GenExpDB

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GenExpDB
Who:	Tyrrell Conway, OU
What:	E. coli Gene Expression Database
Where:	GenExpDB
Updates	Incremental, as site is modified with data and applications
Upcoming events	link to event calendar, if applicable
Web Services

About GenExpDB

The University of Oklahoma Bioinformatics Core hosts the E. coli Gene Expression Database. EcoliGenExpDB was designed from the biologist’s perspective, with a tool box-style, integrated and interactive display interface and a simplified warehouse architecture, for analyzing a large and growing body of over 1200 multiplatform microarray experiments (currently 132 public) and 450 mouse intestinal colonization assays (curently 23 public) for the model organism Escherichia coli.

Content

Microarray Data

• Membrane (Macro) Array data sets generated on Sigma-GenoSys Ecoli Panorama arrays
• Microarray data generated on glass slides printed with Operon, Inc. E. coli ver. 1.0 oligonucleotide probe set
• Affymetrix data generated on custom E. coli GeneChip designed by Conway Laboratory group
• Affymetrix data generated on commercial E. coli GeneChip

Mouse intestinal colonization data

• Generated by the Conway laboratory at OU and Paul Cohen's laboratory at the University of Rhode Island

E. coli Annotations

• ECOLI_K-12: MG1655: NC_000913.2 GI:49175990
• ECOLI_K-12: MG1655: U00096.2 GI:48994873
• ECOLI_K-12: MG1655: K12_SnapShot
• ECOLI_K-12: MG1655: RegulonDB TF-gene interactions file (http://regulondb.ccg.unam.mx/data/NetWorkSet.txt)
• ECOLI_K-12: W3110: AP009048.1 GI:85674274
• ECOLI_042: OUBCF action: Blasted file EC042.art against K12 MG1655 to get gene name
• ECOLI_CFT073: NC_004431.1 GI:26245917
• ECOLI_EDL933: NC_002655.2 GI:16445223
• ECOLI_HS: NZ_AAJY01000001.1 GI:75194227

Using GenExpDB

Usage examples

Add links to additional pages describing success stories here.

Discussion

Trackbacks

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References

A DB-specific article has not yet been published.
Several papers published by the Conway laboratory reference data on EcoliGenExpDB, including:

• Traxler, M. F., D.-E. Chang, and T. Conway. 2006. Guanosine 5’,3’-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli. Proc. Nat. Acad. Sci. 103: 2374-2379.
  
• Chang, D.E., D. Smalley, D. L. Tucker, M. P. Leatham, W. E. Norris, S. J. Stevenson, A. B. Anderson, J. E. Grissom, D. C. Laux, P. S. Cohen, and T. Conway. Carbon nutrition of Escherichia coli in the mouse intestine. 2004. Proc. Nat. Acad. Sci. 101: 7427–7432.

External Links

GenExpDB

Metalinks from external sites to microarray data at EcoliGenExpDB

Using syntax http://chase.ou.edu/oubcf/ecoli/searchlink.php?bnum="b_number"

• EcoCyc
• EcoGene
• RegulonDB

Links out

• ASAP
• ColiBase
• Colibri
• EchoBase
• EcoCyc
• EcoGene
• GenoBase
• KEGG
• NCBI
• RegulonDB
• SwissProt