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jiang-junyao / IReNA

R package IReNA
GNU General Public License v3.0
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About TF motif datasets for other species #5

Open LalicJ opened 1 year ago

LalicJ commented 1 year ago

Hi, do you have any suggestions for building TF motif datasets for other species, like Macaca fascicularis? I see it in the tutorial user-defined motif dataset which should have the same format as these from TRANSFAC database., but I don't know how to prepare my own dataset. Hope to your reply. Thanks for your time.

jiang-junyao commented 1 year ago

Hi, You just need to make a table that context type in each column is the same as our inner TF motif db. For example, the first column should be motif accession, the second column should be motif ID, and so on.... If you still dont know how to make such db, you can send me your motif-tf db, i will help you to complete this part.

LalicJ commented 1 year ago

Thanks for your understanding and help. Actually, I have a set of multi-omics data for macaca fascicularis, but I have been using data from JASPAR[Vertebrata] for motif analysis in the past. Can I use human data from TRANSFAC database directly for analysis?

jiang-junyao commented 1 year ago

I think only the conserved transcription factor related motifs in human TRANSFAC db are make-sense to do further analysis, and if you can send me your JASPAR table, I can help you to make appropriate rdata file to do IRENA analysis.

At 2023-02-27 09:20:11, "LalicJ" @.***> wrote:

Thanks for your understanding and help. Actually, I have a set of multi-omics data for macaca fascicularis, but I have been using data from JASPAR[Vertebrata] for motif analysis in the past. Can I use human data from TRANSFAC database directly for analysis?

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LalicJ commented 1 year ago

Thank you!

I can send them all to you. Thanks again for your help! Also, I found another annotated TF motifs in macaca fascicularis in another database[CIS-BP Database], but I don't know which data is better. Maybe the latter (the compressed file) the latter fits the bill.

At 2023-02-27 21:37:10, "jiang_junyao" @.***> wrote:

I think only the conserved transcription factor related motifs in human TRANSFAC db are make-sense to do further analysis, and if you can send me your JASPAR table, I can help you to make appropriate rdata file to do IRENA analysis.

At 2023-02-27 09:20:11, "LalicJ" @.***> wrote:

Thanks for your understanding and help. Actually, I have a set of multi-omics data for macaca fascicularis, but I have been using data from JASPAR[Vertebrata] for motif analysis in the past. Can I use human data from TRANSFAC database directly for analysis?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

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