Subnetwork analysis

bedtools %

Cut off of target gene predict methods

Function introduction Users can submit a genomic region list, TFs, probes or genes to extract subnet (composed of input nodes and their one-step neighbors) from backgroud network, which contains nine kinds of nodes: probes, genes, TFs by CHIP-seq, TFs by motif, SE, enchancer, ATAC region,3D chromotion interaction regions and CpG islands. Edges were linked by probes to the other seven kinds of nodes in the backround network. 1) Cancer type: Select a cancer type. 2) Input regions: input genomic regions to get overlapping 5 kinds of regulation elements with bedtools. 3) Input node names: input node names directly, including TFs, probes and genes. TFs consist of TFs by CHIP-seq and TFs predicted by fimo with motif. 4) Cut off of target gene predict methods: select thresholds for for probe to gene edges.