Is there a way to find out which enhancer regions associated with the TFs that were kept in the final results?

[YaoLi3]

Dear team and fellow Scenic+ users,

I'm wondering if is there a way to find out which enhancer regions associated with the TFs that were kept in the final results?

If I understand correctly, in Scenic+ workflow there is a step where enhancers (start:end) were linked to TFs? If so, where could I find that information, was it stored in any output data file?

Any help will be appreciated!

Best,
Yao

[SeppeDeWinter]

Hi @YaoLi3

Yes, that's stored in the output.

It's stored in the generated mudata object scplus_mdata.uns["direct_e_regulon_metadata"] and scplus_mdata.uns["extended_e_regulon_metadata"] as a pandas dataframe that looks like this

Region | Gene | importance_R2G | rho_R2G | importance_x_rho | importance_x_abs_rho | TF | is_extended | eRegulon_name | Gene_signature_name | Region_signature_name | importance_TF2G | regulation | rho_TF2G | triplet_rank

The Region column contains the inferred enhancers.

All the best,

Seppe

[YaoLi3]

That's great to hear! Thanks a lot for your swift reply.

However, my results were generated by the older version of Scenic+. Is this as same as scplus_obj.uns['eRegulon_metadata']?

Thanks,

Yao

[SeppeDeWinter]

Hi @YaoLi3

Yes, it's the same as scplus_obj.uns['eRegulon_metadata']

Best,

Seppe