Most transcription factor binding sites are in a few mosaic classes of the human genome.

ABSTRACT:

Background

Many algorithms for finding transcription factor binding sites have concentrated on the characterisation of the binding site itself: and these algorithms lead to a large number of false positive sites. The DNA sequence which does not bind has been modeled only to the extent necessary to complement this formulation.

Results

We find that the human genome may be described by 19 pairs of mosaic classes, each defined by its base frequencies, (or more precisely by the frequencies of doublets), so that typically a run of 10 to 100 bases belongs to the same class. Most experimentally verified binding sites are in the same four pairs of classes. In our sample of seventeen transcription factors - taken from different families of transcription factors - the average proportio

SUBMITTER: Evans KJ 

PROVIDER: S-EPMC2881025 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature