TY - JOUR AU - Wang, Xin AU - Lin, Peijie AU - Ho, Joshua W. K. PY - 2018 DA - 2018/01/19 TI - Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest JO - BMC Genomics SP - 929 VL - 19 IS - 1 AB - 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. SN - 1471-2164 UR - https://doi.org/10.1186/s12864-017-4340-z DO - 10.1186/s12864-017-4340-z ID - Wang2018 ER -