#acl All:read

Official course homepage: http://bimib.disco.unimib.it/index.php/InBiMedDoctoralCourse

 * Lab resources
  * Module 1 lab: (on your own)
   * http://llama.mshri.on.ca/synergizer/translate/
   * http://useast.ensembl.org/biomart/martview
   * http://cytoscape.org/
   * Introductory Cytoscape tutorial: http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape
   * [[attachment:module1YeastGenes.txt]]
  * Module 2 lab: 
   * http://david.abcc.ncifcrf.gov/
   * Gene lists for DAVID lab
     * [[attachment:Module1_AbnormalArteryTree_Sy.txt|HPO: Abnormal Artery Tree]]
     * [[attachment:Module1_HallucinPsychosis_Sy.txt|HPO: Hallucinations or Psychosis]]
  * Module 3 lab:
   * http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin
  * Module 4 lab:
   * http://baderlab.org/Software/EnrichmentMap
  * Module 5 lab: GeneMANIA protocol/tutorial
   * http://www.genemania.org/
   * [[attachment:genemania_exercises_v1-updatedMar2011.pdf|PDF]]

 * Background reading:
  * [[http://www.ncbi.nlm.nih.gov/pubmed/19816451|How to visually interpret biological data using networks]]
   * [[http://baderlab.org/Publications?action=AttachFile&do=get&target=2009_Merico_Primer_NatBiotech_Oct.pdf|PDF]]
  * [[http://www.ncbi.nlm.nih.gov/pubmed/17947979|Integration of biological networks and gene expression data using Cytoscape]]
   * [[http://baderlab.org/Publications?action=AttachFile&do=get&target=2007_Cytoscape_Cline_NatureProtocols_Oct.pdf|PDF]]
  * [[http://www.ncbi.nlm.nih.gov/pubmed/14597658|Cytoscape: a software environment for integrated models of biomolecular interaction networks]]
   * [[attachment:Genome Res.-2003-Shannon-2498-504.pdf|PDF]]
  * [[http://www.nature.com/nprot/journal/v4/n1/abs/nprot.2008.211.html|Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources]]
  * [[http://www.ncbi.nlm.nih.gov/pubmed/20576703|The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function]]
   * [[http://baderlab.org/Publications?action=AttachFile&do=get&target=2010_GeneMANIA_Warde-Farley_NAR_Jun.pdf|PDF]]

 * Multiple Testing Correction tutorial
  * [[attachment:mtc.pdf]]

 * Slides:
  * [[attachment:Pathways_Milan2012_Module1-GeneListIntro.ppt]] - !PowerPoint format
  * [[attachment:Pathways_Milan2012_Module2-EnrichmentAnalysis.ppt]] - !PowerPoint format
  * [[attachment:Pathways_Milan2012_Module3-Pathways.ppt]] - !PowerPoint format
  * [[attachment:Pathways_Milan2012_Module4-part1-NetworkVisualizationAndAnalysis.ppt]] - !PowerPoint format
  * [[attachment:Pathways_Milan2012_Module4-part2-EnrichmentMap.pptx]] - !PowerPoint format
  * [[attachment:Pathways_Milan2012_Module5-Gene function prediction.ppt]] - !PowerPoint format