Sombrero: Integrating self-organizing neural networks in the search for dna binding motifs

Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Identification of the short DNA sequence motifs that serve as binding domains for transcription factors continues to be a challenging problem in computational biology. Currently popular methods of motif discovery are based on unsupervised techniques from the statistical learning theory literature. We present here a working prototype of a neural networks based system that aims to tackle the DNA regulatory motif identification problem. The system consists of three modules, the core module being a SOM-based motif-finder named SOMBRERO. The motif-finder is integrated in the prototype with a SOM-based pre-processing method that initialises SOMBRERO with relevant biological knowledge, as well as a self-organizing tree method that helps the user to interpret SOMBRERO's results. The system is demonstrated here using various datasets.

Original languageEnglish (US)
Title of host publicationWSOM 2005 - 5th Workshop on Self-Organizing Maps
Pages677-685
Number of pages9
StatePublished - 2005
Externally publishedYes
Event5th Workshop on Self-Organizing Maps, WSOM 2005 - Paris, France
Duration: Sep 5 2005Sep 8 2005

Other

Other5th Workshop on Self-Organizing Maps, WSOM 2005
CountryFrance
CityParis
Period9/5/059/8/05

Fingerprint

Transcription factors
DNA sequences
DNA
Neural networks
Processing

Keywords

  • Motif-finding
  • Self-Organizing Map
  • Self-Organizing Tree
  • Transcription factor binding sites

ASJC Scopus subject areas

  • Information Systems

Cite this

Mahony, S., Benos, P. V., Smith, T. J., & Golden, A. (2005). Sombrero: Integrating self-organizing neural networks in the search for dna binding motifs. In WSOM 2005 - 5th Workshop on Self-Organizing Maps (pp. 677-685)

Sombrero : Integrating self-organizing neural networks in the search for dna binding motifs. / Mahony, Shaun; Benos, Panayiotis V.; Smith, Terry J.; Golden, Aaron.

WSOM 2005 - 5th Workshop on Self-Organizing Maps. 2005. p. 677-685.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mahony, S, Benos, PV, Smith, TJ & Golden, A 2005, Sombrero: Integrating self-organizing neural networks in the search for dna binding motifs. in WSOM 2005 - 5th Workshop on Self-Organizing Maps. pp. 677-685, 5th Workshop on Self-Organizing Maps, WSOM 2005, Paris, France, 9/5/05.
Mahony S, Benos PV, Smith TJ, Golden A. Sombrero: Integrating self-organizing neural networks in the search for dna binding motifs. In WSOM 2005 - 5th Workshop on Self-Organizing Maps. 2005. p. 677-685
Mahony, Shaun ; Benos, Panayiotis V. ; Smith, Terry J. ; Golden, Aaron. / Sombrero : Integrating self-organizing neural networks in the search for dna binding motifs. WSOM 2005 - 5th Workshop on Self-Organizing Maps. 2005. pp. 677-685
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