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vanheeringen-lab / ANANSE

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.
http://anansepy.readthedocs.io
MIT License
77 stars 16 forks source link

enhancer regions #181

Closed liyangyang12 closed 1 year ago

liyangyang12 commented 2 years ago

Hi, Can user-provided enhancer regions contain promotor regions? Why not train the enhancer region and the promotor region together when training the model?

Thanks a lot for your time and effort!

siebrenf commented 2 years ago

Can user-provided enhancer regions contain promotor regions?

Yes! If you wish, you can even remove promoters during ANANSE network with the --exclude-promoter flag.

Why not train the enhancer region and the promotor region together when training the model?

Unless I'm mistaken, they are trained together!

liyangyang12 commented 2 years ago

Thanks! But in development version, I noticed that the calculation of distance weight in Inference of "gene regulatory networks" didn't consider the promotor regions in 2kb? 1651929603(1)

By the way, do you recommend using ANANSE for non-model organisms?

Thanks a lot for your time and effort!

siebrenf commented 2 years ago

I double checked the code to be sure :) Starting from version 0.2, we include both promoters and enhancers by default (with the option to exclude them). So that picture is outdated, thank you for pointing that out!

We have done several analyses with non-model organisms, which did show promising results! I highly recommend using the development branch for this. Which files you need, and how to prepare them, can be found on the input data page.

Good luck!

liyangyang12 commented 2 years ago

OK, Thank you very much!