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.

Veber et al. BMC Bioinformatics 2008 9:228   doi:10.1186/1471-2105-9-228

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