Functional annotation and pathway integration of hits in genome-wide - PowerPoint PPT Presentation

Functional annotation and pathway integration of hits in genome-wide RNAi screens Pathways, enrichment and all that Florian Markowetz markowetzlab.org

Phenotyping produces partslists Keith Haring, Untitled , 1986 Urs Wehrli, Tidying Up Art , 2003

A challenge for computation and statistics

HTS analyze R

Over-representation analysis Collection of gene sets Weak Phenotype Strong Hits in GO term All Hits Hyper-geometric test Genes in GO term All genes

Gene Set Enrichment Analysis (GSEA) Subramanian et al. (2005) Signifcant trend Weak Phenotype Strong No signifcant trend Weak Phenotype Strong

Diferential GSEA Phenotype 1 Weak Phenotype Strong Phenotype 2 Weak Phenotype Strong

High-scoring subnetworks

HTS analyze R

From phenotypes to clusters A B C A B

From clusters to mechanisms ?? A B A B B A A B A B A B

Markowetz et al 2005, 2007 Tresch and Markowetz 2008 Nested Efgects Models TF1 TF2 Kinase TF2 TF1 Kinase 1 TF1 TF2 Kinase 2 TF3 TF

Nested Efgects Models 1. Set of candidate pathway genes INPUT 2. High-dimensional phenotypic profjle, e.g. microarray OUTPUT Graph representation of information fow explaining the phenotypes Phenotypic profiles Inferred pathway Gene perturbations A A B B C D E F C D E F G G H H Efgects Markowetz et al (’05, ‘07), Fröhlich et al (’07,’08,’09), Zeller et al (‘08), Markowetz and Tresch (‘07), Vaske et al (‘09)

Anatomy of the NF � B pathway Step 1 Roland ? Schwarz + MPI IB Berlin Hits Weak Phenotype Strong NF � B Step 2 Knock-down Compare Known pathway expression members phenotypes New RNAi Hits by NEMs

Nested Efgect Models for NF � B Roland Schwarz

Software NEM HTSanalyzeR • Froehlich et al (2008) • Terfve, Rose et al (in preparation) • Learning nested efgects models from data • geneset and network analysis of gene perturbation screens. http://www. markowetzlab .org/ software /

Acknowledgements • NFkB: Meyer lab at MPI for Infection Biology Berlin, esp. Andrè Mäurer and Cindy Rechner • The NEM community: Rainer Spang, Achim Tresch, Holger Fröhlich, Tim Beißbarth, … • and my group

Functional annotation and pathway integration of hits in genome-wide RNAi screens Thank you ! Florian Markowetz markowetzlab.org