Regulatorynetworksareusuallypresentedasgraphstructuresshowingthe(combinatorial)regulatorye¿ectoftranscriptionfactors(TF¿s)onmodulesofsimilarlyexpressedorotherwiserelatedgenes.However,fromthesenetworksitisnotclearwhenandhowTF¿sareactivated.TheactualconditionsorperturbationsthattriggerachangeintheactivityofTF¿sshouldbeacrucialpartofthegeneratedregulatorynetwork. Here,wedemonstratethepowertouncoverTFactivitybyfocusingonasmall,homogeneous,yetwellde¿nedsetofchemostatcultivationexperiments,wherethetranscriptionalresponseofyeastgrownunderfourdi¿erentnutrientlimitations,bothaerobicallyaswellasanaerobicallywasmeasured.Wede¿neaconditiontransitionasaninstantchangeinyeast¿sextracellularenvironmentbycomparingtwocultivationconditions,whereeitherthelimitednutrientortheoxygenavailabilityisdi¿erent.Di¿erentialgeneexpressionasaconsequenceofsuchaconditiontransitionisrepresentedinatertiarymatrix,wherezeroindicatesnochangeinexpression;1and-1respectivelyindicateanincreaseanddecreaseinexpressionasaconsequenceofaconditiontransition.WeuncoverTFactivitybyassessingsigni¿cantTFbindinginthepromotorregionofgenesthatbehaveaccordinglyataconditiontransition.Theinterrelatednessoftheconditionsinthecombinatorialsetupisexploitedbyperformingspeci¿chypergeometricteststhatallowforthediscoveryofbothindividualandcombinede¿ectsofthecultivationparametersonTFactivity.Additionally,wecreateaweight-matrixindicatingtheinvolvementofeachTFineachoftheconditiontransitionsbyposingourproblemasanorthogonalProcrustesproblem.WeshowthattheProcrustesanalysisstrengthensandbroadenstheuncoveredrelationships. Theresultingregulatorynetworkrevealsnutrient-limitation-speci¿ce¿ectsofoxygenpresenceonexpressionbehaviorandTFactivity.Ouranalysisidenti¿esmanyTF¿sthatseemtoplayaveryspeci¿cregulatoryroleatthenutrientandoxygenavailabilitytransitions.@en

Abstract Markov blanket filtering based on discretized features (MBF) has been proposed as a feature selection strategy. Critical evaluation of MBF has demonstrated its contradictory and counterintuitive nature, which results in undesirable properties for small sample size applications such as classification based on microarray gene expression data. Keywords: Pattern recognition; Feature evaluation and selection@en

Within the first 5 min after a sudden relief from glucose limitation, Saccharomyces cerevisiae exhibited fast changes of intracellular metabolite levels and a major transcriptional reprogramming. Integration of transcriptome and metabolome data revealed tight relationships between the changes at these two levels. Transcriptome as well as metabolite changes reflected a major investment in two processes: adaptation from fully respiratory to respiro‐fermentative metabolism and preparation for growth acceleration. At the metabolite level, a severe drop of the AXP pools directly after glucose addition was not accompanied by any of the other three NXP. To counterbalance this loss, purine biosynthesis and salvage pathways were transcriptionally upregulated in a concerted manner, reflecting a sudden increase of the purine demand. The short‐term dynamics of the transcriptome revealed a remarkably fast decrease in the average half‐life of downregulated genes. This acceleration of mRNA decay can be interpreted both as an additional nucleotide salvage pathway and an additional level of glucose‐induced regulation of gene expression.@en