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PMID: 19741703 Published · ppublish English Journal Article Review

Molecular networks as sensors and drivers of common human diseases.

Nature ·Vol. 461 ·No. 7261 ·2009-09-10 ·Pages 218-23

Schadt EE

Abstract

The molecular biology revolution led to an intense focus on the study of interactions between DNA, RNA and protein biosynthesis in order to develop a more comprehensive understanding of the cell. One consequence of this focus was a reduced attention to whole-system physiology, making it difficult to link molecular biology to clinical medicine. Equipped with the tools emerging from the genomics revolution, we are now in a position to link molecular states to physiological ones through the reverse engineering of molecular networks that sense DNA and environmental perturbations and, as a result, drive variations in physiological states associated with disease.

MeSH Terms
Animals Disease/genetics Gene Regulatory Networks Genome-Wide Association Study Genomics Humans Metabolic Networks and Pathways Molecular Biology
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Schadt Eric E
Pacific Biosciences, 1505 Adams Drive, Menlo Park, California 94025, USA. eschadt@pacificbiosciences.com
References (48)
48 references, click to expand
  1. A common genetic risk factor for colorectal and prostate cancer.
    Nat Genet. 2007 Aug;39(8):954-6 PMID: 17618282
  2. Genetic analysis of radiation-induced changes in human gene expression.
    Nature. 2009 May 28;459(7246):587-91 PMID: 19349959
  3. Multiple regions within 8q24 independently affect risk for prostate cancer.
    Nat Genet. 2007 May;39(5):638-44 PMID: 17401364
  4. Integrating genetic and network analysis to characterize genes related to mouse weight.
    PLoS Genet. 2006 Aug 18;2(8):e130 PMID: 16934000
  5. An integrated genomic analysis of human glioblastoma multiforme.
    Science. 2008 Sep 26;321(5897):1807-12 PMID: 18772396
  6. Embracing complexity, inching closer to reality.
    Sci STKE. 2005 Aug 02;2005(295):pe40 PMID: 16077086
  7. CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration.
    Nat Genet. 2006 Sep;38(9):1049-54 PMID: 16936733
  8. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma.
    Nature. 2007 Jul 26;448(7152):470-3 PMID: 17611496
  9. Integrative genomics and drug development.
    Pharmacogenomics. 2009 Feb;10(2):203-12 PMID: 19207021
  10. Genetic analysis of genome-wide variation in human gene expression.
    Nature. 2004 Aug 12;430(7001):743-7 PMID: 15269782
  11. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
    Nat Genet. 2008 May;40(5):638-45 PMID: 18372903
  12. A network view of disease and compound screening.
    Nat Rev Drug Discov. 2009 Apr;8(4):286-95 PMID: 19337271
  13. Nonvalidation of reported genetic risk factors for acute coronary syndrome in a large-scale replication study.
    JAMA. 2007 Apr 11;297(14):1551-61 PMID: 17426274
  14. Genetic mapping in human disease.
    Science. 2008 Nov 7;322(5903):881-8 PMID: 18988837
  15. An integrative genomics approach to the reconstruction of gene networks in segregating populations.
    Cytogenet Genome Res. 2004;105(2-4):363-74 PMID: 15237224
  16. Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids.
    Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12741-6 PMID: 16912112
  17. Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations.
    PLoS Comput Biol. 2007 Apr 13;3(4):e69 PMID: 17432931
  18. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
    Science. 2009 Apr 10;324(5924):218-23 PMID: 19213877
  19. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    Nat Genet. 2008 Aug;40(8):955-62 PMID: 18587394
  20. Common genetic variation and human traits.
    N Engl J Med. 2009 Apr 23;360(17):1696-8 PMID: 19369660
  21. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
    Nat Genet. 2008 Jul;40(7):854-61 PMID: 18552845
  22. RNA-Seq: a revolutionary tool for transcriptomics.
    Nat Rev Genet. 2009 Jan;10(1):57-63 PMID: 19015660
  23. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
    Nature. 2008 Mar 13;452(7184):215-9 PMID: 18278030
  24. Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits.
    Nat Genet. 2005 Nov;37(11):1224-33 PMID: 16200066
  25. Inferring subnetworks from perturbed expression profiles.
    Bioinformatics. 2001;17 Suppl 1:S215-24 PMID: 11473012
  26. Evidence for dynamically organized modularity in the yeast protein-protein interaction network.
    Nature. 2004 Jul 1;430(6995):88-93 PMID: 15190252
  27. Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics.
    Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4530-5 PMID: 17360558
  28. Common polymorphic transcript variation in human disease.
    Genome Res. 2009 Apr;19(4):567-75 PMID: 19189928
  29. Distilling free-form natural laws from experimental data.
    Science. 2009 Apr 3;324(5923):81-5 PMID: 19342586
  30. Genomewide association studies and human disease.
    N Engl J Med. 2009 Apr 23;360(17):1759-68 PMID: 19369657
  31. Genetic basis of proteome variation in yeast.
    Nat Genet. 2007 Nov;39(11):1369-75 PMID: 17952072
  32. Genetic risk prediction--are we there yet?
    N Engl J Med. 2009 Apr 23;360(17):1701-3 PMID: 19369656
  33. Adipose tissue macrophages.
    Immunol Lett. 2007 Oct 15;112(2):61-7 PMID: 17719095
  34. Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease.
    Genome Biol. 2009;10(5):R55 PMID: 19463160
  35. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
    Nat Genet. 2008 Feb;40(2):189-97 PMID: 18193044
  36. Genetics of gene expression surveyed in maize, mouse and man.
    Nature. 2003 Mar 20;422(6929):297-302 PMID: 12646919
  37. Towards a proteome-scale map of the human protein-protein interaction network.
    Nature. 2005 Oct 20;437(7062):1173-8 PMID: 16189514
  38. Genomics and biology come together to fight HIV.
    PLoS Biol. 2008 Mar 25;6(3):e76 PMID: 18366259
  39. Mapping the genetic architecture of gene expression in human liver.
    PLoS Biol. 2008 May 6;6(5):e107 PMID: 18462017
  40. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.
    Science. 2008 Sep 26;321(5897):1801-6 PMID: 18772397
  41. Genomic analysis of metabolic pathway gene expression in mice.
    Genome Biol. 2005;6(7):R59 PMID: 15998448
  42. Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
    Nat Genet. 2008 Feb;40(2):161-9 PMID: 18193043
  43. Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity.
    Nat Genet. 2009 Jan;41(1):18-24 PMID: 19079260
  44. Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration.
    Nat Genet. 2006 Sep;38(9):1055-9 PMID: 16936732
  45. Genetic inheritance of gene expression in human cell lines.
    Am J Hum Genet. 2004 Dec;75(6):1094-105 PMID: 15514893
  46. A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility.
    Genome Res. 2008 May;18(5):706-16 PMID: 18347327
  47. Real-time DNA sequencing from single polymerase molecules.
    Science. 2009 Jan 2;323(5910):133-8 PMID: 19023044
  48. Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks.
    Nat Genet. 2009 Apr;41(4):415-23 PMID: 19270708
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
Published
2009-09-10
Pages
218-23
Language
English
Region
England
NLM ID
0410462
Subset
IM
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