Inferring the role of transcription factors in regulatory networks

BMC Bioinformatics

Table 4 Ambiguous modules of Type I found for 3 transcriptional networks of S. cerevisiae.

Interaction network	Actor	Target	Experiment 1	Experiment 2
(A) Core of Transc. Network	YAP6	CIN5	Expression during Sporulation [41]	YPD Broth to Stationary Phase [44]
	GRF10	MBP1	YPD Broth to Stationary Phase [44]	Mec1 mutant + Heat [45]
	PDH1	MSN4	Nitrogen Depletion [44]	Heat shock 21°C to 37°C [44]
(B) Extended Transc. Network	YAP6	CIN5	Expression during Sporulation [41]	YPD Broth to Stationary Phase [44]
	RAP1	SIP4	Expression during Sporulation [41]	Expression during the diauxic shift [40]
	SKN7	NRG1	YPD Broth to Stationary Phase [44]	Expression during the diauxic shift [40]
	PHD1	SOK2	Heat shock 21°C to 37°C [44]	YPD Broth to Stationary Phase [44]
	RAP1	RCS1	Wild type + Heat [45]	Transition from fermentative to glycerol- based respiratory growth [47]
	PHD1	MSN4	Nitrogen Depletion [44]	Heat shock 21°C to 37°C [44]
	HAP4	PUT3	Expression during the diauxic shift [40]	Snf2 mutant, YPD [42]
(C) MacIssac inferred network	SWI5	ASH1	Expression regulated by the PHO path- way [43]	YPD Broth to Stationary Phase [44]
	SKN7	NRG1	YPD Broth to Stationary Phase [44]	Nitrogen Depletion [44]
	NRG1	YAP7	Expression regulated by the PHO path- way [43]	Transition from fermentative to glycerol- based respiratory growth [47]
	NRG1	GAT3	Glycosylation [46]	Transition from fermentative to glycerol- based respiratory growth [47]

For each ambiguous module, we list two inconsistent experiments that infer a different role of regulation.

ISSN: 1471-2105