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.
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation / Neretti N; Remondini D; Tatar M; Sedivy JM; Pierini M; Mazzatti D; Powell J; Franceschi C; Castellani GC.. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - ELETTRONICO. - 8:(2007), pp. 1-14. [10.1186/1471-2105-8-S1-S16]
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation.
REMONDINI, DANIEL;PIERINI, MICHELA;FRANCESCHI, CLAUDIO;CASTELLANI, GASTONE
2007
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.