DOE Human Genome Program Contractor-Grantee Workshop
125. The DOTS Resource for Gene Expression Analysis and Genome Annotation
Chris Overton, Brian Brunk, Jonathan
Crabtree, Philip Le, and Jules Milgram
We have created a linking database that integrates a wide range of high quality, carefully analyzed information on eukaryotic transcribed sequences. This new resource, termed DOTS (Database of Transcribed Sequences, builds upon and substantially expands previous work on creating LENS, a database linking information on ESTs generated in the IMAGE/WashU/Merck project ( http://agave.humgen.upenn.edu/lens). The DOTS resource supports gene expression analyses ongoing at Penn and large-scale genome annotation as part of the DOE sponsored Genome Annotation Collaboratory. The central organizing concept of the database is a representation for mature messenger and structural RNAs and their predicted sequences accompanied by links to genomic sequences and proteins, and associated information, e.g., gene expression arrays and gene expression experiments. Construction of DOTS requires ongoing computational analyses to identify putative transcribed sequences as determined from databases of experimentally identified mRNAs, ESTs and genomic sequences. In the long term, however, most of the effort in building and maintaining DOTS involves integration of data from across multiple online resources (and to some extent directly from the scientific literature). For example, DOTS incorporates keywords and functional taxonomies from GenBank, OMIM, SwissProt, and EGAD among others, enabling complex queries such as "Display all transcription factors with a greater than 4-fold difference in mRNA abundance level at day 11 of erythropoiesis in adult and cord blood." The integration process is facilitated through the K2 system, developed at Penn, for integration of information in distributed, heterogenous databases. Presentation of data is through the bioWidgets visualization toolkit also developed Penn.
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