Dataset Information

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.

ABSTRACT:

Summary

We introduce ProfileChaser, a web server that allows for querying the Gene Expression Omnibus based on genome-wide patterns of differential expression. Using a novel, content-based approach, ProfileChaser retrieves expression profiles that match the differentially regulated transcriptional programs in a user-supplied experiment. This analysis identifies statistical links to similar expression experiments from the vast array of publicly available data on diseases, drugs, phenotypes and other experimental conditions.

Availability

http://profilechaser.stanford.edu

Contact

abutte@stanford.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Engreitz JM

PROVIDER: S-EPMC3223361 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Publications

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.

Engreitz Jesse M JM Chen Rong R Morgan Alexander A AA Dudley Joel T JT Mallelwar Rohan R Butte Atul J AJ

Bioinformatics (Oxford, England) 20111003 23

<h4>Summary</h4>We introduce ProfileChaser, a web server that allows for querying the Gene Expression Omnibus based on genome-wide patterns of differential expression. Using a novel, content-based approach, ProfileChaser retrieves expression profiles that match the differentially regulated transcriptional programs in a user-supplied experiment. This analysis identifies statistical links to similar expression experiments from the vast array of publicly available data on diseases, drugs, phenotype ...[more]

PMID: 21967760

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Project description:BackgroundUnderstanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant.ResultsWe have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database 1 was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability.ConclusionThis new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global studies in citrus by using it to catalogue genes expressed in citrus globular embryos.

Dataset Information

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.

Summary

Availability

Contact

Supplementary information

Publications

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.

Similar Datasets

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