EGRIN Session II Broadening the Model Baliga lab retreat 2010

Network inference with cMonkey and Inferelator Co-expression Functional Associations de novo Motif Detection Image: Christopher Plaisier

Information flow in the cell Images: Wikipedia and OmniGraffle

Transcription…

…plus motif detection

…and protein-protein interactions

transcription Post-transcriptional regulation post-translational modification genetics / epigenetics proteomics metabolomics Information flow in the cell

Data types genetic modifications environmental perturbations transcription motif detection protein-protein interactions epigenetics post-transcriptional regulation post-translational modification protein-DNA binding protein quantification metabolites ncRNAs degradation of transcript degradation of proteins

Current EGRIN

? Effect of bicluster on metabolites

Can we broaden the network and prediction by laying EGRIN on top of metabolic network?

Causal Inference (Conditional Independence) TFEnzymeMetabolite

Using Causal Inference Hole filling in the metabolic network – Correct inconsistencies using causal inference Link expression of regulators to expression of genes to levels of metabolites Nice because it can be done using only SEMs based on linear regression, just like cMonkey and Inferelator

Conditional Independence (4/12 ) * (6/12) = 2/12 = 1/6 (2/12) = 1/6 (12/37) * (12/37) = (4/37) = 0.108

Conditional Dependence Democrat Republican