Self-organizing neural networks to support the discovery of DNA-binding motifs

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

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Identification of the short DNA sequence motifs that serve as binding targets for transcription factors is an important challenge in bioinformatics. Unsupervised techniques from the statistical learning theory literature have often been applied to motif discovery, but effective solutions for large genomic datasets have yet to be found. We present here three self-organizing neural networks that have applicability to the motif-finding problem. The core system in this study is a previously described SOM-based motif-finder named SOMBRERO. The motif-finder is integrated in this work with a SOM-based method that automatically constructs generalized models for structurally related motifs and initializes SOMBRERO with relevant biological knowledge. A self-organizing tree method that displays the relationships between various motifs is also presented, and it is shown that such a method can act as an effective structural classifier of novel motifs. The performance of the three self-organizing neural networks is evaluated here using various datasets.

Original languageEnglish (US)
Pages (from-to)950-962
Number of pages13
JournalNeural Networks
Volume19
Issue number6-7
DOIs
StatePublished - Jul 2006
Externally publishedYes

Fingerprint

Nucleotide Motifs
DNA
Neural networks
Transcription factors
DNA sequences
Bioinformatics
Classifiers
Computational Biology
Transcription Factors
Learning
Datasets

Keywords

  • DNA-binding motif identification
  • Self-organizing map
  • Self-organizing tree

ASJC Scopus subject areas

  • Artificial Intelligence
  • Neuroscience(all)

Cite this

Self-organizing neural networks to support the discovery of DNA-binding motifs. / Mahony, Shaun; Benos, Panayiotis V.; Smith, Terry J.; Golden, Aaron.

In: Neural Networks, Vol. 19, No. 6-7, 07.2006, p. 950-962.

Research output: Contribution to journalArticle

Mahony, Shaun ; Benos, Panayiotis V. ; Smith, Terry J. ; Golden, Aaron. / Self-organizing neural networks to support the discovery of DNA-binding motifs. In: Neural Networks. 2006 ; Vol. 19, No. 6-7. pp. 950-962.
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