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Abstract Detail

Genomics / Proteomics

Russell, Scott D. [1].

RiceChip: Annotational Support for Rice (Oryza sativa) Microarray Analysis.

RiceChip is a database that integrates TIGR/MSU and IRGSP (International Rice Genome Sequencing Project) annotations with expressional data. The site uses the widely adopted Affymetrix 57K Rice Genome GeneChip®, providing 57,381 experimental and control probe sets using multiple 25-mer oligonucleotides that cover most of the genome. This site reports all 25-mer exact probe matches to the available pseudochromosomes TIGR pseudochromosomes (version 5, which represents 56,278 loci and 66,710 folding models), integrated with authoritative annotational and expressional databases, providing a single source of data for profiling and data mining. A lexicon of all annotational headers assigned to genes is a good starting point for assessing coverage; this is indexed with number of matching loci and probes, number of TIGR/MSU loci and folding models proposed. Linkouts to other databases are available through these links and separate search capabilities. A probe set search portal includes data on all matching loci and folding models, tBLASTx matches for the rice and Arabidopsis genomes, and expressional data from the NCBI GEO database, generating dynamic bar charts including a mouseover feature that provides experimental data, intensity, reference files and signal intensity. Data on probe matches provide information on coding sequences, UTRs, introns, cDNAs and intergenic regions, so the nature of matches and potential mismatches are clearly documented. A gene locus/model/protein database includes such characteristics such as annotated description, ESTs, Pfams, Interpros, GO (Gene Ontology) codes, predicted signal peptides, transmembrane domains, subcellular targets, nucleic acid constitution, matching probes and probe sets, and Arabidopsis TAIR8 best homolog (with similar descriptions, chromosome location, Pfams, Interpros, ESTs, GO codes, percent match, ratio of identically matched amino acids, and length) and a link to alignments, MSU and Gramene genome browsers and to MPSS as well, which can be used to conveniently corroborate transcript and tissue prevalence information.

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Related Links:
RiceChip Database

1 - University of Oklahoma, Department of Botany and Microbiology, Norman, OK, 73019, USA

microarray analysis
Oryza sativa
transcript profiling
data integration
genome tools

Presentation Type: Poster:Posters for Topics
Session: P1
Location: Event Tent/Cliff Lodge
Date: Monday, July 27th, 2009
Time: 5:30 PM
Number: P1GP001
Abstract ID:930