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Discovering sequences with potential regulatory characteristics.

Publication ,  Journal Article
Bina, M; Wyss, P; Lazarus, SA; Shah, SR; Ren, W; Szpankowski, W; Crawford, GE; Park, SP; Song, XC
Published in: Genomics
April 2009

We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes.

Duke Scholars

Published In

Genomics

DOI

EISSN

1089-8646

Publication Date

April 2009

Volume

93

Issue

4

Start / End Page

314 / 322

Location

United States

Related Subject Headings

  • Regulatory Sequences, Nucleic Acid
  • Promoter Regions, Genetic
  • Humans
  • Homeodomain Proteins
  • Genome, Human
  • Genetics & Heredity
  • DNA
  • Computational Biology
  • Chromosomes, Human, Pair 7
  • Binding Sites
 

Citation

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Bina, M., Wyss, P., Lazarus, S. A., Shah, S. R., Ren, W., Szpankowski, W., … Song, X. C. (2009). Discovering sequences with potential regulatory characteristics. Genomics, 93(4), 314–322. https://doi.org/10.1016/j.ygeno.2008.11.008
Bina, Minou, Phillip Wyss, Sheryl A. Lazarus, Syed R. Shah, Wenhui Ren, Wojciech Szpankowski, Gregory E. Crawford, Sang P. Park, and Xiaohui C. Song. “Discovering sequences with potential regulatory characteristics.Genomics 93, no. 4 (April 2009): 314–22. https://doi.org/10.1016/j.ygeno.2008.11.008.
Bina M, Wyss P, Lazarus SA, Shah SR, Ren W, Szpankowski W, et al. Discovering sequences with potential regulatory characteristics. Genomics. 2009 Apr;93(4):314–22.
Bina, Minou, et al. “Discovering sequences with potential regulatory characteristics.Genomics, vol. 93, no. 4, Apr. 2009, pp. 314–22. Pubmed, doi:10.1016/j.ygeno.2008.11.008.
Bina M, Wyss P, Lazarus SA, Shah SR, Ren W, Szpankowski W, Crawford GE, Park SP, Song XC. Discovering sequences with potential regulatory characteristics. Genomics. 2009 Apr;93(4):314–322.
Journal cover image

Published In

Genomics

DOI

EISSN

1089-8646

Publication Date

April 2009

Volume

93

Issue

4

Start / End Page

314 / 322

Location

United States

Related Subject Headings

  • Regulatory Sequences, Nucleic Acid
  • Promoter Regions, Genetic
  • Humans
  • Homeodomain Proteins
  • Genome, Human
  • Genetics & Heredity
  • DNA
  • Computational Biology
  • Chromosomes, Human, Pair 7
  • Binding Sites