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Article: An evaluation of new criteria for CpG islands in the human genome as gene markers

TitleAn evaluation of new criteria for CpG islands in the human genome as gene markers
Authors
Issue Date2004
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2004, v. 20 n. 7, p. 1170-1177 How to Cite?
AbstractMotivation: Recently, more stringent criteria for CpG islands have been introduced to exclude Alu repeats, thereby enabling a higher proportion of CpG islands associating with genes to be identified. Using these new criteria, several types of associations between CpG islands and genes were investigated to further establish the importance of CpG islands as gene markers. Results: The CpG islands were searched by CpGIE, a java software program developed for CpG island identification. CpGIE was advanced in identification accuracy compared with other tools. According to our results, about 70% of the identified CpG islands were associating with the human genes and over half of them are in the promoters. Furthermore, the investigation of genes in the confirmed gene model showed that 56% of them had a CpG island overlapping the transcription start sites. In comparison, the new criteria were found capable of filtering a large fraction of Alu repeats that was identified as CpG islands by the generally accepted criteria within the genes, but very few CpG islands associating with the promoters were affected. The genes in the predicted gene model were not obviously associated with CpG islands, suggesting that CpG islands can be used to evaluate the accuracy of gene annotation. © Oxford University Press 2004; all rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/43523
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_HK
dc.contributor.authorLeung, FCCen_HK
dc.date.accessioned2007-03-23T04:47:54Z-
dc.date.available2007-03-23T04:47:54Z-
dc.date.issued2004en_HK
dc.identifier.citationBioinformatics, 2004, v. 20 n. 7, p. 1170-1177en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/43523-
dc.description.abstractMotivation: Recently, more stringent criteria for CpG islands have been introduced to exclude Alu repeats, thereby enabling a higher proportion of CpG islands associating with genes to be identified. Using these new criteria, several types of associations between CpG islands and genes were investigated to further establish the importance of CpG islands as gene markers. Results: The CpG islands were searched by CpGIE, a java software program developed for CpG island identification. CpGIE was advanced in identification accuracy compared with other tools. According to our results, about 70% of the identified CpG islands were associating with the human genes and over half of them are in the promoters. Furthermore, the investigation of genes in the confirmed gene model showed that 56% of them had a CpG island overlapping the transcription start sites. In comparison, the new criteria were found capable of filtering a large fraction of Alu repeats that was identified as CpG islands by the generally accepted criteria within the genes, but very few CpG islands associating with the promoters were affected. The genes in the predicted gene model were not obviously associated with CpG islands, suggesting that CpG islands can be used to evaluate the accuracy of gene annotation. © Oxford University Press 2004; all rights reserved.en_HK
dc.format.extent183841 bytes-
dc.format.extent25088 bytes-
dc.format.mimetypeapplication/pdf-
dc.format.mimetypeapplication/msword-
dc.languageengen_HK
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshAlgorithmsen_HK
dc.subject.meshCpg islands - geneticsen_HK
dc.subject.meshGene expression profiling - methodsen_HK
dc.subject.meshGenetic markers - geneticsen_HK
dc.subject.meshGenome, humanen_HK
dc.titleAn evaluation of new criteria for CpG islands in the human genome as gene markersen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2105&volume=20&issue=7&spage=1170&epage=1177&date=2004&atitle=An+evaluation+of+new+criteria+for+CpG+islands+in+the+human+genome+as+gene+markersen_HK
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1093/bioinformatics/bth059en_HK
dc.identifier.pmid14764558-
dc.identifier.scopuseid_2-s2.0-2442684104en_HK
dc.identifier.hkuros86193-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-2442684104&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume20en_HK
dc.identifier.issue7en_HK
dc.identifier.spage1170en_HK
dc.identifier.epage1177en_HK
dc.identifier.isiWOS:000221139700020-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWang, Y=8710320600en_HK
dc.identifier.scopusauthoridLeung, FCC=7103078633en_HK
dc.identifier.citeulike5239149-

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