Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription

Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16577-82. doi: 10.1073/pnas.0406767101. Epub 2004 Nov 15.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Cell Cycle
  • DNA Replication / genetics*
  • DNA, Fungal / biosynthesis
  • DNA, Fungal / genetics
  • Databases, Genetic
  • Genome, Fungal*
  • Least-Squares Analysis
  • Mathematics
  • Models, Genetic*
  • Protein Binding
  • RNA, Fungal / genetics*
  • RNA, Messenger / genetics
  • Saccharomyces cerevisiae / cytology
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transcription, Genetic

Substances

  • DNA, Fungal
  • RNA, Fungal
  • RNA, Messenger
  • Saccharomyces cerevisiae Proteins