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
  • Database entry query box for gene or list of genes (query history is recorded) (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 displays Gene expression ration data in a blue/yellow heat map of concentric rings, one for each experiment, with all displayed Transcription Factor (TF) genes labeled on outside ring(s) and with hyperbolas connecting to all target genes regulated by each TF
  • Mouse-over on data rings displays Experiment_name, Gene_name, Locus_tag, LogRatio (expression value), Operon, Regulated by, and position on the ring
  • Select Data to choose datasets to be loaded into E-Ring display
    • Select User Data to upload Data file, and/or Regulator file, and/or Gene information file
    • Select OUBCF Data to load local data from lists of Experiments and Experiment sets
  • Select Regulators to display a list of all TF genes in the display, with check boxes to select/deselect TFs and hyperbola connecting lines for display on redraw
  • Select Filter for redrawing display by user defined fold-changes, standard deviation value or expression ratio value by chosen experiment(s)
  • Select Log to display information about the display, including nuber of experiments, genes, and regulatory connections displayed; a list of genes not found in the display, as well as lists of locus tags and synonym calls; and regulators not found in display
  • Select Stats to access popup window display of regulatory information displayed
    • All TFs in display
    • The number of target genes regulated by that TF
      • Click on Number of regulated genes to access popup window displaying blue/yellow heatmap of all genes in operon/regulon and lists of TFs that regulate each gene
    • For each experiment ring, the average log expression ratio value for all target genes in the operon/regulon
    • A list of all other regulators that control genes regulated by that TF
  • A Gene query box accesses a popup window to indicate location of gene(s) on data rings
• 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