Literature and Links to sites mentioned in Lecture 15

Literature

• Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
  Khatri P, Sirota M, Butte AJ
  PLOS Computational Biology, 2012 8(2):e1002375.

• Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?
  Wood V, Lock A, Harris MA, Rutherford K, Bahler J, Oliver SG.
  Open Biology, 2019 9(2):180241.

• Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
  Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD.
  Nature Protocols, 2019 14:482-517

• WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs
  Liao Y, Wang J, Jaehnig EJ, Shi Z, Zhang B.
  Nucleic Acids Research, 2019 47(W1):W199-W205

• g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)
  Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, Vilo J.
  Nucleic Acids Research, 2019 47(W1):W191-W198

Links

Selected Pathway tools:

• g:Profiler: https://biit.cs.ut.ee/gprofiler/gost
• GSEA: http://software.broadinstitute.org/gsea/index.jsp
• WebGestalt: http://www.webgestalt.org/
• Cytoscape: https://cytoscape.org/

• KEGG (Kyoto Encyclopedia of Genes and Genomes): https://www.genome.jp/kegg/
• BioCyc: https://biocyc.org
• Reactome: https://reactome.org
• Wikipathways: https://www.wikipathways.org/index.php/WikiPathways

• Identifier Conversion Tools: http://bip.weizmann.ac.il/toolbox/seq_analysis/annotation.html