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Questions tagged [transcription-factor]

Transcription factors are proteins which regulate the expression of genes. They are divided into two groups: The group of the general transcription factors which are present in every transcription and the special transcription factors, which are present in specific tissues or cells.

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Does every protein encoding gene necessarily have a transcription factor?

For instance, transcription factor gene A is responsible for activating gene B that encodes protein 1. However, it is possible for genes like gene B to encode proteins without having transcription ...
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Finding targets of transcription factors

I'm trying to find an easy way to get a list of putative targets of a particular transcription factor (for example, STAT1). I'm interested in targets determined using both experimental and ...
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How might the distance from the transcript start site affect genetic interactions?

How might the distance from the transcript start site affect the extent to which a nearby noncoding variant may vary the level of expression at a coding variant? My guess would be that a greater ...
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response elements in transcription regulation

I'm studying eukaryotic gene regulation and I want to know whether there are some instances where transcription factors don't need to bind to response elements to initiate transcription. RNA ...
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What's the difference in roles of GATA-2 and BMI-1 in guiding Hematopietic cells?

I've discovered that hematopoietic cells become lineage-positive (Lin+) and go down the path of becoming lymphoblasts and myeloblasts, and that both BMI-1 and GATA-2 are transcription factors that ...
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Can the same target gene be regulated differently by the same transcription factor under different conditions?

I'm very new in biology and doing more computational analysis. I'm confused with the type of interactions between Transcription Factors (TF) and target genes. Is it possible that the same ...
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Are transcription factors some kind of eQTLs?

Cause of working on Allele-Specific expression, working I am trying to know more about expression quantitative trait loci (eQTLs). based on definition, eQTLs are loci that control the expression level ...
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How to find transcription factors?

I need to find master transcription factor(s) regulating secreted proteases in a fungus to be disrupted toward upregulation and overexpresion of extracellular recombinant proteins. How can I detect ...
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Where can I find a list of transcription factors that are used in somatic embryogenesis? [closed]

Where can I find a list of TFs that are used in somatic embryogenesis or zygotic embryogenesis?
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Etymology of PAX proteins

What is the reasoning behind naming proteins first found in Drosophila as paired box? All I could find on internet is that it was first found in Drosophila as a protein with paired domain, but I ...
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Do transcription factors block transcription entirely?

Transcription factors bind to the DNA to block the transcription of a certain gene, right? But while they are bound to the DNA, do they completely block any transcription of this gene for as long as ...
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What regulates production of first transcription factors during development?

In my biochemistry class, we learned that transcription factors regulate the transcription of genes. However, transcription factors are also coded by genes, so what activates the transcription of ...
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TRANSFAC Matrix.dat retrieve count matrix using BA or CC field

In the TRANSFAC Matrix.dat most of the motifs are given in the form of count matrix, but a few of them are given as some kind of frequency matrix. Those aren't ordinary PWMs because rows don't sum to ...
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What are in common between transcription factors?

In terms of their structures (primary to tertiary) and locations? Why do they have these commonalities? Or are any of these commonalities critical to their functions?
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How would one identify cellular transcription factors associated with a viral protein in a treated cell line?

I've been working as the computer guy for a microbiology lab for the past few months. I've always been interested in bench work, but my wet lab experience is rather limited and thus so is my ...
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curly braces in sequence motifs

what do curly braces in sequence motifs stand for? e.g. in RTCRYBN{4}ACG what is N{4}? moreover, i notice that in TRANSFAC ...
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Toll Like Receptors Vs Toll Receptors

What are the major differences between them, apart from one being in humans and other in Drosophilla?
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General transcription factors vs. DNA Binding transcription factors

I know that DNA binding transcription factors are trans-acting, but what about general transcription factors? Are they cis or trans acting?
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How do DNA-binding proteins recognize the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-...
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Is there a consensus on the CaMV 35S minimal promoter sequence?

We have an algal enhancer element and a transcription factor that probably binds it. Basal expression of the enhancer element or full promoter driving luciferase in tobacco protoplast was extremely ...
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Are upstream activating factor (UAF) and upstream binding factor (UBF) the same thing?

During ribosome pre-40S and pre-60S synthesis, many sources state the importance of UAF or UBF in initiation complex of ribosome DNA transcription. None of the sources I've seen mentions the other ...
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Is RNA polymerase affected by proteins bound to the coding sequence of a gene?

I am designing a synthetic gene construct to express genes in E. coli driven by either Ptet or PLacO. The construct would look like: -Ptet-(Gene1)-PLacO-(Gene2)- I want to express each gene using ...
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Do transcription factors bind to both strands of DNA?

Do transcription factors (or generally proteins) bind to only single strand of DNA or both strands? Since it can have non covalent bonds to both strands in theory. I would like to know the mechanism. ...
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Why are most transcription factors enhancing the expression rather than repressing?

One can classify the effects of Transcription Factors (TF) on gene expression into two types: it either enhance or repress the gene expression. I have always been told that most of transcription ...
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Resource for finding Repressive/Inhibitory factors for a given gene?

I have a list of genes for each of which I'd like to find: A list of transcription factors that up-regulate the gene A list of inhibitory factors that down-regulate it. I used this tool on Qiagen's ...
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what is the biggest known functional distance between an enhancer and its target gene (TSS) in cis?

since the title seems self explanatory; It would be nice if anybody could provide a reference. I'm looking for a paper that I belive stated around 1.5 Mb but anything above will be cordialy welcomed. ...
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Number of autoregulation and FFL motifs in a network

Suppose we have a network with N* nodes (N* is the number of internal nodes). Every directed link in this network exists with probability p. What would be the number of: motifs that are auto-...
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How can I re-format my DNA motifs' position weight matrices?

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites). The motifs belong to several species, and I wanted to cluster these ...
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How many transcription factors are there?

In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to ...