E Coli Expression2

Published E. coli Microarray-based Gene Expression Data

The MS Excel file below contains 213 normalized Affymetrix microarray gene expression profiles from several published studies conducted in the Palsson Lab, and summarized in Lewis, et al. (J. Bact., 2009, PMID:19363119):

Published Data - current as of 12.14.08

The "ArrayInfo" worksheet contains sample and environmental information for each profile. The "GenExpVal" worksheet contains the log base 2 transformed normalized data. In the latter worksheet, individual probesets are represented in each row, and each column corresponds to a single expression profile as specified in the top header row.

Normalization Specifications

  • Normalization method / Software: GCRMA / Bioconductor

  • CDF File: Ecoli_ASv2.CDF

  • Microarrays: Affymetrix E. coli Antisense Genome Array

Study Descriptions

Briefly, in Covert et al. (Nature, 2004, PMID:15129285), gene expression data was used to infer regulatory interactions associated with E. coli's response to oxygen availability. Fong et al. (Genome Research, 2005, PMID:16204189) assessed genome-wide transcriptional changes associated with adaptive evolution of E. coli to growth on glycerol- and lactate-supplemented minimal medium. Finally, Fong et al. (2006, J. Biol. Chem., PMID:16319065) sought to identify gene expression changes associated with metabolic flux re-routing following adaptive evolution of E. coli strains following single gene deletions of central metabolic genes. Information on additional datasets can be found in the excel data file above and in the the MIAME worksheets here.


Contact Nathan Lewis at n1lewis@ucsd.dt.edu.