Schematic of gene region annotated with predicted TF binding sites

[JP]

Hello,

I am currently trying to recreate and conduct analysis for a gene using from a publication using JASPAR but am unable to. I am trying to recreate figure 1B from the following paper: doi: 10.1242/dev.194019

I was hoping someone can point me in the correct direction on how I can do this for a different but similar gene (in humans).

Thank you in advance!

[Jaime Castro]

Hi Justin

One possibility is to identify TFBSs within your region of interest.
You can use this tool https://unibind.uio.no/TFBS_extraction/ to detect TFBS annotated in Unibind (which are predicted from the JASPAR PFMs) in a region of interest provided as a BED file.
Alternatively you can use bedtools intersect of your region vs all jaspar TFBSs (both files in BED format)

To make the figure you can use this python package (https://edinburgh-genome-foundry.github.io/DnaFeaturesViewer/), you can make pretty nice figures, specially when your region is not so long.

I hope this info helps you,

Thanks for using JASPAR

[JP]

Hi!

Thank you so much for this. I have used the tool and used IGV to view the BED file. However, it is only showing me experiment names and not transcription factor names (see screenshot). How can I fix this?