A database of annotated promoters of genes associated with common respiratory and related diseases

Handle URI:
http://hdl.handle.net/10754/562236
Title:
A database of annotated promoters of genes associated with common respiratory and related diseases
Authors:
Chowdhary, Rajesh; Tan, Sinlam; Pavesi, Giulio; Jin, Gg; Dong, Difeng; Mathur, Sameer K.; Burkart, Arthur; Narang, Vipin; Glurich, Ingrid E.; Raby, Benjamin A.; Weiss, Scott T.; Limsoon, Wong; Liu, Jun; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Many genes have been implicated in the pathogenesis of common respiratory and related diseases (RRDs), yet the underlying mechanisms are largely unknown. Differential gene expression patterns in diseased and healthy individuals suggest that RRDs affect or are affected by modified transcription regulation programs. It is thus crucial to characterize implicated genes in terms of transcriptional regulation. For this purpose, we conducted a promoter analysis of genes associated with 11 common RRDs including allergic rhinitis, asthma, bronchiectasis, bronchiolitis, bronchitis, chronic obstructive pulmonary disease, cystic fibrosis, emphysema, eczema, psoriasis, and urticaria, many of which are thought to be genetically related. The objective of the present study was to obtain deeper insight into the transcriptional regulation of these disease-associated genes by annotating their promoter regions with transcription factors (TFs) and TF binding sites (TFBSs). We discovered many TFs that are significantly enriched in the target disease groups including associations that have been documented in the literature. We also identified a number of putative TFs/TFBSs that appear to be novel. The results of our analysis are provided in an online database that is freely accessible to researchers at http://www.respiratorygenomics.com. Promoter-associated TFBS information and related genomic features, such as histone modification sites, microsatellites, CpG islands, and SNPs, are graphically summarized in the database. Users can compare and contrast underlying mechanisms of specific RRDs relative to candidate genes, TFs, gene ontology terms, micro-RNAs, and biological pathways for the conduct of metaanalyses. This database represents a novel, useful resource for RRD researchers. Copyright © 2012 by the American Thoracic Society.
KAUST Department:
Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Applied Mathematics and Computational Science Program
Publisher:
American Thoracic Society
Journal:
American Journal of Respiratory Cell and Molecular Biology
Issue Date:
Jul-2012
DOI:
10.1165/rcmb.2011-0419OC
PubMed ID:
22383585
Type:
Article
ISSN:
10441549
Sponsors:
This study was supported by Marshfield Clinic disease specific research funding (SP code: CHO10310).
Appears in Collections:
Articles; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorChowdhary, Rajeshen
dc.contributor.authorTan, Sinlamen
dc.contributor.authorPavesi, Giulioen
dc.contributor.authorJin, Ggen
dc.contributor.authorDong, Difengen
dc.contributor.authorMathur, Sameer K.en
dc.contributor.authorBurkart, Arthuren
dc.contributor.authorNarang, Vipinen
dc.contributor.authorGlurich, Ingrid E.en
dc.contributor.authorRaby, Benjamin A.en
dc.contributor.authorWeiss, Scott T.en
dc.contributor.authorLimsoon, Wongen
dc.contributor.authorLiu, Junen
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2015-08-03T09:57:28Zen
dc.date.available2015-08-03T09:57:28Zen
dc.date.issued2012-07en
dc.identifier.issn10441549en
dc.identifier.pmid22383585en
dc.identifier.doi10.1165/rcmb.2011-0419OCen
dc.identifier.urihttp://hdl.handle.net/10754/562236en
dc.description.abstractMany genes have been implicated in the pathogenesis of common respiratory and related diseases (RRDs), yet the underlying mechanisms are largely unknown. Differential gene expression patterns in diseased and healthy individuals suggest that RRDs affect or are affected by modified transcription regulation programs. It is thus crucial to characterize implicated genes in terms of transcriptional regulation. For this purpose, we conducted a promoter analysis of genes associated with 11 common RRDs including allergic rhinitis, asthma, bronchiectasis, bronchiolitis, bronchitis, chronic obstructive pulmonary disease, cystic fibrosis, emphysema, eczema, psoriasis, and urticaria, many of which are thought to be genetically related. The objective of the present study was to obtain deeper insight into the transcriptional regulation of these disease-associated genes by annotating their promoter regions with transcription factors (TFs) and TF binding sites (TFBSs). We discovered many TFs that are significantly enriched in the target disease groups including associations that have been documented in the literature. We also identified a number of putative TFs/TFBSs that appear to be novel. The results of our analysis are provided in an online database that is freely accessible to researchers at http://www.respiratorygenomics.com. Promoter-associated TFBS information and related genomic features, such as histone modification sites, microsatellites, CpG islands, and SNPs, are graphically summarized in the database. Users can compare and contrast underlying mechanisms of specific RRDs relative to candidate genes, TFs, gene ontology terms, micro-RNAs, and biological pathways for the conduct of metaanalyses. This database represents a novel, useful resource for RRD researchers. Copyright © 2012 by the American Thoracic Society.en
dc.description.sponsorshipThis study was supported by Marshfield Clinic disease specific research funding (SP code: CHO10310).en
dc.publisherAmerican Thoracic Societyen
dc.subjectAllergic rhinitisen
dc.subjectAsthmaen
dc.subjectBronchiectasisen
dc.subjectBronchiolitisen
dc.subjectBronchitisen
dc.subjectCOPDen
dc.subjectCystic fibrosisen
dc.subjectEczemaen
dc.subjectEmphysemaen
dc.subjectPathwaysen
dc.subjectPromoter analysisen
dc.subjectPromoter motifsen
dc.subjectPsoriasisen
dc.subjectRespiratory/pulmonary disease genesen
dc.subjectSNPsen
dc.subjectSystems/network biologyen
dc.subjectTranscription factor binding sitesen
dc.subjectUrticariaen
dc.titleA database of annotated promoters of genes associated with common respiratory and related diseasesen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.identifier.journalAmerican Journal of Respiratory Cell and Molecular Biologyen
dc.contributor.institutionMarshfield Clin Fdn Med Res & Educ, Biomed Informat Res Ctr, MCRF, Marshfield, WI 54449 USAen
dc.contributor.institutionUniv Milan, Dept Biomol Sci & Biotechnol, Milan, Italyen
dc.contributor.institutionNatl Univ Singapore, Sch Comp, Kent Ridge, Singaporeen
dc.contributor.institutionUniv Wisconsin, Dept Med, Madison, WI USAen
dc.contributor.institutionSingapore Immunol Network, Singapore, Singaporeen
dc.contributor.institutionBrigham & Womens Hosp, Channing Lab, Boston, MA 02115 USAen
dc.contributor.institutionHarvard Univ, Dept Stat, Cambridge, MA 02138 USAen
kaust.authorBajic, Vladimir B.en
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.