GUS We have created the Genomic Unified Schema

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. Userfriendly 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 #146 A for details of the Genomics Unified Schema (GUS).

GUS Supports Multiple Projects All. Genes Allgenes is based on a comprehensive mouse and human gene index. The genes are approximated by transcripts predicted from EST and m. RNA clustering Plasmo. DB 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 EPCon. DB is an index of genes expressed in endocrine pancreas. Expression is defined either through microarray experiments or sequence annotation.

allgenes. org query "Is my c. DNA 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 • RHMap • GOFunction • Sequence Data Analysis Tools • GOFunction assigments • Boolean function • History function • BLAST http: //www. allgenes. org/

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

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

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

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

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

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 CAP 4 assembly EST expression profile UCSC BLAT

Plasmo. DB 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 • Predicted genome translation • Microarray expression Data Analysis • Spot intensity http: //plasmodb. org/ Tools • History function

Select Text Search from the Plasmo. DB homepage Choose signal peptide

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

Choose gene expression-microarray from the homepage Then choose an experiment, chromosome, and Gene/prediction type submit There are 12170 gene predictions that satisfy this query

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

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

EPCon. DB query: "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 • Sequence • Microarray experiment • Transduction pathway Data Analysis • BLAST Tools • History function http: //www. cbil. upenn. edu/EPCon. DB

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

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

Return to the gene information query page and select clones sets. Choose chip 2. 0 - submit There are 3242 assemblies represented on chip 2

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.

Acknowledgements and References The Plasmodium Genome Consortium Sanger http: //www. sanger. ac. uk/Projects/P_falciparum TIRG/NMRC http: //www. tigr. org/tdb/edb 2/pfal/htmls Stanford http: //sequence-www. stanford. edu/group/malaria/ 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. K 2/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): 300 -308 3. The GUS schema is available at http: //www. allgenes. org/cgi-bin/schema. Browser. pl 4. The RAD schema is available at http: //www. cbil. upenn. edu/cgi-bin/RAD 2/schema. Browser. RAD. pl

Acknowledgements Funding: National Institutes of Health, Wellcome Trust, US Dep’t of Defense, Burroughs Wellcome Fund, World Health Organization, etc EPCon. DB is part of the NIDDK-sponsored consortium on "Functional Genomics of the Developing Endocrine Pancreas". We gratefully acknowledge support through NIDDK 56947 and 56954 with cosponsorship from the JDFI. allgenes. org Funding for allgenes. org is provided by NIH grant RO 1 -HG 01539 -03 and DOE grant DE-FG 02 -00 ER 62893

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. , Mc. Weeney, S. K. , Milgram, A. J. , Roos, D. S. , Schug, J. , Stoeckert, C. J. (2002) Plasmo. DB: 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. 2002 30: 87 -90 Davidson, S. B. , Crabtree, J. , Brunk, Brian P. , Schug, J. , Tannen, V. , Overton, G. C. , Stoeckert, C. J. Jr. (2001) K 2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources. IBM Systems Journal: 40(2), p. 512 -531. Scearce, L. Marie, Brestelli, John E. , Mc. Weeney, 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 Panc. Chip, New Resources for Diabetes Research Diabetes 51: 1997 -2004, 2002. The Plasmodium Genome Database Collaborative (2001) Plasmo. DB: 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. 1 66 -69