charlesbreeze
commented
5 months ago Hi Isaac,
Motifs from FORGE2-TF and eFORGE-TF come from several main sources: a) TRANSFAC, b) JASPAR, c) UniPROBE, and d) the TF motifs obtained from Jussi Taipale’s lab -which are coded “Taipale”. These admittedly are a range of sources, have you tried searching for the TF motif "V_AP4_Q6" in google/pubmed? For some motifs we have to go back to these sources, for others there are multiple annotations present online, available via google/pubmed.
A google search for "V_AP4_Q6" brings up more details for this TRANSFAC motif for the gene transcription factor AP-4 (activating enhancer binding protein 4):
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text with details: https://www2.stat.duke.edu/~sayan/assess/genesets/Jan2006/cards/C3/V_AP4_Q6.shtml
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TF motif logos for AP-4 motifs, among others: http://www.mauranolab.org/CATO/weblogos/DataS2.pdf
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consensus sequence: https://www.bioinformatics.org/grn/matrix_list
Given the many sources, it is admittedly not always easy to pinpoint data in every single case, but searching in these repositories should cover most motifs.
Let me know if you have any more questions!
Best,
Charles
Y-Isaac
HI,
Thanks for this tools. I would like to inquire about how to further understand the TF Motif information related to the SNP I submitted. For example, I submitted the SNP rs10409243, the result shows that it belong to TF Motif _V_AP4Q6, but I don't understand what it actually represents, and the TF Motif _V_AP4Q6 is not a standard name. I also try to query it in url https://eforge-tf.altiusinstitute.org/, but there doesn't seem to have the information I'm looking for either.
May be my quetion is a little silly, I am new in this field. Thanks for your help in advanced!
Best regards, Issac