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

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    Type
    Article
    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. cc
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Applied Mathematics and Computational Science Program
    Date
    2012-07
    Permanent link to this record
    http://hdl.handle.net/10754/562236
    
    Metadata
    Show full item record
    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.
    Citation
    Chowdhary, R., Tan, S. L., Pavesi, G., Jin, J., Dong, D., Mathur, S. K., … Bajic, V. B. (2012). A Database of Annotated Promoters of Genes Associated with Common Respiratory and Related Diseases. American Journal of Respiratory Cell and Molecular Biology, 47(1), 112–119. doi:10.1165/rcmb.2011-0419oc
    Sponsors
    This study was supported by Marshfield Clinic disease specific research funding (SP code: CHO10310).
    Publisher
    American Thoracic Society
    Journal
    American Journal of Respiratory Cell and Molecular Biology
    DOI
    10.1165/rcmb.2011-0419OC
    PubMed ID
    22383585
    ae974a485f413a2113503eed53cd6c53
    10.1165/rcmb.2011-0419OC
    Scopus Count
    Collections
    Articles; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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