Targeting c-Myc-activated genes with a correlation method: Detection of global changes in large gene expression network dynamics

D. Remondini, B. O'Connell, N. Intrator, J. M. Sedivy, N. Neretti, G. C. Castellani, L. N. Cooper

Research output: Contribution to journalArticlepeer-review

Abstract

This work studies the dynamics of a gene expression time series network. The network, which is obtained from the correlation of gene expressions, exhibits global dynamic properties that emerge after a cell state perturbation. The main features of this network appear to be more robust when compared with those obtained with a network obtained from a linear Markov model. In particular, the network properties strongly depend on the exact time sequence relationships between genes and are destroyed by random temporal data shuffling. We discuss in detail the problem of finding targets of the c-myc protooncogene, which encodes a transcriptional regulator whose inappropriate expression has been correlated with a wide array of malignancies. The data used for network construction are a time series of gene expression, collected by microarray analysis of a rat fibroblast cell line expressing a conditional Myc-estrogen receptor oncoprotein. We show that the correlation-based model can establish a clear relationship between network structure and the cascade of c-myc-activated genes.

Original languageEnglish
Pages (from-to)6902-6906
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume102
Issue number19
DOIs
StatePublished - 10 May 2005

Keywords

  • Complex systems
  • Gene interaction
  • Time series

Fingerprint

Dive into the research topics of 'Targeting c-Myc-activated genes with a correlation method: Detection of global changes in large gene expression network dynamics'. Together they form a unique fingerprint.

Cite this