Questions tagged [transcription-factors]

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Where to get BED files for regions that contain binding site motifs for specific transcription factors?

Quick question, is there a place where one can download BED files for the binding motifs of certain transcription factors. In my case, I'm looking for a BED file for the genomic regions (enhancers) ...
user305902's user avatar
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If regulatory proteins decide the gene regulation, is it necessary for every cell to have a different look? [closed]

Transcription factors regulate the genes in different cells. That is, different cells have different sequence of genes that are transcribed (set on or off) by the RNA polymerase. This will help ...
Deepak Tatyaji Ahire's user avatar
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What's the meaning of Txn factor?

The transcription factor track in UCSC is named as Txn factor. Why Txn == Transcription?
Jie's user avatar
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Is there a software that can predict protein-DNA binding?

Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
Anthony Guterres's user avatar
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Profile HMM to find sequence motif using Baum-Welch instead of using a given multiple sequence alignment?

I know this can be very problem-specific -- but it seemed to me the standard approach to train an HMM to recognize a binding pattern of a protein is to use the multiple sequence alignment (MSA), ...
skc's user avatar
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Biological replicates on Chip-seq Transcription factor data

I have 2 biological replicates for chip-seq transcription factor data and I have applied macs2 peak calling for each replicate separately. How can i make use of the biological replicates to extract ...
Dimtiris's user avatar
1 vote
1 answer

how to obtain GRCh38 bed and symbol files for HOCOMOCOv11

I am trying to a recently published software called diffTF and contacted the authors on how to obtain the input HOCOMOCO files for GRCh38. While I wait for the answer, I thought I would post the ...
719016's user avatar
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