FINDING REGULATORY ELEMENTS USING JOINT LIKELIHOODS FOR SEQUENCE AND EXPRESSION PROFILE DATA.

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A recent, popular method of finding promoter sequences is to look for conserved motifs up-stream of genes clustered on the basis of expression data. This method presupposes that the clustering is correct. Theoretically, one should be better able to find promoter sequences and create more relevant gene clusters by taking a unified approach to these two problems. We present a likelihood function for a sequence-expression model giving a joint likelihood for a promoter sequence and its corresponding expression levels. An algorithm to estimate sequence-expression model parameters using Gibbs sampling and Expectation/Maximization is described. A program, called kimono, that implements this ... continued below

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10 p.

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IAN HOLMES, UC BERKELEY, CA, WILLIAM J. BRUNO, LANL August 20, 2000.

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Description

A recent, popular method of finding promoter sequences is to look for conserved motifs up-stream of genes clustered on the basis of expression data. This method presupposes that the clustering is correct. Theoretically, one should be better able to find promoter sequences and create more relevant gene clusters by taking a unified approach to these two problems. We present a likelihood function for a sequence-expression model giving a joint likelihood for a promoter sequence and its corresponding expression levels. An algorithm to estimate sequence-expression model parameters using Gibbs sampling and Expectation/Maximization is described. A program, called kimono, that implements this algorithm has been developed and the source code is freely available over the internet.

Physical Description

10 p.

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OSTI as DE00752619

Medium: P; Size: 10 pages

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  • ISMB 2000 CONFERENCE, San Diego, CA (US), 08/20/2000--08/23/2000

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  • Report No.: LA-UR-00-965
  • Grant Number: W-7405-ENG-36
  • Office of Scientific & Technical Information Report Number: 752619
  • Archival Resource Key: ark:/67531/metadc703543

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  • August 20, 2000

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  • Sept. 12, 2015, 6:31 a.m.

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  • April 6, 2017, 6:54 p.m.

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IAN HOLMES, UC BERKELEY, CA, WILLIAM J. BRUNO, LANL. FINDING REGULATORY ELEMENTS USING JOINT LIKELIHOODS FOR SEQUENCE AND EXPRESSION PROFILE DATA., article, August 20, 2000; New Mexico. (digital.library.unt.edu/ark:/67531/metadc703543/: accessed September 23, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.