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Module 3: Pathway Analysis

Lesson #: Intro to Gene ontology and pathway analysis

  • Discuss what this is
  • Where can we find descriptors
  • geneontology.org
  • organism specific databases
  • What is KEGG?

Lesson #: More on ORA, GSEA, GSVA

  • pros and cons
    • https://alexslemonade.github.io/refinebio-examples/03-rnaseq/pathway-analysis_rnaseq_01_ora.html
  • Where to find tools?

Lesson #: Example run of one of these tools

Lesson #: Qiagen IPA

Notes: PANTHER DAVID

Qiagen IPA - more detailed

R Bioconductor clusterProfiler GSVA goseq GOexpress (for GO annotation) pathview EGSEA seqGSEA

CRAN GANPA GOxploreR geneset

GSEA, GSVA, ORA

https://www.rna-seqblog.com/blitzgsea-efficient-computation-of-gene-set-enrichment-analysis-in-python/

https://github.com/iDEP-SDSU/idep http://bioinformatics.sdstate.edu/idep96/ http://bioinformatics.sdstate.edu/go/

http://revigo.irb.hr/

https://yulab-smu.top/biomedical-knowledge-mining-book/index.html

https://maayanlab.cloud/Enrichr/#

http://www.funrich.org/

https://biit.cs.ut.ee/gprofiler/gost

http://geneontology.org/docs/tools-overview/