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

Ari B. Kahn, Michael C. Ryan, Hongfang D Liu, Barry R. Zeeberg, Curtis Jamison, John N. Weinstein

Research output: Contribution to journalArticle

19 Citations (Scopus)

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). 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.

Original languageEnglish (US)
Article number75
JournalBMC Bioinformatics
Volume8
DOIs
StatePublished - Mar 5 2007
Externally publishedYes

Fingerprint

Microarrays
Microarray
High Throughput
Throughput
Databases
Genes
Alternative Splicing
Probe
Microarray Analysis
Gene expression
Gene
Gene Expression
Batch
Evidence
5' Untranslated Regions
Bioelectric potentials
3' Untranslated Regions
Human Genome
Bioinformatics
Computational Biology

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

SpliceMiner : A high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. / Kahn, Ari B.; Ryan, Michael C.; Liu, Hongfang D; Zeeberg, Barry R.; Jamison, Curtis; Weinstein, John N.

In: BMC Bioinformatics, Vol. 8, 75, 05.03.2007.

Research output: Contribution to journalArticle

Kahn, Ari B. ; Ryan, Michael C. ; Liu, Hongfang D ; Zeeberg, Barry R. ; Jamison, Curtis ; Weinstein, John N. / SpliceMiner : A high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. In: BMC Bioinformatics. 2007 ; Vol. 8.
@article{30197f4e7dc443ef831f25394075c6d6,
title = "SpliceMiner: A high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis",
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). 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.",
author = "Kahn, {Ari B.} and Ryan, {Michael C.} and Liu, {Hongfang D} and Zeeberg, {Barry R.} and Curtis Jamison and Weinstein, {John N.}",
year = "2007",
month = "3",
day = "5",
doi = "10.1186/1471-2105-8-75",
language = "English (US)",
volume = "8",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",

}

TY - JOUR

T1 - SpliceMiner

T2 - A high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis

AU - Kahn, Ari B.

AU - Ryan, Michael C.

AU - Liu, Hongfang D

AU - Zeeberg, Barry R.

AU - Jamison, Curtis

AU - Weinstein, John N.

PY - 2007/3/5

Y1 - 2007/3/5

N2 - 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). 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.

AB - 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). 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.

UR - http://www.scopus.com/inward/record.url?scp=34047187150&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34047187150&partnerID=8YFLogxK

U2 - 10.1186/1471-2105-8-75

DO - 10.1186/1471-2105-8-75

M3 - Article

C2 - 17338820

AN - SCOPUS:34047187150

VL - 8

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

M1 - 75

ER -