If you need an accessible version of this item please contact JSTOR User Support

Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation between DNA Replication and RNA Transcription

Orly Alter and Gene H. Golub
Proceedings of the National Academy of Sciences of the United States of America
Vol. 101, No. 47 (Nov. 23, 2004), pp. 16577-16582
Stable URL: http://www.jstor.org/stable/3373867
Page Count: 6
  • Download PDF
  • Cite this Item

You are not currently logged in.

Access your personal account or get JSTOR access through your library or other institution:

login

Log in to your personal account or through your institution.

If you need an accessible version of this item please contact JSTOR User Support
Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation between DNA Replication and RNA Transcription
Preview not available

Abstract

We describe an integrative data-driven mathematical framework that formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the "basis" set. By using pseudoinverse projection, the molecular biological profiles of the data samples are least-squares-approximated as superpositions of the basis profiles. Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis and gives a global picture of the correlations and possibly also causal coordination of these two sets of states. We illustrate this framework with an integration of yeast genome-scale proteins' DNA-binding data with cell cycle mRNA expression time course data. Novel correlation between DNA replication initiation and RNA transcription during the yeast cell cycle, which might be due to a previously unknown mechanism of regulation, is predicted.

Page Thumbnails

  • Thumbnail: Page 
[16577]
    [16577]
  • Thumbnail: Page 
16578
    16578
  • Thumbnail: Page 
16579
    16579
  • Thumbnail: Page 
16580
    16580
  • Thumbnail: Page 
16581
    16581
  • Thumbnail: Page 
16582
    16582