for all publications, posters, and presentations:
[software name] licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh was used for data analysis.