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George M. Church Laboratory

mRNA Abundance Home Page

Welcome to the new and (as usual) evolving Church Lab home page for whole genome mRNA abundance studies. 

The purpose of this page is to share the mRNA abundance data that our lab has generated, as well as software tools for data analysis. 

At present, this site contains only data and tools developed in the context of a recent article: 
Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences Clustered by Whole-Genome mRNA Quantitation, Roth, F.R., Hughes, J. D., Estep, P. E. & G.M. Church, Nature Biotechnology 1998 
This article describes a method for discovery of DNA motifs which regulate gene transcription, using mRNA abundance data and a computer.  This approach does not require prior information about transcription factors or their binding sites. 

Briefly the approach is: 

  • Choose a set of genes which are similar in their pattern of expression, based on large scale mRNA abundance measurements 
  • Collect the 5' non-coding sequence of this set of genes.
  • Apply an algorithm which finds conserved elements in unaligned nucleic acid sequence
  • Score each motif (a motif is defined by a set of conserved DNA elements) by the 'goodness' of alignment
  • Score each motif by its frequency of occurrence in non-coding dequences of an entire genome
The method was applied to a set of four whole-genome scale mRNA abundance experiments in the yeast Saccharomyces cerevisiae, using Affymetrix DNA microarrays. 

The data from these four experiments can be found here

Protocols used in these experiments can be found here

AlignACE software, which Aligns Nucleic Acid Conserved Elements, as well as other software for analysis of mRNA data, can be found here 

Please direct any questions or comments to Jason Hughes or Fritz Roth
This page was last modified 3 Oct 98 by FR.