Figure 2.

The algorithmic scheme to extract functional TF-gene binding pairs. We used a network approach to combine the ChIP-chip data and the TFKO data. The central notion of our method is based on the deduced hypostatic TF-gene regulation. This extended the low overlap between the binding data and the TFKO data. For a given TF-gene binding pair, we first sought for regulation evidence for this pair. The regulation evidence can be either the direct literature-curated TFKO TF-gene regulation or the deduced hypostatic TF-gene regulation. Then we calculated the confidence for the TF-gene regulation by comparing the regulation pair with the same pairs in randomly generated TFKO networks. A final RCS was calculated for confidence measurement. A TF-gene binding pair is called functional if it also has confident TF-gene regulation information (with RCS > 1000).