English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands

Pape, U. J., Rahmann, S., Sun, F., & Vingron, M. (2008). Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 15(6), 547-564. doi:10.1089/cmb.2007.0084.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7E7F-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7E80-B
Genre: Journal Article

Files

show Files
hide Files
:
cmb.2007.pdf (Any fulltext), 536KB
 
File Permalink:
-
Name:
cmb.2007.pdf
Description:
-
Visibility:
Restricted (Max Planck Institute for Molecular Genetics, Berlin; )
MIME-Type / Checksum:
application/pdf
Technical Metadata:
Copyright Date:
-
Copyright Info:
eDoc_access: INSTITUT
License:
-

Locators

show

Creators

show
hide
 Creators:
Pape, Utz J.1, Author              
Rahmann, Sven1, Author              
Sun, Fengzhu, Author
Vingron, Martin2, Author              
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

Content

show
hide
Free keywords: binding site clumps compound Poisson distribution count statistics DNA motif overlapping occurrences PFM Position Frequency Matrix p-value
 Abstract: Transcription factors play a key role in gene regulation by interacting with specific binding sites or motifs. Therefore, enrichment of binding motifs is important for genome annotation and efficient computation of the statistical significance, the p-value, of the enrichment of motifs is crucial. We propose an efficient approximation to compute the significance. Due to the incorporation of both strands of the DNA molecules and explicit modeling of dependencies between overlapping hits, we achieve accurate results for any DNA motif based on its Position Frequency Matrix (PFM) representation. The accuracy of the p-value approximation is shown by comparison with the simulated count distribution. Furthermore, we compare the approach with a binomial approximation, (compound) Poisson approximation, and a normal approximation. In general, our approach outperforms these approximations or is equally good but significantly faster. An implementation of our approach is available at http://mosta.molgen.mpg.de.

Details

show
hide
Language(s): eng - English
 Dates: 2008-12-23
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Journal of Computational Biology : A Journal of Computational Molecular Cell Biology
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 15 (6) Sequence Number: - Start / End Page: 547 - 564 Identifier: ISSN: 1066-5277