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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
- Our K-12 annotation database holds information from all 5 of the listed sources and is unique in combining genetic network information with gene function and biological process information.
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

Browsing

Searching

Display Interfaces

Database-wide heatmap display of gene(s)-specific queries; user defined blue/yellow or red/green color scheme; user defined wrap or no wrap of heatmap output (http://chase.ou.edu/oubcf/ecoli/searchlink.php?query="gene_name or b_number or synonym)
- Mouse-over reveals Gene expression ratio value, Experiment set and Experiment
- One-click access from DB-wide heatmap to experiment-specific data in graphic display or overlay on E. coli metabolic pathway chart
- Graphic display of gene expression ratio vs. genome location (http://chase.ou.edu/oubcf/ecoli/searchlink.php?clr=1&dly=0&wrp=1&plt=1&esid=21&eid=193&query="gene_name or b_number#ShowGraph")
  - Mouse-over on graph shows gene name and gene expression ratio value
  - One-click on graph-data point returns DB-wide heatmap query for for any gene in graphic display
  - User defined significance values shown on graph
  - Genome browser line shows genome location and neighboring genes (clickable for DB-wide heatmap query)
  - Annotation line shows information in local annotation database for queried gene(s)
  - Select information from local annotation database and metalinks to external sites listed below
- Display of gene expression ratio values in Omics Viewer (Biocyc Pathway Tools 9.0 running locally) (http://chase.ou.edu/ouma/omics/"filename".html
Browse Experiment sets
- Select experiment information to access tab-delimited data
- Select experiment design and publication information
- Select graphic display of experiment set data; user defined graphic display options including...
- Select heatmap display of experiment set data
- Select hierarchical cluster of data in heatmap display
- Select Expression Ring display of selected experiments or experiment sets

Usage examples

Technology

Web Services/API

Discussion

Trackbacks

What are trackbacks? This feature is not yet functional

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

Discussion of GenExpDB on other websites