SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysisReport as inadecuate




SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis - Download this document for free, or read online. Document in PDF available to download.

BMC Bioinformatics

, 8:75

First Online: 05 March 2007Received: 03 October 2006Accepted: 05 March 2007

Abstract

BackgroundThere are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and design of new arrays for alternative splicing require assessment of probes at the sequence and exon levels.

DescriptionSpliceMiner is a web interface for querying Evidence Viewer Database EVDB. EVDB is a comprehensive, non-redundant compendium of splice variant data for human genes. We constructed EVDB as a queryable implementation of the NCBI Evidence Viewer EV. EVDB is based on data obtained from NCBI Entrez Gene and EV. The automated EVDB build process uses only complete coding sequences, which may or may not include partial or complete 5- and 3- UTRs, and filters redundant splice variants. Unlike EV, which supports only one-at-a-time queries, SpliceMiner supports high-throughput batch queries and provides results in an easily parsable format. SpliceMiner maps probes to splice variants, effectively delineating the variants identified by a probe.

ConclusionEVDB can be queried by gene symbol, genomic coordinates, or probe sequence via a user-friendly web-based tool we call SpliceMiner http:-discover.nci.nih.gov-spliceminer. The EVDB-SpliceMiner combination provides an interface with human splice variant information and, going beyond the very valuable NCBI Evidence Viewer, supports fluent, high-throughput analysis. Integration of EVDB information into microarray analysis and design pipelines has the potential to improve the analysis and bioinformatic interpretation of gene expression data, for both batch and interactive processing. For example, whenever a gene expression value is recognized as important or appears anomalous in a microarray experiment, the interactive mode of SpliceMiner can be used quickly and easily to check for possible splice variant issues.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-8-75 contains supplementary material, which is available to authorized users.

Ari B Kahn, Michael C Ryan contributed equally to this work.

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Author: Ari B Kahn - Michael C Ryan - Hongfang Liu - Barry R Zeeberg - D Curtis Jamison - John N Weinstein

Source: https://link.springer.com/







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