1. GUS
We have created the Genomic Unified Schema (GUS), a relational database that warehouses and integrates biological sequence, sequence annotation, and gene expression data from a large number of heterogeneous sources. User-friendly web interfaces present slices of the GUS database and allow researchers to execute structured queries for information concerning gene structure, function, and expression.
Please visit poster #146A for details of the Genomics Unified Schema (GUS).

2. GUS Supports Multiple Projects
AllGenes
Allgenes is based on a comprehensive mouse and human gene index. The genes are approximated by transcripts predicted from EST and mRNA clustering
PlasmoDB
PlasmoDB is the official database of the Plasmodium falciparum genome project which provides an integrated view of genome sequence data including expression data from EST, SAGE, and microarray projects
Now implementing these websites.
Add ones to come on-line ‘soon’.
Could also go as slide 2 to emphasize range of applications.
DB box gives away some of the guts before they’ve been explained.
EPConDB
EPConDB is an index of genes expressed in endocrine pancreas. Expression is defined either through microarray experiments or sequence annotation.

3. allgenes.org query
"Is my cDNA similar to any mouse genes that are predicted to encode transcription factors and have been localized to mouse chromosome 5?"
This query illustrates several aspects of the GUS database including:
Data Integration
Data Analysis
Tools
RHMap
GOFunction
Sequence
GOFunction assigments
Boolean function
History function
BLAST

4. Select the allgenes.org boolean query page
Click on the "AND" button

5. Choose the RH map and GO function queries
Select mouse chromosome 5 and "transcription factor"

6. There are 22 mouse RNAs (assemblies) that meet these criteria:
This query result set now appears on the query "history" page:

7. Now use the BLAST page to identify RNAs similar to my cDNA
The results of the BLAST search appear in the query history

8. Intersect ("AND") the BLAST search with the previous query:
And we have our answer (the third row on the query history page):

9. Mapping information Protein/motif hits Gene trap insertions, etc.
Other transcripts from
the same gene
Predicted GO function(s)
(some manually reviewed)
External links
Mapping information
Protein/motif hits
Gene trap insertions,
etc.
predicted protein
CAP4 assembly
EST expression profile
UCSC BLAT

10. PlasmoDB query:
"List all genes whose proteins are predicted to contain a signal peptide and for which there is evidence that they are expressed in Plasmodium falciparum's late schizont stage."
This query illustrates several aspects of the GUS database including:
Data Integration
Data Analysis
Tools
Predicted genome translation
Microarray expression
Spot intensity
History function

11. Select Text Search from the PlasmoDB homepage
Choose signal peptide

12. Choose chromosome and Gene/prediction type-submit
There are 1952 genes with predicted signal peptides

13. Choose gene expression-microarray from the homepage
Then choose an experiment, chromosome, and Gene/prediction type - submit
There are gene predictions that satisfy this query

14. Go to the history page and choose which simple queries to combine
Go to the history page and choose which simple queries to combine. Select intersect.
We have an answer. There are 949 predicted genes that satisfy our complex query
Click on a gene to get a full report

15. There is a variety of information available from the report page including:
Gene models predicted using a variety of approaches
and mRNA and protein predictions

16. EPConDB query: http://www.cbil.upenn.edu/EPConDB Data Analysis Tools
"Which DOTS assemblies (RNA) represented on the Endocrine Pancreas Consortium’s chip 2.0 are constituents of the insulin initiated signal transduction pathway ?"
Data Integration
Data Analysis
Tools
Sequence
Microarray experiment
Transduction pathway
BLAST
History function

18. Go to the gene information query page and click on “DOTS assemblies involved in a pathway”

19. Choose the insulin pathway, a p-value, pancreas, the species, and whether an assembly must include an mRNA - submit
There are 59 dots assemblies that are constituents of the insulin pathway

20. Return to the gene information query page and select clones sets
Return to the gene information query page and select clones sets. Choose chip submit
There are 3242 assemblies represented on chip 2

21. Go to the history page, select the queries to combine and select intersect – view the results
There are 8 assemblies that satisfy the complex query. Clicking on an RNA retrieves an allgenes report.

23. Acknowledgements and References
The Plasmodium Genome Consortium
Sanger
TIRG/NMRC
Stanford
The many researchers who have contributed data and software to the database
Funding Agencies
National Institutes of Health, Wellcome Trust, US Dep’t of Defense,
Burroughs Wellcome Fund, World Health Organization, etc
The research community who has supported these large-scale ventures for the benefit of all
References
1. K2/Kleisli and GUS: Experiments in integrated access to genomic data sources (2001) Davidson, S.B., J. Crabtree, B.P. Brunk, J. Schug, V.Tannen, G.C. Overton and C.J. Stoeckert, Jr. IBM Systems Journal 40(2):1-20
2. A relational schema for both array-based and SAGE gene expression experiments (2001) Stoeckert, C., A. Pizarro, E. Manduchi, M. Gibson, B. Brunk, J. Crabtree, J. Schug, S. Shen-Orr and G.C. Overton. Bioinformatics 17(4):
3. The GUS schema is available at
4.The RAD schema is available at

25. Acknowledgements Funding:
National Institutes of Health, Wellcome Trust, US Dep’t of Defense,
Burroughs Wellcome Fund, World Health Organization, etc
EPConDB is part of the NIDDK-sponsored consortium on "Functional Genomics of the Developing Endocrine Pancreas". We gratefully acknowledge support through NIDDK and with cosponsorship from the JDFI.
allgenes
.org
Funding for allgenes.org is provided by NIH grant RO1-HG and DOE grant DE-FG02-00ER62893

26. References
Bahl, A., Brunk, B., Coppel, R.L., Crabtree, J., Diskin, S.J., Fraunholz, M.J., Grant, G.R., Gupta, D., Huestis, R.L., Kissinger, J.C., Labo, P., Li, L., McWeeney, S.K., Milgram, A.J., Roos, D.S., Schug, J., Stoeckert, C.J. (2002) PlasmoDB: The Plasmodium Genome Resource. An integrated database providing tools for accessing and analyzing mapping, expression and sequence data (both finished and unfinished). Nucleic Acids Res : 87-90
Davidson, S.B., Crabtree, J., Brunk, Brian P., Schug, J., Tannen, V., Overton, G.C., Stoeckert, C.J. Jr. (2001) K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources. IBM Systems Journal: 40(2), p
Scearce, L. Marie, Brestelli, John E., McWeeney, Shannon K., Lee, Catherine S., Mazzarelli, Joan, Pinney, Deborah F., Pizarro, Angel, Stoeckert, C. J. Jr., Clifton, Sandra, Permutt, M. Alan, Brown, Juliana, Melton, Douglas A., Kaestner, Klaus H. (2002) Functional Genomics of the Endocrine Pancreas: The Pancreas Clone Set and PancChip, New Resources for Diabetes Research Diabetes 51: , 2002.
The Plasmodium Genome Database Collaborative (2001) PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. Nucleic Acids Res., 2001, Vol. 29, No