skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data

Abstract

Genome wide disease association analysis using SNPs is being explored as a method for dissecting complex genetic traits and a vast number of SNPs have been generated for this purpose. As there are cost and throughput limitations of genotyping large numbers of SNPs and statistical issues regarding the large number of dependent tests on the same data set, to make association analysis practical it has been proposed that SNPs should be prioritized based on likely functional importance. The most easily identifiable functional SNPs are coding SNPs (cSNPs) and accordingly cSNPs have been screened in a number of studies. SNPs in gene regulatory sequences embedded in noncoding DNA are another class of SNPs suggested for prioritization due to their predicted quantitative impact on gene expression. The main challenge in evaluating these SNPs, in contrast to cSNPs is a lack of robust algorithms and databases for recognizing regulatory sequences in noncoding DNA. Approaches that have been previously used to delineate noncoding sequences with gene regulatory activity include cross-species sequence comparisons and the search for sequences recognized by transcription factors. We combined these two methods to sift through mouse human genomic sequences to identify putative gene regulatory elements and subsequently localized SNPs withinmore » these sequences in a 1 Megabase (Mb) region of human chromosome 5q31, orthologous to mouse chromosome 11 containing the Interleukin cluster.« less

Authors:
; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Director. Office of Science. Biological and Environmental Research (US)
OSTI Identifier:
825304
Report Number(s):
LBNL-50366
R&D Project: LGFGAA; TRN: US200421%%195
DOE Contract Number:  
AC03-76SF00098
Resource Type:
Journal Article
Journal Name:
Mammalian Genome
Additional Journal Information:
Journal Volume: 13; Other Information: Journal Publication Date: 2002; PBD: 1 Jan 2002
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; ALGORITHMS; CHROMOSOMES; DISEASES; DNA; FUNCTIONALS; GENES; GENETICS; HUMAN CHROMOSOMES; LYMPHOKINES; TRANSCRIPTION FACTORS

Citation Formats

Banerjee, Poulabi, Bahlo, Melanie, Schwartz, Jody R., Loots, Gabriela G., Houston, Kathryn A., Dubchak, Inna, Speed, Terence P., and Rubin, Edward M. SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data. United States: N. p., 2002. Web. doi:10.1007/s00335-002-2169-4.
Banerjee, Poulabi, Bahlo, Melanie, Schwartz, Jody R., Loots, Gabriela G., Houston, Kathryn A., Dubchak, Inna, Speed, Terence P., & Rubin, Edward M. SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data. United States. doi:10.1007/s00335-002-2169-4.
Banerjee, Poulabi, Bahlo, Melanie, Schwartz, Jody R., Loots, Gabriela G., Houston, Kathryn A., Dubchak, Inna, Speed, Terence P., and Rubin, Edward M. Tue . "SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data". United States. doi:10.1007/s00335-002-2169-4. https://www.osti.gov/servlets/purl/825304.
@article{osti_825304,
title = {SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data},
author = {Banerjee, Poulabi and Bahlo, Melanie and Schwartz, Jody R. and Loots, Gabriela G. and Houston, Kathryn A. and Dubchak, Inna and Speed, Terence P. and Rubin, Edward M.},
abstractNote = {Genome wide disease association analysis using SNPs is being explored as a method for dissecting complex genetic traits and a vast number of SNPs have been generated for this purpose. As there are cost and throughput limitations of genotyping large numbers of SNPs and statistical issues regarding the large number of dependent tests on the same data set, to make association analysis practical it has been proposed that SNPs should be prioritized based on likely functional importance. The most easily identifiable functional SNPs are coding SNPs (cSNPs) and accordingly cSNPs have been screened in a number of studies. SNPs in gene regulatory sequences embedded in noncoding DNA are another class of SNPs suggested for prioritization due to their predicted quantitative impact on gene expression. The main challenge in evaluating these SNPs, in contrast to cSNPs is a lack of robust algorithms and databases for recognizing regulatory sequences in noncoding DNA. Approaches that have been previously used to delineate noncoding sequences with gene regulatory activity include cross-species sequence comparisons and the search for sequences recognized by transcription factors. We combined these two methods to sift through mouse human genomic sequences to identify putative gene regulatory elements and subsequently localized SNPs within these sequences in a 1 Megabase (Mb) region of human chromosome 5q31, orthologous to mouse chromosome 11 containing the Interleukin cluster.},
doi = {10.1007/s00335-002-2169-4},
journal = {Mammalian Genome},
number = ,
volume = 13,
place = {United States},
year = {2002},
month = {1}
}