[Integration of data obtained by different experimental methods to determine the motifs in DNA sequences recognized by transcription-regulating factors]

Biofizika. Nov-Dec 2009;54(6):965-74.
[Article in Russian]

Abstract

For 39 proteins regulating the transcription of Drosophila melanogaster, refined motifs typical for nucleotide sequences specifically interacting with these proteins have been constructed using the new logarithm ChiPMunk. The entire spectrum of available experimental data, including the data of DNAse footprinting, SELEX, ChIP-chip, and B1H-system, has been used. Motifs constructed by integrating the data obtained by independent experimental methods show the highest sensitivity. The collection of motifs can be used to refine the immediate binding sites of transcription factors in DNA nucleotide sequences. The collection of motifs and the results of the estimation of motif quality are available at: http://line.imb.ac.ru/iDMMPMM. The realization of the algorithm ChIPmunk is accessible at http://line.imb.ac.ru/Chipmunk.

Publication types

  • English Abstract
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Binding Sites
  • DNA / chemistry*
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Databases, Factual
  • Drosophila Proteins / chemistry*
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster
  • Nucleic Acid Conformation
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism
  • Transcription, Genetic

Substances

  • DNA-Binding Proteins
  • Drosophila Proteins
  • Transcription Factors
  • DNA