Profiling Cell/Tissue Specific Gene Regulatory Networks
summary
Analyzes 41 cell-specific TF regulatory networks (from a 2012 dataset) with ~475 TFs and ~1,100 predicted interactions each, finds hierarchical layout with ~23% TFs in a top layer and 60–70% in a middle layer, reports feed-forward loops ~10× feedback loops and stem cells showing the smallest motif counts relative to network size, derives closed-form estimators to recover global motif counts from incomplete noisy subnetwork data and estimator validated on ER / preferential-attachment / duplication / geometric models, notes estimator breaks down with high false-positive/negative rates and that human PPI shows ~194× more triangles than yeast (caveat: network size and noise).
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