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Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.

Author
Abstract
:

It has been observed that many transcription factors (TFs) can bind to different genomic loci depending on the cell type in which a TF is expressed in, even though the individual TF usually binds to the same core motif in different cell types. How a TF can bind to the genome in such a highly cell-type specific manner, is a critical research question. One hypothesis is that a TF requires co-binding of different TFs in different cell types. If this is the case, it may be possible to observe different combinations of TF motifs - a motif grammar - located at the TF binding sites in different cell types. In this study, we develop a bioinformatics method to systematically identify DNA motifs in TF binding sites across multiple cell types based on published ChIP-seq data, and address two questions: (1) can we build a machine learning classifier to predict cell-type specificity based on motif combinations alone, and (2) can we extract meaningful cell-type specific motif grammars from this classifier model.

Year of Publication
:
2018
Journal
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BMC genomics
Volume
:
19
Issue
:
Suppl 1
Number of Pages
:
929
Date Published
:
2018
URL
:
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4340-z
DOI
:
10.1186/s12864-017-4340-z
Short Title
:
BMC Genomics
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