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rdf:type |
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lifeskim:mentions |
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pubmed:dateCreated |
2007-4-13
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pubmed:abstractText |
Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynamics. In this paper we apply a correlation based approach to network reconstruction to three datasets of time series gene expression following system perturbation: 1) Conditional, Tamoxifen dependent, activation of the cMyc proto-oncogene in rat fibroblast; 2) Genomic response to nutrition changes in D. melanogaster; 3) Patterns of gene activity as a consequence of ageing occurring over a life-span time series (25y-90y) sampled from T-cells of human donors. We show that the three datasets undergo similar transitions from an "uncorrelated" regime to a positively or negatively correlated one that is symptomatic of a shift from a "ground" or "basal" state to a "polarized" state. In addition, we show that a similar transition is conserved at the pathway level, and that this information can be used for the construction of "meta-networks" where it is possible to assess new relations among functionally distant sets of molecular functions.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10077610,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10371154,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10380183,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10391217,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10523523,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10566452,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10592173,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10676951,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10700174,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10783168,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10902182,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-10952317,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-11027309,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-11099258,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-11108481,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-11700590,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-11700594,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-11847076,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-12529326,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-15284096,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-15479708,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-15535868,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-15575966,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-15867157,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-17090700,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-9697172,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-9843569,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17430560-9843981
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:issn |
1471-2105
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:volume |
8 Suppl 1
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
S16
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
pubmed-meshheading:17430560-Adaptation, Physiological,
pubmed-meshheading:17430560-Computer Simulation,
pubmed-meshheading:17430560-Gene Expression,
pubmed-meshheading:17430560-Gene Expression Regulation,
pubmed-meshheading:17430560-Models, Biological,
pubmed-meshheading:17430560-Models, Statistical,
pubmed-meshheading:17430560-Oligonucleotide Array Sequence Analysis,
pubmed-meshheading:17430560-Proteome,
pubmed-meshheading:17430560-Signal Transduction,
pubmed-meshheading:17430560-Statistics as Topic
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pubmed:year |
2007
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pubmed:articleTitle |
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation.
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pubmed:affiliation |
Institute for Brain and Neural Systems, Brown University, Providence RI, USA. nicola_neretti@brown.edu
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pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't,
Research Support, N.I.H., Extramural
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