Description
This track contains the location and score of transcription factor binding sites predicted to have transcriptional regulatory functions.
Methods
According to binding motifs, the sequence affinities of TFs to genome are different among base pairs within binding sites. The mutations in different base pairs have different effects on the binding of TFs and thus the selective constrains are different. So for functional binding sites, the base pairs with higher affinity are more conserved across species. Hinted by this, a method called "FunTFBS" was developed to identify functional TFBSs based on the correlation between frequencies in binding motifs and conservation scores.
There are four types of input:
The predicted TFBS from motif scanning using FIMO were downloaded from PlantRegMap.
The TF binding motifs were downloaded from PlantTFDB.
The conservation data (PhyloP) was calculated based on multiple genome alignments across species (See Conservation track).
The genome sequence was downloaded from PlantRegMap.
For each binding site from motif scanning, the motif base frequency (MBF) of each base pair are extracted according to the genome sequence. The PhyloP scores in the same region are also extracted and then Pearson correlation is calculated between motif base frequencies and the absolute value of PhyloP scores. If the correlation test is significant (p<=0.05) with correlation score > 0.5, the corresponding binding site will be treated as functional TFBS.
References
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202-208.
Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G. 2017. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 45:D1040-D1045.
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