Skip to main content
6 votes

Relative abundance of transcription factors and protein kinases

Summary The abundance of protein kinases and transcription factors vary among and between these broad classes of protein. General Considerations Let us first think what might be expected for the ...
David's user avatar
  • 26.2k
4 votes
Accepted

How can a nucleotide falling *outside* a binding site affect a transcription factor's ability to bind to said site?

This is an answer to the general question posed in the title and not what is happening in the specific case of C/EBPβ. How can a nucleotide falling outside a binding site affect a transcription ...
acvill's user avatar
  • 8,296
3 votes

How to find transcription factors?

How can I detect transcription factors and preferably master TFs (master regulators) in an organism? The easiest approach to find transcription factors for any given organism would be based on ...
Nicolai's user avatar
  • 4,391
3 votes

Etymology of PAX proteins

In addition to the other answer, the following is some historical context on the naming of these genes. 1980 October: Discovery of pair-rule genes in Drosophila. Nusslein-Volhard C, Wieschaus E. ...
canadianer's user avatar
  • 17.8k
3 votes
Accepted

Etymology of PAX proteins

According to InterPro, a paired domain is a DNA-binding element consisting of paired N-terminal and C-terminal subdomains, separated by a linker. PAX proteins follow this motif, and as such typically ...
CKM's user avatar
  • 8,119
2 votes

How does a cell identify itself?

This has been studied this in Drosophila, and a lot of development hinges on where the cell is in the body. An initial asymmetry of mRNA in the pre-fertilized ovum leads to the establishment of the ...
swbarnes2's user avatar
  • 5,230
2 votes
Accepted

Are transcription factors some kind of eQTLs?

No, eQTLs and transcption factor are very different things. Like you described TFs are proteins that control the expression level of genes. eQTLs are nothing that is physically present in the cell. ...
Nicolai's user avatar
  • 4,391
2 votes

What is the meaning of NF-kB (transcription factor) "activity"?

The word activity has at least two meanings in biochemistry. One is chemical activity as in the effective concentration of a chemical. This comes up a lot because biomolecules often behave non-ideally....
Ryan's user avatar
  • 1,321
1 vote
Accepted

model organism for maize

Why not maize itself? (And other grasses) If for some reason you need something that is more explicitly a model organism, I suppose you could look at Arabidopsis. That link actually includes a large ...
Maximilian Press's user avatar
1 vote

Is there a resource/paper containing information about which co-activators are often associated with a given transcription factor?

This website can be used to search for protein interactomes: http://www.interactome-atlas.org/ might help you.
Paul Goodman's user avatar
1 vote
Accepted

What is sigma factor PvdS?

Clarification of the Question It appears to me that the question posed in the title of this question, “What is sigma factor PvdS?” is answered by the poster — it is a sigma factor that is specific for,...
David's user avatar
  • 26.2k
1 vote

Finding targets of transcription factors

If you were interested in human targets, one easy way is GeneCards, which aggregates other resources, and combines computational and (some) experimental data: In this case the inverse problem is ...
tsttst's user avatar
  • 1,597
1 vote
Accepted

Can the same target gene be regulated differently by the same transcription factor under different conditions?

Short answer - yes but probably somewhat rarely. Transcription factors aren't necessarily limited to being either repressors or activators. In practice they mostly do one a lot more than the other - ...
Dermot Harnett's user avatar
1 vote
Accepted

Origins of transcription factors and RNA Polymerase

This is one of the main features of the RNA World. What I mean by that is, RNA not only acts as a repository of genetic information, it also acts as an enzyme. This enzyme is known as Ribozyme. ...
Vasundhara Gray's user avatar
1 vote

How do enhancers induce transcription?

The activators are proteins that bind to specific DNA sequences in the enhancer region. These activators also bind to the RNA polymerase and other associated members of the transcription complex, ...
Thymine's user avatar
  • 259
1 vote

General Enhancer Questions (Methylation Patterns, ect.)

This subject is actually both complicated and incompletely understood. For example, there is evidence that some enhancers don't result in loops at all — instead their influence travels along the ...
tyersome's user avatar
  • 5,598
1 vote

How does a cell identify itself?

If all cells have identical genomes and, therefore, identical transcription factors Important comment: all cells do indeed have identical genomes, and all cells are therefore equipped with DNA that ...
S Pr's user avatar
  • 6,272
1 vote

Do transcription factors block transcription entirely?

Of course it's never 100%. The protein still has a measurable Kd for the DNA, meaning that there's always some part that's not bound (or some time that it's not bound. Besides that, you're talking ...
VonBeche's user avatar
  • 1,473
1 vote
Accepted

What regulates production of first transcription factors during development?

The first transcription factors for the first transcription after fertilization are already present in the ovum (egg) before it is fertilized. Generally, all the machinery needed for transcription, ...
mgkrebbs's user avatar
  • 9,054
1 vote
Accepted

TRANSFAC Matrix.dat retrieve count matrix using BA or CC field

So databases like TRANSFAC are of somewhat... variable quality. Those matrices maybe have been derived from a program that just doesn't output a count matrix, but instead outputs a frequency matrix ...
Dermot Harnett's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible