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

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.

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

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.

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

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

Acknowledgements

This study was supported by Marshfield Clinic disease specific research funding (SP code: CHO10310).