JASPAR familial binding sites

Description

We provide here the track hub corresponding to the JASPAR familial binding profiles that can be downloaded from the JASPAR database. In the track hub, users can find one track per species and genome assembly. Very briefly, familial profiles are an average representation of a cluster of TF motifs. After hierarchical clustering, motifs from each cluster are aligned and the average IC for each base and position is computed to obtain the familial binding profile. JASPAR TFBSs for each of the profiles are then adjusted to fit the length of the familial profile, followed by removal of identical familial profile binding sites after TFBS readjustment.

Display Conventions and Configuration

Boxes represent predicted binding sites for each of the familial binding profiles in JASPAR.

Each familial profile is named with the cluster number it belongs to (i.e. Familial profile 42). Furthermore, each familial profile is displayed using a specific RGB color.

Methods

We adapted the methodology from (Vierstra et al Nature 2020) to generate familial binding profiles from the clusters found by the RSAT matrix clustering tool. We explicitly aimed at providing distinct familial binding profiles for motifs derived from dimer or monomer TF binding. Except for the motif clustering step, we used the default parameters in (Vierstra et al Nature 2020). As a final step, we removed the familial binding sites whose start coordinates were lower than 0 or end coordinates were greater than the chromosome size. These correspond to artifacts related to the expansion of original binding sites to fit the familial profile size.

Data Availability

References

Contact

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