Saccharomyces cerevisiae TFs
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3 months ago
Deepblue ▴ 10

Hello. I want to predict transcription factor binding motifs in my rna-seq data. Is there any database that stores S. cerevisiae TFs as a list? I have found JASPAR, but that doesn't give me a list. Thanks in advance...

RNA-SEQ • 621 views
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you might want to consider elaborating on what you consider "a list" . Perhaps add some dummy example?

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I agree with lieven.sterck - that said, you might want to take a look at what is available via the JASPAR REST API https://jaspar.genereg.net/api

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Thanks both. Sorry, probably I should have mentioned that I'd like to predict transcription regulatory network from my rna-seq data and some packages need the transcription factors as an input. The JASPAR rest gives the binding motifs only as far as I understood?

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some packages need the transcription factors as an input

And what is the format of this transcription factor data that you need? Do you need to know what S. cerevisiae genes are transcription factors? Do you need to know where transcription factors are bind in the genome?

I only suggested the JASPAR REST API b/c you mentioned it as a potential resource for the information that you are seeking.

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I only need the transcription factors of S. cerevisiae

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3 months ago
jv ▴ 400

One option for getting a list of S. cerevisiae genes that are annotated as transcription factors would be BioMart and filtering for genes with gene ontologies (GO terms) associated with transcription factor activity. You can also add filters for protein domains related to transcription factor activity as well.

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YeastMine is also great for making lists for genes specific to S. cerevisiae. I note in the browser-based QueryBuilder they list 'GO Term' as a choice among many others. To get an idea how to use the QueryBuild, I find studying examples available in Templates are very helpful. You can view the full-built Query for these, by selecting one from the list, and then select Edit Query button down on the right side. Then you can adapt basic ones to do what you need.

I do note that one of the templates at YeastMine is:


Retrieve all Regulators and their Summary Paragraphs


And we can use that as example of running a Query and how to get a list. If you select 'Retrieve all Regulators and their Summary Paragraphs' from templates and then click green 'Show Results' button on the next page, you'll get a Table with lots of genes. For each table like this that YeastMine makes, there's a button in the upper right side that you can choose 'Save as List'. (If you make an account with YeastMine, you can actually save your lists so there are there when you log back in.) And you can also use 'Export' in the upper right. This is what you want to use to download the type of list where each gene is on a single line. The 'Export' dialog lets you toggle off columns, by selecting 'All columns' and then toggling off ones you don't want to include so that you can just leave the gene's standard name and choose to Download the file with 'Download TSV file'. Also while in the 'Export' dialog window, you can use the 'Preview' feature on the lower left side at any time to get a sense of what your list will look like as you select your columns.

YeastMine lists the source of regulation related data (Transcription Factor and Target relationships) here.