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).
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 EPConDB EPConDB is an index of genes expressed in endocrine pancreas. Expression is defined either through microarray experiments or sequence annotation.
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: 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 cDNA 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. UCSC BLAT CAP4 assembly EST expression profile predicted protein
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: http://plasmodb.org/
Select Text Search from the PlasmoDB 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 mRNA and protein predictions
EPConDB query: "Which DOTS assemblies (RNA) represented on the Endocrine Pancreas Consortium’s chip 2.0 are constituents of the insulin initiated signal transduction pathway ?" http://www.cbil.upenn.edu/EPConDB
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 mRNA - 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 Sangerhttp://www.sanger.ac.uk/Projects/P_falciparum TIRG/NMRChttp://www.tigr.org/tdb/edb2/pfal/htmls Stanfordhttp://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. 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):300-308 3. The GUS schema is available at http://www.allgenes.org/cgi-bin/schemaBrowser.pl 4.The RAD schema is available at http://www.cbil.upenn.edu/cgi-bin/RAD2/schemaBrowserRAD.pl
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 56947 and 56954 with cosponsorship from the JDFI. allgenes .org Funding for allgenes.org is provided by NIH grant RO1-HG-01539-03 and DOE grant DE-FG02-00ER62893
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. 2002 30: 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. 512-531. 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: 1997-2004, 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. 1 66-69