Abstract:
: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.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Neretti N,Remondini D,Tatar M,Sedivy JM,Pierini M,Mazzatti D,Powell J,Franceschi C,Castellani GCdoi
10.1186/1471-2105-8-S1-S16subject
Has Abstractpub_date
2007-03-08 00:00:00pages
S16issn
1471-2105pii
1471-2105-8-S1-S16journal_volume
8 Suppl 1pub_type
杂志文章abstract:BACKGROUND:As whole-genome sequencing is becoming a routine technique, it is important to identify a cost-effective depth of sequencing for such studies. However, the relationship between sequencing depth and biological results from the aspects of whole-genome coverage, variant discovery power and the quality of varian...
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pub_type: 杂志文章
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更新日期:2019-11-08 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2016-09-05 00:00:00
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2014-12-14 00:00:00
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2017-01-05 00:00:00
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pub_type: 杂志文章
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更新日期:2004-07-26 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2013-11-14 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2014-10-24 00:00:00
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更新日期:2014-06-11 00:00:00
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2009-04-03 00:00:00
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