Florian Markowetz markowetzlab.org Joining the dots… Network analysis of gene perturbation data

Functional Genomics: “What I cannot break, I do not understand.” Richard Feynman: “What I cannot create, I do not understand.” M. mycoides JCVI-syn1.0 How to understand a complex system?

Breaking the system DNA mRNA Protein RNAi Knockout Drugs Small molecules Stress Somatic aberrations Pathway

Today’s lecture What information do we get out of gene perturbations? –Phenotypes and their ‘richness’ How do we use this information to infer the internal architecture of a cell? –Guilt-by-association –Nested Effects Models

Phenotype: viability versus cell death WT B- A-

Phenotype: organism morphology Boutros and Ahringer, Nat Rev 2008

Phenotype: cell morphology Boutros and Ahringer, Nat Rev 2008 RNAi control After gene silencing

Phenotype: pathway activity Receptors A- B- C-

Phenotype: global gene expression A- B- C- … … … A- B- C- All the genes in the genome Transcriptional phenotypes by microarrays

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

A challenge for computation and statistics

From phenotypes to clusters ABC A B Guilt by association

From clusters to mechanisms ?? A B ABBAA B ABA B

TF1TF2 Kinase TF1TF2 TF3 Nested effect models: subset relations Guilt-by-assocation: similarity Markowetz et al 2005, 2007 Tresch and Markowetz 2008 Nested Effects Models

Inferred pathway A B C D E F G H 1.Set of candidate pathway genes 2.High-dimensional phenotypic profile, e.g. microarray INPUT OUTPUT Graph explaining the phenotypes

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

Roland Schwarz Nested Effect Models for NF  B

Take-home messages Phenotyping screens probe a cell’s reaction to targeted perturbations Guilt-by-assocation is a powerful predictor of gene/protein function … … but Guilt-by-assocation has limited ability to infer mechanisms Inferring subset relations by Nested Effects Models provides hierarchical view of cellular organisation

PLoS Comput Biol 6(2) 2010

the team

Florian Markowetz markowetzlab.org Thank you ! Joining the dots …