Condition transition analysis reveals TF activity to nutrient-limitation-specific effects of oxygen presence in yeast

TA Knijnenburg; LFA Wessels; MJT Reinders

Condition transition analysis reveals TF activity to nutrient-limitation-specific effects of oxygen presence in yeast

TA Knijnenburg, LFA Wessels, MJT Reinders

Multimedia Computing

Research output: Chapter in Book/Conference proceedings/Edited volume › Conference contribution › Scientific › peer-review

Abstract

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.

Original language	Undefined/Unknown
Title of host publication	Computational Methods in Systems Biology
Editors	C Priami
Place of Publication	Berlin,Heidelberg
Publisher	Springer
Pages	271-284
Number of pages	14
ISBN (Print)	3-540-46166-3
Publication status	Published - 2006
Event	International Conference Computational Methods in Systems Biology, Trento, Italy - Berlin,Heidelberg Duration: 18 Oct 2006 → 19 Oct 2006

Publication series

Name
Publisher	Springer

Name
Volume	4210

Conference

Conference	International Conference Computational Methods in Systems Biology, Trento, Italy
Period	18/10/06 → 19/10/06

Bibliographical note

Dit is opgenomen in Lecture Notes in Bioinformatics (4210) maar dat komt niet voor op de lijst en kan ook niet door mij worden toegevoegd

Keywords

Wiskunde en Informatica
Techniek
technische Wiskunde en Informatica
conference contrib. refereed
Conf.proc. > 3 pag

Cite this

@inproceedings{e37433efdc0943538ee9aef227069893,

title = "Condition transition analysis reveals TF activity to nutrient-limitation-specific effects of oxygen presence in yeast",

abstract = "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.",

keywords = "Wiskunde en Informatica, Techniek, technische Wiskunde en Informatica, conference contrib. refereed, Conf.proc. > 3 pag",

author = "TA Knijnenburg and LFA Wessels and MJT Reinders",

note = "Dit is opgenomen in Lecture Notes in Bioinformatics (4210) maar dat komt niet voor op de lijst en kan ook niet door mij worden toegevoegd; International Conference Computational Methods in Systems Biology, Trento, Italy ; Conference date: 18-10-2006 Through 19-10-2006",

year = "2006",

language = "Undefined/Unknown",

isbn = "3-540-46166-3",

publisher = "Springer",

pages = "271--284",

editor = "C Priami",

booktitle = "Computational Methods in Systems Biology",

}

Condition transition analysis reveals TF activity to nutrient-limitation-specific effects of oxygen presence in yeast. / Knijnenburg, TA; Wessels, LFA ; Reinders, MJT.
Computational Methods in Systems Biology. ed. / C Priami. Berlin,Heidelberg: Springer, 2006. p. 271-284.

Research output: Chapter in Book/Conference proceedings/Edited volume › Conference contribution › Scientific › peer-review

TY - GEN

T1 - Condition transition analysis reveals TF activity to nutrient-limitation-specific effects of oxygen presence in yeast

AU - Knijnenburg, TA

AU - Wessels, LFA

AU - Reinders, MJT

N1 - Dit is opgenomen in Lecture Notes in Bioinformatics (4210) maar dat komt niet voor op de lijst en kan ook niet door mij worden toegevoegd

PY - 2006

Y1 - 2006

N2 - 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.

AB - 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.

KW - Wiskunde en Informatica

KW - Techniek

KW - technische Wiskunde en Informatica

KW - conference contrib. refereed

KW - Conf.proc. > 3 pag

UR - http://www.springerlink.com/content/01342gt6h02k533h/fulltext.pdf

M3 - Conference contribution

SN - 3-540-46166-3

SP - 271

EP - 284

BT - Computational Methods in Systems Biology

A2 - Priami, C

PB - Springer

CY - Berlin,Heidelberg

T2 - International Conference Computational Methods in Systems Biology, Trento, Italy

Y2 - 18 October 2006 through 19 October 2006

ER -

Condition transition analysis reveals TF activity to nutrient-limitation-specific effects of oxygen presence in yeast

Abstract

Publication series

Conference

Bibliographical note

Keywords

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Cite this