Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks
Fig 4
Evolution of the integrated human TF-miRNA-mRNA network with increasing number of ChIP’ed transcription factors and cell types in which transcription factors have been ChIP’ed.
As more TFs are ChIP’ed, while the shape of TF out-degree distribution remains the same (a), a proportionate number of edges are added to the network (b). Addition of these new edges leads to a linear increase in the in-degrees of mRNA nodes both for average in-degree and high in-degree mRNAs (c,d). This is similar to percolation dynamics where the frequency of both average and large size clusters increases as an increasing number of lattice spaces are filled up (e). ChIP of the same TFs in more cell types adds fewer new edges to the network (f) and the TF nodes (g) with a plateau reached beyond 10 cell types. Shown in (h) is an extrapolation of mRNA in-degree if all known TFs in the human genome (~1400) were to be ChIP’ed.