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Table 4 Replacing regulatory coupling strength by response to transcription factor deletion.

From: Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

Transcription Factor Number of genes in each group GO category
  B- B+/D+ B+/D- Not available B+/D+ B+/D-
Dig1 5881 1 30 115 32 16
Gcn4 5928 16 63 60 19 17
Hir2 5941 2 19 105 24 5
Mbp1 5647 2 103 315 22 12
Swi4 5535 19 106 407 9 6
Swi5 5368 10 82 607 2 0
Yap1 5968 7 37 55 0 0
  1. We analyzed the performance of a scheme in which our TF-gene coupling factor was replaced by the change in mRNA abundance in response to transcription factor deletion as a predictor of true targets. Significant binding (B+) was defined as before, while a significant response to deletion (D+) required P < 10-2. The number of significantly over-represented GO categories is listed for both the B+/D+ and the B+/D- gene groups. The results indicate that TF deletion data is less useful than our coupling factor for distinguishing functional target genes from non-functional ones.
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