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