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

Table 2 Analysis of transcriptional response to transcription factor deletion.

Transcription Factor	Genomewide		B+/C+			B+/C-
	Mean	SD	Mean	SD	-log ₁₀ (p)	Mean	SD	-log ₁₀ (p)
Dig1	0.759	0.198	0.567	0.360	3.76	0.846	0.080	0.04
Gcn4	0.785	0.177	0.294	0.329	28.23	0.793	0.170	0.24
Hir2	0.724	0.218	0.180	0.295	4.00	0.760	0.194	0.14
Mbp1	0.830	0.121	0.541	0.324	27.86	0.770	0.172	2.79
Swi4	0.524	0.338	0.348	0.352	4.89	0.533	0.333	0.24
Swi5	0.744	0.204	0.583	0.373	5.98	0.759	0.186	0.17
Yap1	0.756	0.201	0.471	0.376	7.66	0.587	0.337	2.67

The mean and the standard deviation of gene expression log-ratio between mutant and wild type as obtained in Hughes et al. were calculated for all genes in the genome as well as for the B+/C+ and B+/C- groups [21]. A sample t-test was performed to determine the significance of the change in expression. The B+/C+ genes show a significant change in mRNA expression for the 7 transcription factors for which deletion and ChIP data is available. By contrast, the response of the B+/C- genes is insignificant for most transcription factors.