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MCB course: Introduction to Integrative Bioinformatics
Module 1: In the context of microarray gene expression data analysis
Files needed for the exercises
- The J-Express .pro file with the course data: http://www.bccs.uni.no/~kjellp/MCBcourse09/CancerPhenotypes.pro
- License instructions to unlock all features of J-Express: license
- GO association file for H. Sapiens: http://www.bccs.uni.no/~kjellp/MCBcourse09/gene_association.goa_human
- Gene set file (.gmt) listing KEGG Pathways and their respective genes by Gene Symbols: http://www.bccs.uni.no/~kjellp/MCBcourse09/pwtable.gmt
- J-Express script for Meta analysis exercise: http://www.bccs.uni.no/~kjellp/MCBcourse09/InvertLogRatiosAndReplace0values.pyt
- KEGG2SBML files: http://www.bccs.uni.no/~mdo041/mcbcourse/kegg2sbml/ (brief description: http://www.bccs.uni.no/~mdo041/mcbcourse/)
Exercises as PDF files
- J-Express basics exercise: http://www.bccs.uni.no/~kjellp/MCBcourse09/Exercise_1_Basics_MCB2009.pdf
- Differential Expression exercise: http://www.bccs.uni.no/~kjellp/MCBcourse09/Exercise_DiffExp_MCB2009.pdf
- Gene Set Enrichment Analysis: http://www.bccs.uni.no/~kjellp/MCBcourse09/Exercise_GSEA_MCB2009.pdf
- Identifier mapping: see presentation slides and http://www.bccs.uni.no/~mdo041/mcbcourse/pdf/exercise_identifiers.pdf
- Meta analysis using Rank Product: http://www.bccs.uni.no/~kjellp/MCBcourse09/Exercise_MetaRP_MCB2009.pdf
- Systematic KEGG PW representation: see presentation slides and http://www.bccs.uni.no/~mdo041/mcbcourse/pdf/exercise_kegg.pdf
- ProMeTra and visualization: http://www.bccs.uni.no/~mdo041/mcbcourse/pdf/exercise_prometra.pdf
Presentations as PDF files
- Introduction and overview: http://www.bccs.uni.no/~kjellp/MCBcourse09/IntroAndOverview.pdf
- Differential Expression: http://www.bccs.uni.no/~kjellp/MCBcourse09/IntroDiffExpAnalysis.pdf
- Gene Set Enrichment Analysis: http://www.bccs.uni.no/~kjellp/MCBcourse09/IntroGSEA.pdf
- Identifier mapping: http://www.bccs.uni.no/~mdo041/mcbcourse/pdf/MCBcourseIdentifiers.pdf
- Meta analysis using Rank Product: http://www.bccs.uni.no/~kjellp/MCBcourse09/MetaAnalysisRankProduct.pdf
- ProMeTra and network visualization: http://www.bccs.uni.no/~mdo041/mcbcourse/pdf/ProMeTra.pdf
- Systematic KEGG PW representation: http://www.bccs.uni.no/~mdo041/mcbcourse/pdf/MCBcourseKegg.pdf
