Read the following papers before coming to the workshop:

• 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
  Nat Protoc. 2019 Feb;14(2):482-517 - Available here as well

• iRegulon: from a gene list to a gene regulatory network using large motif and track collections
  Janky R, Verfaillie A, Imrichová H, Van de Sande B, Standaert L, Christiaens V, Hulselmans G, Herten K, Naval Sanchez M, Potier D, Svetlichnyy D, Kalender Atak Z, Fiers M, Marine JC, Aerts S
  PLoS Comput Biol. 2014 Jul 24;10(7)

• The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
  Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q
  Nucleic Acids Res 2010 Jul 1;38 Suppl:W214-20 - Available here as well

• GeneMANIA update 2018
  Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q
  Nucleic Acids Res. 2018 Jun 15 - Available here as well

• How to visually interpret biological data using networks
  Merico D, Gfeller D, Bader GD
  Nature Biotechnology 2009 Oct 27, 921-924 - Available here as well

• g:Profiler–a web-based toolset for functional profiling of gene lists from large-scale experiments.
  Reimand J, Kull M, Peterson H, Hansen J, Vilo J
  Nucleic Acids Res. 2007 Jul;35

• 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 Res. 2019 May 8

• Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
  Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP
  Proc Natl Acad Sci U S A. 2005 Oct 25;102(43)

• Expression data analysis with Reactome
  Jupe S, Fabregat A, Hermjakob H
  Curr Protoc Bioinformatics. 2015 Mar 9;49:8.20.1-9

Do these exercises before coming to the workshop:

1. Sequencing Terminology

2. Cytoscape Preparation tutorials: From introductory tutorial to Cytoscape, complete:

• 1. Tour of Cytoscape
• 1. Basic Data Visualization