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Jumitti / TFinder

Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.
https://tfinder-ipmc.streamlit.app/
MIT License
9 stars 15 forks source link

[FEATURE] multiple TF search #59

Open Darius-bit opened 4 months ago

Darius-bit commented 4 months ago

Is it possible to integrate the search for multiple TF? possibly all from TRANSFAC database. I am particularly interested in human ones.

Jumitti commented 4 months ago

Hello @Darius-bit,

Thank you for your proposal, we are thinking about it seriously and it is in our perspectives.

The TRANSFAC database is interesting yes but TFinder does not have its own server, this is what it does so that it can support several work sessions at the same time. Not having a server, we cannot use a downloadable database (like TRANSFAC) and we have focused on APIs which are more modular and up-to-date without worrying about the version of the databases used (NCBI, JASPAR). I know that TRANSFAC also has an API, but you need a paid license. I need to find out if we can make TRANSFAC available if we pay for the license.

In any case, multi TF is developing. Also, your TF is not available on JASPAR?

Darius-bit commented 3 months ago

The main goal is to find differential TFs from two set of organ-specific promoters. To do this task I need to discover all TF present in one set, and not in the other. So finding a specific TF is easy, but I do not know which tissue-specific TF are guiding the expression of my genes. Best Dario Balestra

Il giorno ven 10 mag 2024 alle ore 17:23 Minniti Julien < @.***> ha scritto:

Hello @Darius-bit https://github.com/Darius-bit,

Thank you for your proposal, we are thinking about it seriously and it is in our perspectives.

The TRANSFAC database is interesting yes but TFinder does not have its own server, this is what it does so that it can support several work sessions at the same time. Not having a server, we cannot use a downloadable database (like TRANSFAC) and we have focused on APIs which are more modular and up-to-date without worrying about the version of the databases used (NCBI, JASPAR). I know that TRANSFAC also has an API, but you need a paid license. I need to find out if we can make TRANSFAC available if we pay for the license.

In any case, multi TF is developing. Also, your TF is not available on JASPAR?

— Reply to this email directly, view it on GitHub https://github.com/Jumitti/TFinder/issues/59#issuecomment-2104800071, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ5CPFDLGNK3W3RILPKHLITZBTQ7LAVCNFSM6AAAAABHQY4ZUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBUHAYDAMBXGE . You are receiving this because you were mentioned.Message ID: @.***>

Darius-bit commented 3 months ago

For sake of completeness, I would like to mention that JASPAR 2020 transcription factor matrices can be freely downloadable from the CiiiDER website, at http://ciiider.com/ Best Dario

Il giorno lun 13 mag 2024 alle ore 16:30 Dario Balestra < @.***> ha scritto:

The main goal is to find differential TFs from two set of organ-specific promoters. To do this task I need to discover all TF present in one set, and not in the other. So finding a specific TF is easy, but I do not know which tissue-specific TF are guiding the expression of my genes. Best Dario Balestra

Il giorno ven 10 mag 2024 alle ore 17:23 Minniti Julien < @.***> ha scritto:

Hello @Darius-bit https://github.com/Darius-bit,

Thank you for your proposal, we are thinking about it seriously and it is in our perspectives.

The TRANSFAC database is interesting yes but TFinder does not have its own server, this is what it does so that it can support several work sessions at the same time. Not having a server, we cannot use a downloadable database (like TRANSFAC) and we have focused on APIs which are more modular and up-to-date without worrying about the version of the databases used (NCBI, JASPAR). I know that TRANSFAC also has an API, but you need a paid license. I need to find out if we can make TRANSFAC available if we pay for the license.

In any case, multi TF is developing. Also, your TF is not available on JASPAR?

— Reply to this email directly, view it on GitHub https://github.com/Jumitti/TFinder/issues/59#issuecomment-2104800071, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ5CPFDLGNK3W3RILPKHLITZBTQ7LAVCNFSM6AAAAABHQY4ZUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBUHAYDAMBXGE . You are receiving this because you were mentioned.Message ID: @.***>

Jumitti commented 3 months ago

I understand your problem better. TFinder is mainly made to facilitate the analysis of promoter and terminal regions of genes and search for a pattern (individual motif) or a TFBS in these same sequences. Example: you are studying the XZ protein which is a transcription factor not available in the database because it is still too recent. You have RNA-seq and you want to look if the TFBS of protein XZ is present on certain RNA-seq genes. This also works with a JASPAR TF.

If your goal is to discover all the FTs that can be fixed, other software is available to do this like PROMO (even if it is old) and other tools. JASPAR also allows you to do this but it is limited to 2000 bp. Other software also exists but is more complicated to use such as HOMER or Homocomo

And yes indeed, we can download the JASPAR databases even 2024 but the problem is that we do not use servers to store the software. Using the API allows you to avoid having an absence of obsolete data (even if the majority of TFs will not be affected by this).