Genome-wide analysis of regions similar to promoters of histone genes

Handle URI:
http://hdl.handle.net/10754/325265
Title:
Genome-wide analysis of regions similar to promoters of histone genes
Authors:
Chowdhary, Rajesh; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Dong, Difeng; Wong, Limsoon; Liu, Jun S
Abstract:
Background: The purpose of this study is to: i) develop a computational model of promoters of human histone-encoding genes (shortly histone genes), an important class of genes that participate in various critical cellular processes, ii) use the model so developed to identify regions across the human genome that have similar structure as promoters of histone genes; such regions could represent potential genomic regulatory regions, e.g. promoters, of genes that may be coregulated with histone genes, and iii/ identify in this way genes that have high likelihood of being coregulated with the histone genes.Results: We successfully developed a histone promoter model using a comprehensive collection of histone genes. Based on leave-one-out cross-validation test, the model produced good prediction accuracy (94.1% sensitivity, 92.6% specificity, and 92.8% positive predictive value). We used this model to predict across the genome a number of genes that shared similar promoter structures with the histone gene promoters. We thus hypothesize that these predicted genes could be coregulated with histone genes. This hypothesis matches well with the available gene expression, gene ontology, and pathways data. Jointly with promoters of the above-mentioned genes, we found a large number of intergenic regions with similar structure as histone promoters.Conclusions: This study represents one of the most comprehensive computational analyses conducted thus far on a genome-wide scale of promoters of human histone genes. Our analysis suggests a number of other human genes that share a high similarity of promoter structure with the histone genes and thus are highly likely to be coregulated, and consequently coexpressed, with the histone genes. We also found that there are a large number of intergenic regions across the genome with their structures similar to promoters of histone genes. These regions may be promoters of yet unidentified genes, or may represent remote control regions that participate in regulation of histone and histone-coregulated gene transcription initiation. While these hypotheses still remain to be verified, we believe that these form a useful resource for researchers to further explore regulation of human histone genes and human genome. It is worthwhile to note that the regulatory regions of the human genome remain largely un-annotated even today and this study is an attempt to supplement our understanding of histone regulatory regions. 2010 Chowdhary et al; licensee BioMed Central Ltd.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Chowdhary R, Bajic VB, Dong D, Wong L, Liu JS (2010) Genome-wide analysis of regions similar to promoters of histone genes. BMC Systems Biology 4: S4. doi:10.1186/1752-0509-4-S1-S4.
Publisher:
BioMed Central
Journal:
BMC Systems Biology
Issue Date:
28-May-2010
DOI:
10.1186/1752-0509-4-S1-S4
PubMed ID:
20522254
PubMed Central ID:
PMC2880410
Type:
Article
ISSN:
17520509
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorChowdhary, Rajeshen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorDong, Difengen
dc.contributor.authorWong, Limsoonen
dc.contributor.authorLiu, Jun Sen
dc.date.accessioned2014-08-27T09:43:34Z-
dc.date.available2014-08-27T09:43:34Z-
dc.date.issued2010-05-28en
dc.identifier.citationChowdhary R, Bajic VB, Dong D, Wong L, Liu JS (2010) Genome-wide analysis of regions similar to promoters of histone genes. BMC Systems Biology 4: S4. doi:10.1186/1752-0509-4-S1-S4.en
dc.identifier.issn17520509en
dc.identifier.pmid20522254en
dc.identifier.doi10.1186/1752-0509-4-S1-S4en
dc.identifier.urihttp://hdl.handle.net/10754/325265en
dc.description.abstractBackground: The purpose of this study is to: i) develop a computational model of promoters of human histone-encoding genes (shortly histone genes), an important class of genes that participate in various critical cellular processes, ii) use the model so developed to identify regions across the human genome that have similar structure as promoters of histone genes; such regions could represent potential genomic regulatory regions, e.g. promoters, of genes that may be coregulated with histone genes, and iii/ identify in this way genes that have high likelihood of being coregulated with the histone genes.Results: We successfully developed a histone promoter model using a comprehensive collection of histone genes. Based on leave-one-out cross-validation test, the model produced good prediction accuracy (94.1% sensitivity, 92.6% specificity, and 92.8% positive predictive value). We used this model to predict across the genome a number of genes that shared similar promoter structures with the histone gene promoters. We thus hypothesize that these predicted genes could be coregulated with histone genes. This hypothesis matches well with the available gene expression, gene ontology, and pathways data. Jointly with promoters of the above-mentioned genes, we found a large number of intergenic regions with similar structure as histone promoters.Conclusions: This study represents one of the most comprehensive computational analyses conducted thus far on a genome-wide scale of promoters of human histone genes. Our analysis suggests a number of other human genes that share a high similarity of promoter structure with the histone genes and thus are highly likely to be coregulated, and consequently coexpressed, with the histone genes. We also found that there are a large number of intergenic regions across the genome with their structures similar to promoters of histone genes. These regions may be promoters of yet unidentified genes, or may represent remote control regions that participate in regulation of histone and histone-coregulated gene transcription initiation. While these hypotheses still remain to be verified, we believe that these form a useful resource for researchers to further explore regulation of human histone genes and human genome. It is worthwhile to note that the regulatory regions of the human genome remain largely un-annotated even today and this study is an attempt to supplement our understanding of histone regulatory regions. 2010 Chowdhary et al; licensee BioMed Central Ltd.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjecthistoneen
dc.subjectBayes theoremen
dc.subjectgeneticsen
dc.subjectgenomicsen
dc.subjecthuman genomeen
dc.subjectpromoter regionen
dc.subjectBayes Theoremen
dc.subjectGenome, Humanen
dc.subjectGenomicsen
dc.subjectHistonesen
dc.subjectPromoter Regions, Geneticen
dc.titleGenome-wide analysis of regions similar to promoters of histone genesen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalBMC Systems Biologyen
dc.identifier.pmcidPMC2880410en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Statistics, Harvard University, Cambridge, MA 02138, United Statesen
dc.contributor.institutionBiomedical Informatics Research Center, MCRF, Marshfield Clinic, 1000 North Oak Avenue, Marshfield, WI 54449, United Statesen
dc.contributor.institutionSchool of Computing, National University of Singapore, Singapore 117417, Singaporeen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorBajic, Vladimir B.en

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