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

    • module1YeastGenes.txt

  • Module 2 lab:

    • http://david.abcc.ncifcrf.gov/

    • Gene lists for DAVID lab

      • HPO: Abnormal Artery Tree

      • 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/

    • PDF

• Background reading:

  • How to visually interpret biological data using networks

    • PDF

  • Integration of biological networks and gene expression data using Cytoscape

    • PDF

  • Cytoscape: a software environment for integrated models of biomolecular interaction networks

    • PDF

  • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

  • The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

    • PDF

• Multiple Testing Correction tutorial

  • mtc.pdf

• Slides:

  • Pathways_Milan2012_Module1-GeneListIntro.ppt - PowerPoint format

  • Pathways_Milan2012_Module2-EnrichmentAnalysis.ppt - PowerPoint format

  • Pathways_Milan2012_Module3-Pathways.ppt - PowerPoint format

  • Pathways_Milan2012_Module4-part1-NetworkVisualizationAndAnalysis.ppt - PowerPoint format

  • Pathways_Milan2012_Module4-part2-EnrichmentMap.pptx - PowerPoint format

  • Pathways_Milan2012_Module5-Gene function prediction.ppt - PowerPoint format

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