Motif model change to transcription factor

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2.6 years ago

zzzZZZ • 0

hi all, I have one file in which the first column is the motifs( model from hocomoco). for example AP2A_HUMAN.H11MO.0.A And I want to change it to a transcription factor, like TFAP2A(from genecards). How can I get the gene names with package biomart?

Thanks in advance.

R biomart hocomoco • 827 views

ADD COMMENT • link 2.6 years ago by zzzZZZ • 0

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Can you show a snapshot of the following file?

one file in which the first column is the motifs( model from hocomoco)

ADD REPLY • link 2.6 years ago by Hamid Ghaedi 3.3k

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hi, here is the file. enter image description here

I want to change the motif_id to the Transcription factor with R. Here for example ERR1 to ESRRA. But I don't know what to do with biomart package. enter image description here

This bild is from https://hocomoco11.autosome.org/search?arity=mono&query=ERR1&species=human

ADD REPLY • link 2.6 years ago by zzzZZZ • 0

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In the file there is no "Transcription factor" column, right? If you have both columns in one file, you do not need to use biomaRt.

I downloaded data by clicking on the largest circle on this page, then on the next page clicked on "CSV" to download the file. It looks like this: enter image description here . Read this file into R, then split the "Transcription factor" column to obtain the string after : and save the second part as a column. The result can be what you are looking for.