title: A database of annotated promoters of genes associated with common respiratory and related diseases.
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.
authors.affiliation: Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield Clinic, Wisconsin 54449, USA. chowdhary.rajesh@mcrf.mfldclin.edu
authors.forename: Rajesh
authors.initials: R
authors.lastname: Chowdhary
authors.forename: Sin Lam
authors.initials: SL
authors.lastname: Tan
authors.forename: Giulio
authors.initials: G
authors.lastname: Pavesi
authors.forename: Jingjing
authors.initials: J
authors.lastname: Jin
authors.forename: Difeng
authors.initials: D
authors.lastname: Dong
authors.forename: Sameer K
authors.initials: SK
authors.lastname: Mathur
authors.forename: Arthur
authors.initials: A
authors.lastname: Burkart
authors.forename: Vipin
authors.initials: V
authors.lastname: Narang
authors.forename: Ingrid
authors.initials: I
authors.lastname: Glurich
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Raby
authors.forename: Scott T
authors.initials: ST
authors.lastname: Weiss
authors.forename: Limsoon
authors.initials: L
authors.lastname: Wong
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
mesh_terms: D030541:Databases, Genetic; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods; D006801:Humans; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic; D012140:Respiratory Tract Diseases / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors