REFERENCES

• HoodL.PerlmutterRM.The impact of systems approaches on biological problems in drug discovery.Nat Biotechnol.2004221215121715470453
   PubMed Web of Science ®Google Scholar
• BoothB.ZemmelR.Prospects for productivity.Nat Rev Drug Discov.2004345145615136792
   PubMed Web of Science ®Google Scholar
• WeinshilboumR.Inheritance and drug response.N Engl J Med.200334852953712571261
   PubMed Web of Science ®Google Scholar
• GolubTR.SlonimDK.TamayoP.et al.Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.Science.199928653153710521349
   PubMed Web of Science ®Google Scholar
• GerholdDL.JensenRV.GullansSR.Better therapeutics through microarrays.Nat Genet.20023254755212454652
   PubMed Web of Science ®Google Scholar
• AdlerAS.LinM.HorlingsH.NuytenDS.van de VijverMJ.ChangHY.Genetic regulators of large-scale transcriptional signatures in cancer.Nat Genet20063842143016518402
   PubMed Web of Science ®Google Scholar
• MischelPS.CloughesyTF.NelsonSF.DNA-microarray analysis of brain cancer: Molecular classification for therapy.Nat Rev Neurosci.2004578279215378038
   PubMed Web of Science ®Google Scholar
• SegalE.FriedmanN.KaminskiN.RegevA.KollerD.From signatures to models: understanding cancer using microarrays.Nat Genet.200537S38S4515920529
   PubMed Web of Science ®Google Scholar
• LockhartDJ.DongH.ByrneMC.et al.Expression monitoring by hybridization to high-density oligonucleotide arrays.Nat Biotechnol.199614167516809634850
   PubMed Web of Science ®Google Scholar
• HughesT.MaoM.JonesA.et al.Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer.Nat Biotechnol.20011934234711283592
   PubMed Web of Science ®Google Scholar
• GundersonKL.KruglyakS.GraigeMS.et al.Decoding randomly ordered DNA arrays.Genome Res.20041487087715078854
   PubMed Web of Science ®Google Scholar
• KuhnK.BakerSC.ChudinE.et al.A novel high-performance random array platform for quantitative gene expression profiling.Genome Res.2004142347235615520296
   PubMed Web of Science ®Google Scholar
• HardimanG.Microarray platforms - comparisons and contrasts.Pharmacogenomics.20045487 50215212585
   PubMed Web of Science ®Google Scholar
• LehrachH.DrmanacR.HoheiselJ.et al.Hybridization fingerprinting in genome mapping and sequencing. In: Davis KE, Tilghman S, eds.Genome Analysis: Genetic and Physical Mapping. Cold Spring Harbor, NY;19903981
   Google Scholar
• LennonG.LehrachH.Hybridization analyses of arrayed cDNA libraries.Trends Genet.199173143171781028
   PubMed Web of Science ®Google Scholar
• SchenaM.ShalonD.DavisR.BrownP.Quantitative monitoring of gene expression patterns with a complementary DNA microarray.Science.9952704674707569999
   PubMed Web of Science ®Google Scholar
• AdjayeJ.HerwigR.HerrmannD.et al.Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays.BMC Genomics.20045814728724
   PubMed Web of Science ®Google Scholar
• NewtonSS.BennettA.DumanRS.Production of custom microarrays for neuroscience research.Methods.20053723824616308153
   PubMed Web of Science ®Google Scholar
• ParrishML.WeiN.DuenwaldS.et al.A microarray platform comparison for neuroscience applications.J Neurosci Meth.20041325768
   PubMed Web of Science ®Google Scholar
• KuoWP.JenssenTK.ButteAJ.Ohno-MachadoL.KohaneIS.Analysis of matched mRNA measurements from two different microarray technologies.Bioinformatics.20021840541211934739
   PubMed Web of Science ®Google Scholar
• TanPK.DowneyTJ.SpitznagelEL.et al.Evaluation of gene expression measurements from commercial microarray platforms.Nucleic Acids Res.2003315676568414500831
   PubMed Web of Science ®Google Scholar
• BarnesM.FreudenbergJ.ThompsonS.AronowB.PavlidisP.Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms.Nucleic Acids Res.2005335914592316237126
   PubMed Web of Science ®Google Scholar
• DaiM.WangP.BoydAD.et al.Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.Nucleic Acids Res.200533e17516284200
   PubMed Web of Science ®Google Scholar
• JainAN.TokuyasuTA.SnijdersAM.SegravesR.AlbertsonDG.PinkelD.Fully automatic quantification of microarray image data.Genome Res.20021232533211827952
   PubMed Web of Science ®Google Scholar
• WierlingCK.SteinfathM.ElgeT.et al.Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis.BMC Bioinformatics.200232912390683
   PubMed Web of Science ®Google Scholar
• SteinfathM.WruckW.SeidelH.LehrachH.RadelofU.O'BrienJ.Automated image analysis for array hybridization experiments.Bioinformatics.20011763464111448881
   PubMed Web of Science ®Google Scholar
• HollemanA.CheokMH.denBoerML.et al.Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment.N Engl J Med.200435153354215295046
   PubMed Web of Science ®Google Scholar
• QuakenbushJ.Microarray data normalization and transformation.Nat Genet.200249650112454644
   PubMed Web of Science ®Google Scholar
• ClevelandWS.Robust locally weighted regression and smoothing scatterplots.J Am Stat Assoc.197974829836
   Web of Science ®Google Scholar
• ClevelandWS.DevlinSJ.Locally weighted regression: an approach to regression analysis by local fitting.J Am Stat Assoc.198383596610
   Google Scholar
• YangH.DudoitS.LuuP.et al.Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variations.Nucleic Acids Res.200230e1511842121
   PubMed Web of Science ®Google Scholar
• LiC.WongWH.Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection.Proc Natl Acad Sel U S A.2001983136
   PubMed Web of Science ®Google Scholar
• lrizarryRA.BolstadBM.CollinsF.CopeLM.HobbsB.SpeedTP.Summaries of Âffymetrix GeneChip probe level data.Nucleic Acids Res.200331e1512582260
   PubMed Web of Science ®Google Scholar
• DraghiciS.Data Analysis Tools for DNA Microarrays. Boca Raton, Fla: Chapman & Hall/CRC Press2003
   Google Scholar
• KahlemP.SultanM.HerwigR.et al.Transcript level alterations reflect gene dosage effects across multiple tissues in a mouse model of Down syndrome.Genome Res.2004141258126715231742
   PubMed Web of Science ®Google Scholar
• HerwigR.AanstadP.ClarkM.LehrachH.Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments.Nucleic Acids Res.200129E11711726700
   PubMed Web of Science ®Google Scholar
• EisenMB.SpellmanPT.BrownPO.BotsteinD.Cluster analysis and display of genome-wide expression patterns.Proc Natl Acad Sel U S A.1998951486314868
   PubMed Web of Science ®Google Scholar
• TamayoP.SlonlmD.MesirovJ.et al.Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation.Proc Natl Acad Sci U S A.1998962907291210077610
   PubMed Web of Science ®Google Scholar
• HerwigR.PoustkaAJ.MullerC.LehrachH.O'BrienJ.Large-scale clustering of cDNA fingerprinting data.Genome Res.199991093110510568749
   PubMed Web of Science ®Google Scholar
• SharanR.ShamirR.CLICK: a clustering algorithm with applications to gene expression analysis. Paper presented at: Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB); Menlo Park, California, USA. 2000
   Google Scholar
• JainAK.DubesRC.Algorithms for Clustering Data. Englewood Cliffs, NJ: Prentice Hall.1988
   Google Scholar
• TavazoieS.HughesJD.CampbellMJ.ChoRJ.ChurchGM.Systematic determination of genetic network architecture.Nat Genet.19992228128510391217
   PubMed Web of Science ®Google Scholar
• GibbonsFD.RothFP.Judging the quality of gene expression-based clustering methods using gene annotation.Genome Res2002121574158112368250
   PubMed Web of Science ®Google Scholar
• GittonY.DahmaneN.BaikS.et al.A gene expression map of human chromosome 21 orthologues in the mouse.Nature.200242058659012466855
   PubMed Web of Science ®Google Scholar
• RhodesDR.BarretteT.RubinMA.GhoshD.ChinnaiyanAM.Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer.Cancer Res.2002624427443312154050
   PubMed Web of Science ®Google Scholar
• RhodesDR.YuJ.ShankerK.et al.Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression.Proc Natl Acad Sci U S A.20041019309931415184677
   PubMed Web of Science ®Google Scholar
• AdjayeJ.HuntrissJ.HerwigR.et al.Primary differentiation in the human blastocyst: Comparative molecular portraits of inner cell mass and trophectoderm cells.Stern Cells.20052315141525
   PubMed Web of Science ®Google Scholar
• MakrantonakiE.AdjayeJ.HerwigR.et al.Signalling and metabolic pathways associated with hormone-induced aging in human sebocyte cells in vitro.Aging Cell.2006533134416805856
   PubMedGoogle Scholar
• KanehisaM.GotoS.KawashimaS.OkunoY.HattoriM.The KEGG resources for deciphering the genome.Nucleic Acids Res.200432D277D28014681412
   PubMed Web of Science ®Google Scholar
• Luthi-CarterR.StrandAD.PetersNL.et al.Decreased expression of striatal signaling genes in a mouse model of Huntington's disease.Hum MolGenet. 2000912591271
   PubMed Web of Science ®Google Scholar
• SipioneS.RigamontiD.ValenzaM.et al.Early transcriptional profiles in huntingtin-inducible striatal cells by microarray analyses.Hum Mol Genet.2002111953196512165557
   PubMed Web of Science ®Google Scholar
• Luthi-CarterR.HansonSA.StrandAD.et al.Polyglutamine and transcription: gene expression changes shared by DRPLA and Huntington's disease mouse models reveal context-independent effects.Hum Mol Genet.2002111927193712165555
   PubMed Web of Science ®Google Scholar
• JiangYM.YamamotoM.KobayashiY.et al.Gene expression profile of spinal motor neurons in sporadic amyotrophic lateral sclerosis.Ann Neurol.20055723625115668976
   PubMed Web of Science ®Google Scholar
• BarrettT.SuzekTO.TroupDB.et al.NCBI GEO: mining millions of expression profiles - database and tools.Nucleic Acids Res.200533(Database lssue)D562D56615608262
   PubMed Web of Science ®Google Scholar
• ParkinsonH.SarkansU.ShojatalabM.et al.ArrayExpress - a public repository for microarray gene expression data at the EBI.Nucleic Acids Res.200533(Databaselssue)D55355515608260
   PubMed Web of Science ®Google Scholar
• ene Ontology Consortium. The gene ontology (GO) project in 2006.Nucleic Acids Res.200634(Database lssue)D322D32616381878
   PubMed Web of Science ®Google Scholar
• HennigS.GrothD.LehrachH.Automated Gene Ontology annotation for anonymous sequence data.Nucleic Acids Res.2003313712371512824400
   PubMed Web of Science ®Google Scholar
• GrothD.LehrachH.HennigS.GOblet: a platform for Gene Ontology annotation of anonymous sequence data.Nucleic Acids Res.200432W31331715215401
   PubMed Web of Science ®Google Scholar
• HewettM.OliverDE.RubinDL.et al.PharmGKB: the pharmacogenetics knowledge base.Nucleic Acids Res.20023016316511752281
   PubMed Web of Science ®Google Scholar
• ThornCF.KleinTE.AltmanRB.PharmGKB: the pharmacogenetics knowledge base.Methods Mol Biol.2005311179191 16100408
   PubMedGoogle Scholar
• KramerR.CohenD.Functional genomics to new drug targets.Nat Rev Drug Discov.2004396597215520818
   PubMed Web of Science ®Google Scholar
• KanehisaM.BorkP.Bioinformatics in the post-sequence era.Nat Genet.20033330531012610540
   PubMed Web of Science ®Google Scholar
• DobrinSE.StephanDA.Integrating microarrays into disease-gene identification strategies.Expert Rev Mol Diagn.2003337538512779011
   PubMed Web of Science ®Google Scholar
• DunckleyT.CoonKD.StephanDA.Discovery and development of biomarkers of neurological disease.Drug Discov Today.20051032633415749281
   PubMed Web of Science ®Google Scholar
• EvansWE.McLeodHL.Pharmacogenomics- drug disposition, drug targets, and side effects.N Engl J Med.200334853854912571262
   PubMed Web of Science ®Google Scholar
• HopkinsAL.GroomCR.The druggable genome.Nat Rev Drug Disc.20021727730
   PubMed Web of Science ®Google Scholar
• RussAP.LampelS.The druggable genome: an update.Drug Discov Today2005101607161016376820
   PubMed Web of Science ®Google Scholar
• LipinskiC.LombardeF.DominyB.FeeneyP.Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings.Adv Drug Deliv Rev.199723225
   Web of Science ®Google Scholar
• MimicsK.PevsnerJ.Progress in the use of microarray technology to study the neurobiology of disease.Nat Neurosci.20045434439
   Google Scholar
• MirnicsK.MiddletonFA.LewisDA.LevittP.Analysis of complex brain disorders with gene expression microarrays: schizophrenia as a disease of the synapse.Trends Neurosci.20012447948611476888
   PubMed Web of Science ®Google Scholar
• ReevesRH.IrvingNG.MoranTH.et al.A mouse model for Down syndrome exhibits learning and behaviour deficits.Nat Genet.1995111771847550346
   PubMed Web of Science ®Google Scholar
• MimicsK.MiddletonFA.MarquezA.LewisDA.LevittP.Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex.Neuron.200028536711086983
   PubMed Web of Science ®Google Scholar
• MiddletonFA.MirnicsK.PierriJN.LewisDA.LevittP.Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia.J Neurosci.2002222718272911923437
   PubMed Web of Science ®Google Scholar
• MischelPS.CloughesyTF.NelsonSF.DNA microarray analysis of brain cancer: molecular classification for therapy.Nat Rev Neurosci.2004578279215378038
   PubMed Web of Science ®Google Scholar
• BIalockEM.GeddesJW.ChenKC.PorterNM.MarkesberyWR.LandfieldPW.Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor response.Proc Natl Acad Sci U S A.20041012173217814769913
   PubMed Web of Science ®Google Scholar
• BoroveckiF.LovrecicL.ZhouJ.et al.Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease.Proc Natl Acad Sci U S A.2005102110231102816043692
   PubMed Web of Science ®Google Scholar
• ButcherE.BergEL.KunkelEJ.Systems biology in drug discovery.Nat Biotechnol.2004221253125915470465
   PubMed Web of Science ®Google Scholar
• KlippE.HerwigR.KowaldA.WierlingC.LehrachH.Systems Biology in Practice. Weinheim, Germany: Wiley-VCH;2005
   Google Scholar
• BhallaUS.IyengarR.Emergent properties of networks of biological signaling pathways.Science.19992833813879888852
   PubMed Web of Science ®Google Scholar
• WileyHS.ShvartsmanSY.LauffenburgerDA.Computational modeling of the EGF-receptor system: a paradigm for systems biology.Trends Cell Biol.200313435012480339
   PubMed Web of Science ®Google Scholar
• SchoeberlB.Eichler-JonssonC.GillesED.MullerG.Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors.Nat Biotechnol.20022037037511923843
   PubMed Web of Science ®Google Scholar
• OdaK.MatsuokaY.FunahashiA.KitanoH.A comprehensive pathway map of epidermal growth factor receptor signaling.Mol Sys Biol.2005 2005.0010Epub2005 May 25
   PubMed Web of Science ®Google Scholar
• ChoKH.ShinSY.LeeHW.WolkenhauerO.Investigations into the analysis and modeling of the TNF alpha-mediated NF-kappa B-signaling pathway.Genome Res2003132413242214559780
   PubMed Web of Science ®Google Scholar
• HoffmannA.LevchenkoA.ScottML.BaltimoreD.The l-kappaB-NFkappaB signaling module: temporal control and selective gene activation.Science.20052981241124512424381
   PubMedGoogle Scholar
• ABmusHE.HerwigR.ChoKH.WolkenhauerO.Understanding the dynamics of biological systems: roles in medical research.Expert Rev Mol Diagn. In press2006
   Google Scholar