A database of annotated promoters of genes associated with common respiratory and related diseases
Mathur, Sameer K.
Glurich, Ingrid E.
Raby, Benjamin A.
Weiss, Scott T.
Bajic, Vladimir B.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Applied Mathematics and Computational Science Program
Permanent link to this recordhttp://hdl.handle.net/10754/562236
MetadataShow full item record
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.
CitationChowdhary, 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
SponsorsThis study was supported by Marshfield Clinic disease specific research funding (SP code: CHO10310).
PublisherAmerican Thoracic Society
- AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors.
- Authors: Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E
- Issue date: 2003 Jun 23
- Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression.
- Authors: Murakami K, Kojima T, Sakaki Y
- Issue date: 2004 Feb 23
- PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.
- Authors: Chow CN, Zheng HQ, Wu NY, Chien CH, Huang HD, Lee TY, Chiang-Hsieh YF, Hou PF, Yang TY, Chang WC
- Issue date: 2016 Jan 4
- A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human.
- Authors: Hatanaka Y, Nagasaki M, Yamaguchi R, Obayashi T, Numata K, Fujita A, Shimamura T, Tamada Y, Imoto S, Kinoshita K, Nakai K, Miyano S
- Issue date: 2008
- Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.
- Authors: Kim SY, Kim Y
- Issue date: 2006 Jul 4