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Article: Finding alternative splicing patterns with strong support from expressed sequences on individual exons/introns

TitleFinding alternative splicing patterns with strong support from expressed sequences on individual exons/introns
Authors
KeywordsAlternative splicing pattern
ESTs
Expressed sequences
Issue Date2008
PublisherImperial College Press. The Journal's web site is located at http://www.worldscinet.com/jbcb/jbcb.shtml
Citation
Journal Of Bioinformatics And Computational Biology, 2008, v. 6 n. 5, p. 1021-1033 How to Cite?
AbstractWe consider the problem of predicting alternative splicing patterns from a set of expressed sequences (cDNAs and ESTs). Some of these expressed sequences may be errorous, thus forming incorrect exons/introns. These incorrect exons/introns may cause a lot of false positives. For example, we examined a popular alternative splicing database, ECgene, which predicts alternate splicing patterns from expressed sequences. The result shows that about 81.3%-81.6% (sensitivity) of known patterns are found, but the specificity can be as low as 5.9%. Based on the idea that errorous sequences are usually not consistent with other sequences, in this paper we provide an alternative approach for finding alternative splicing patterns which ensures that individual exons/introns of the reported patterns have enough support from the expressed sequences. On the same dataset, our approach can achieve a much higher specificity and a slight increase in sensitivity (38.9% and 84.9%, respectively). Our approach also gives better results compared with popular alternative splicing databases (ASD, ECgene, SpliceNest) and the software ClusterMerge. © 2008 Imperial College Press.
Persistent Identifierhttp://hdl.handle.net/10722/60613
ISSN
2015 Impact Factor: 0.785
2015 SCImago Journal Rankings: 0.525
References

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorYang, Wen_HK
dc.contributor.authorYiu, SMen_HK
dc.date.accessioned2010-05-31T04:14:59Z-
dc.date.available2010-05-31T04:14:59Z-
dc.date.issued2008en_HK
dc.identifier.citationJournal Of Bioinformatics And Computational Biology, 2008, v. 6 n. 5, p. 1021-1033en_HK
dc.identifier.issn0219-7200en_HK
dc.identifier.urihttp://hdl.handle.net/10722/60613-
dc.description.abstractWe consider the problem of predicting alternative splicing patterns from a set of expressed sequences (cDNAs and ESTs). Some of these expressed sequences may be errorous, thus forming incorrect exons/introns. These incorrect exons/introns may cause a lot of false positives. For example, we examined a popular alternative splicing database, ECgene, which predicts alternate splicing patterns from expressed sequences. The result shows that about 81.3%-81.6% (sensitivity) of known patterns are found, but the specificity can be as low as 5.9%. Based on the idea that errorous sequences are usually not consistent with other sequences, in this paper we provide an alternative approach for finding alternative splicing patterns which ensures that individual exons/introns of the reported patterns have enough support from the expressed sequences. On the same dataset, our approach can achieve a much higher specificity and a slight increase in sensitivity (38.9% and 84.9%, respectively). Our approach also gives better results compared with popular alternative splicing databases (ASD, ECgene, SpliceNest) and the software ClusterMerge. © 2008 Imperial College Press.en_HK
dc.languageengen_HK
dc.publisherImperial College Press. The Journal's web site is located at http://www.worldscinet.com/jbcb/jbcb.shtmlen_HK
dc.relation.ispartofJournal of Bioinformatics and Computational Biologyen_HK
dc.subjectAlternative splicing patternen_HK
dc.subjectESTsen_HK
dc.subjectExpressed sequencesen_HK
dc.subject.meshAlgorithmsen_HK
dc.subject.meshAlternative Splicing - geneticsen_HK
dc.subject.meshBase Sequenceen_HK
dc.subject.meshExons - geneticsen_HK
dc.subject.meshGene Expression - geneticsen_HK
dc.subject.meshIntrons - geneticsen_HK
dc.subject.meshMolecular Sequence Dataen_HK
dc.subject.meshRNA Splice Sites - geneticsen_HK
dc.subject.meshSequence Analysis, DNA - methodsen_HK
dc.titleFinding alternative splicing patterns with strong support from expressed sequences on individual exons/intronsen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0219-7200&volume=6&issue=5&spage=1021&epage=1033&date=2008&atitle=Finding+Alternative+Splicing+Patterns+with+Strong+Support+from+Expressed+Sequences+on+Individual+Exons/Intronsen_HK
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYang, W:yangwl@hkucc.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYang, W=rp00524en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1142/S0219720008003825en_HK
dc.identifier.pmid18942164-
dc.identifier.scopuseid_2-s2.0-54049115762en_HK
dc.identifier.hkuros155950en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-54049115762&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume6en_HK
dc.identifier.issue5en_HK
dc.identifier.spage1021en_HK
dc.identifier.epage1033en_HK
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWong, TKF=25423289800en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridYang, W=23101349500en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK

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