Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation.
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.
Neretti
Nicola
N
Institute for Brain and Neural Systems, Brown University, Providence RI, USA. nicola_neretti@brown.edu
Remondini
Daniel
D
Tatar
Marc
M
Sedivy
John M
JM
Pierini
Michela
M
Mazzatti
Dawn
D
Powell
Jonathan
J
Franceschi
Claudio
C
Castellani
Gastrone C
GC
D000222:Adaptation, Physiological / Q000502:physiology*; D003198:Computer Simulation; D015870:Gene Expression / Q000502:physiology*; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D000090063:Proto-Oncogene Mas; D015398:Signal Transduction / Q000502:physiology*; D013223:Statistics as Topic
C000715470:MAS1 protein, human; D020543:Proteome; D000090063:Proto-Oncogene Mas