1. EPConDB: Endocrine Pancreas Consortium Database
A web resource of the Beta Cell Biology Consortium
Concepts and data used in the web site
Overview of web site pages
Using EPConDB
Four Query Examples
Going over

2. Other Microarray Platforms
Data In EPConDB
PancChips &
Other Microarray Platforms
mRNA
Expression
Studies
DoTS
transcripts
(mRNA + EST
Transcript
Assemblies)
TF binding sites
Data in EPConDB consists of relating the transcripts on expression arrays to results from expression studies performed using these arrays
Also relationships between transcripts/genes with transcription factor binding sites to identify transcription factor target genes
Overall, relating transcription factor target genes and their expression
Promoter Chip
TF Target genes

3. EPConDB is transcript based and uses DoTS transcripts (DTs)
A DoTS Transcript or DT is a consensus sequence generated using ESTs and mRNAs
EST + mRNA Assembly
Example FoxA2 transcript
Assembly alignment view
DT sequence

4. For each gene, e.g., foxA2, there maybe more than one DoTS transcript,
possibly representing alternative forms (Genome Browser alignments) *
There maybe more than one FoxA2 DoTS transcript since alternative transcripts are possible.
Shows additional FoXA2 exon
DoTS provides a snap shot of the transcriptional activity at a gene locus

5. Integrated Websites BCBC EPConDB T1DBase
EPConDB is integrated with other web sites, can get to EPConDB from BCBC and T1DBAse web sites
Reciprocal links with both web sites
Antibody reagent links with BCBC
Common gene page with T1DBase and EPConDB uses GBrowse

6. Overview of EPConDB pages
EPConDB Home Page
Navigation Bar
Has links to EPConDB pages
What is on Chips?
Queries to quickly find transcripts genes and those associated with Chips
Home Page Queries to quickly find transcripts genes and those associated with Chips
Navigation Bar has links to other EPConDB web pages
What’s New
Items about new EPConDB features

7. Navigation Bar (NavBar)
Has links to all different kinds of pages
Chips
Downloads
BLAST
Query Transcripts
Experiments
Analysis
Help
Can try to go though these pages live before exercises
Headings on Query transcript page (all available queries) favor of queries available

8. Query #1 “Find a Particular Gene”
Use Query on Home Page
Insert gene name/symbol into gene name text search box, e.g, Foxa2
Click Search
Result is list of DTs associated with name
Choose or click on mouse Foxa2 transcript DT to get RNA Page

9. RNA Page Items on RNA Page and Other RNA View Links (examples)
Highlight particular info
Gene
Expression profile
GBrowse (which we saw before)

10. Detailed Views
Gene
ExpressionProfile

11. Query # 2 “Find a list of transcripts with down-regulated expression when FoxA2 is deleted”
Goto Query Transcripts Page (use NavBar!)
Select Down-Regulated Expression
Click on “Submit” on Query Form
Have option to change parameters but for now use defaults
Query Form

12. Result Page: 15 transcripts with Down regulated Expression
Click on the My Transcripts button to view query History
Query Results
are saved in your
Query History

13. Query # 3
“Find transcripts expressed in the islet with IPF1 (PDX1) sites in their promoters”
uses intersection of two query result sets
Goto Query Transcripts Page
Click on Predicted Transcription Factor Target Genes
Choose IPF1
Click Submit
Result Set

14. Query # 3 - continued * Go to the Query Transcript Page again
Click on the Down regulated Expression query
choose a different study from list, Affymetrix MOE430v2 vs Mouse PancChip 5.0 comparison
Click Submit *

15. From Result Page for Down Regulated Expression Query, Click on My Transcripts Button
Check
boxes
Click Intersect
Intersection Result
Click on view
to see Result Page

16. Query # 4 “Find genes with a gata6 and FoxA2 site within 300 base pairs of one another
in a promoter region”
Binding Site Collection Query
Select Analysis Link
Click on Submit Binding Site Collection Query
Form allows searching for TF binding sites (single or multiple) that are found upstream of transcript genomic alignments
Select TF from pull down list of TFs or user defined
Can take 15 minutes to an hour to run analysis so look at previously run query and results
An Example Search
Go to home page
Under What’s new, click on FORM link
Example form already filled in
Click on RESULTS (page generated is Tabular Results)
Add Results to History (to find how many of these genes are expressed in islet)
Perform intersection with transcripts expressed in islet (should already be in your query history)
How many genes do you get from intersection?
Use this tf binding site model to search for a particular binding site
User (add your own binding site) consensus for binding site, distance constraints

17. *