A dynamic network of transcription in LPS-treated human subjects

Junhee Seok, Wenzhong Xiao, Lyle L. Moldawer, Ronald W. Davis, Markus W. Covert

Research output: Contribution to journalArticlepeer-review

36 Citations (Scopus)


Background: Understanding the transcriptional regulatory networks that map out the coordinated dynamic responses of signaling proteins, transcription factors and target genes over time would represent a significant advance in the application of genome wide expression analysis. The primary challenge is monitoring transcription factor activities over time, which is not yet available at the large scale. Instead, there have been several developments to estimate activities computationally. For example, Network Component Analysis (NCA) is an approach that can predict transcription factor activities over time as well as the relative regulatory influence of factors on each target gene. Results: In this study, we analyzed a gene expression data set inblood leukocytes from human subjects administered with lipopolysaccharide (LPS), a prototypical inflammatory challenge, in the context of a reconstructed regulatory network including 10 transcription factors, 99 target genes and 149 regulatory interactions. We found that the computationally estimated activities were well correlated to their coordinated action. Furthermore, we found that clustering the genes in the context of regulatory influences greatly facilitated interpretation of the expression data, as clusters of gene expression corresponded to the activity of specific factors or more interestingly, factor combinations which suggest coordinated regulation of gene expression. The resulting clusters were therefore more biologically meaningful, and also led to identification of additional genes under the same regulation. Conclusion: Using NCA, we were able to build a network that accounted for between 8-11% genes in the known transcriptional response to LPS in humans. The dynamic network illustrated changes of transcription factor 0activities and gene expressions as well as interactions of signaling proteins, transcription factors and target genes.

Original languageEnglish
Article number78
JournalBMC Systems Biology
Publication statusPublished - 2009 Jul 28
Externally publishedYes

Bibliographical note

Funding Information:
This work was funded by the NIH through the Inflammation and the Host Response to Injury research project (U54-GM62119), as well as a K99/R00 award to MWC (CA125994-01A1). We thank Jonathan Karr and Robert Winfield for critical reading of the manuscript. The following is a list of participating investigators of the Inflammation and the Host Response to Injury research project: Henry V. Baker, Ulysses GJ. Balis, Paul E. Bankey, Timothy R. Billiar, Bernard H. Brownstein, Steven E. Calvano, David G. Camp II, Irshad H. Chaudry, J. Perren Cobb, Joseph Cuschieri, Ronald W. Davis, Asit K. De, Celeste C. Finnerty, Bradley Freeman, Richard L. Gamelli, Nicole S. Gibran, Brian G. Harbrecht, Douglas L. Hayden, Laura Hennessy, David N. Herndon, Marc G. Jeschke, Jeffrey L. Johnson, Matthew B. Klein, James A. Lederer, Stephen F. Lowry, Ronald V. Maier, John A. Mannick, Philip H. Mason, Grace P. McDonald-Smith, Carol L. Miller-Graziano, Michael N. Mindrinos, Joseph P. Minei, Lyle L. Moldawer, Ernest E. Moore, Avery B. Nathens, Grant E. O’Keefe, Laurence G. Rahme, Daniel G. Remick, David A. Schoenfeld, Michael B. Shapiro, Geoffrey M. Silver, Richard D. Smith, John D. Storey, Robert Tibshirani, Ronald G. Tompkins, Mehmet Toner, H. Shaw Warren, Michael A. West, Rebbecca P. Wilson, Wenzhong Xiao.

ASJC Scopus subject areas

  • Structural Biology
  • Modelling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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