Description

This track contains the location and score of transcription factor binding sites conserved (in DNA level) across species. A binding site is considered to be conserved across the alignment if at least half of the length fall into conserved elements.

Methods

The predicted TFBS from motif scanning using FIMO were downloaded from PlantRegMap and the conserved elements were calculated based on multiple genome alignments across species (See Conservation track).

The conserved TFBS were filtered using Bedtools, which only filtered for ones with at least half of the length overlapped with conserved elements.

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.

Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841-842.