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.
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 9 Feb 00 by JH.