Table 4 (supplementary): Replacing regulatory coupling strength by transcription factor deletion data

Transcription factor	Gene number in each group				GO category
Transcription factor	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

Replacing regulatory coupling strength by response to transcription factor deletion. 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 overrepresented 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.