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

Ari B Kahn12, Michael C Ryan123, Hongfang Liu24, Barry R Zeeberg2, D Curtis Jamison15 and John N Weinstein2*

Author Affiliations

1 Department of Bioinformatics, George Mason University, Fairfax, Virginia, USA

2 Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA

3 Tiger Team Consulting, Fairfax, VA, USA

4 Georgetown University, Washington, DC, USA

5 School of Informatics, Northern Kentucky University, Highland Heights, KY, USA

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BMC Bioinformatics 2007, 8:75  doi:10.1186/1471-2105-8-75

Published: 5 March 2007

Abstract

Background

There 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.

Description

SpliceMiner 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.

Conclusion

EVDB 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 webcite). 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.