How can I get Nanog PWM

Question

[jesselee516]

Hi everyone,

I am trying to find motif in mouse ChIP-seq data set. One of my interested motif is Nanog. But I can't find Nanog PWM in all Jaspar2010, Jaspar2016 and Transfac. Can anyone help me out???

Answer 1

[Satyajeet Khare]

There is mouse nanog entry in CIS-BP database.

Here is the link to the page.

Here is the link to PWM.

[Santosh Anand]

Do you know which are the resources used by CIS-BP? Why some of the factors are not found in JASPAR (2016), but they are present here?

[Satyajeet Khare]

Hi Santosh,

I found this on their faq page.

CisBP collects data from >25 sources, including other database such as Transfac, JASPAR, HOCOMOCO, FactorBook, UniProbe, Fly Factor Survey, and dozens of additional publications.

I guess this explains why CIS-BP has some extra entries.

[Santosh Anand]

That explains it. Thanks!

[Santosh Anand]

BTW, +1 for CIS-BP. I was going to write that P :)