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 Annotation Data

• 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

Display Interfaces

• Database-wide heatmap display
  • Gene or list of genes queried from primary query box (records query history) (http://chase.ou.edu/oubcf/ecoli/searchlink.php?query="gene_name or b_number or synonym)
    • User defined blue/yellow or red/green color scheme
    • User defined wrap or no wrap of heatmap output
  • Mouse-over on DB-wide heatmap reveals Gene expression ratio value, Experiment set, and Experiment
  • One-click access from DB-wide heatmap to graphic display of individual experiment data: 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 executes DB-wide heatmap query for for any gene in graphic display
    • User defined significance values shown on graph
    • Displays lists of up-regulated and down-regulated genes
  • One-click access from DB-wide heatmap to overlay on E. coli metabolic pathway chart in Omics Viewer (Biocyc Pathway Tools 9.0 running locally) (http://chase.ou.edu/ouma/omics/"filename".html
  • 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
    • Select metalinks to external sites listed below
    • Select gene-specific query of Mouse Colonization Data
• Expression Ring display

• Browse Experiment sets
  • Select Experiment to access tab-delimited data and array information
  • Select Cluster to display hierarchical clustered data in heatmap
  • Select Heatmap tp display experiment set data ordered by genome location
  • Select Genome to display experiment set data in concentric rings for each time point
  • Select Time Series for graphic display of experiment set data (optimized for time series data)
    • User defined display of genes selected from lists (soon to include operons, regulons, biological processes)
    • User defined selection of experiments to be displayed from experiments set
  • Select Experiment Design for biological protocols and publication information

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

Links out

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