How to find transcription factors list?

Question

[Sky]

Hello everyone I am new to bioinformatics and I am really confused about Transcription factors. I want to find TF lists of some genes and I tried to read a lot of other people questions and posts and different websites they provide in the comments. But when I try to open those websites I don't understand anything and how to find transcription factors of certain genes. A lot of people recommended Transfac but I don't know how to find there. And in some websites I can't find the list of certain genes.

So can anyone help me to explain how I can find transcription factors list and it's proper way.

Thank you so much

[Ram]

Please do not use bioinformatics as a tag unless your post is about the field of bioinformatics itself. For proper examples, please see Forum and News type posts under https://www.biostars.org/tag/bioinformatics/

I've removed the tag this time but please be more mindful in the future.

Answer 1

[gglim]

try decoupleR

library(decoupleR)
library(OmnipathR)
net <- get_collectri(organism='human', split_complexes=FALSE)

> str(net)
tibble [42,595 × 3] (S3: tbl_df/tbl/data.frame)
 $ source: chr [1:42595] "MYC" "SPI1" "SMAD3" "SMAD4" ...
 $ target: chr [1:42595] "TERT" "BGLAP" "JUN" "JUN" ...
 $ mor   : num [1:42595] 1 1 1 1 1 1 1 1 1 1 ...

[Sky]

Can you explain a bit more how to open this.

[gglim]

It's an R package, you can download the RStudio and use the R language conveniently.

[ATpoint]

I'll note though that transcription factor targets are very celltype-specific so I would probably not trust such a general resource. Is there information available how the package created these lists?

For example, Spi1 (PU.1) is very canonically expressed in hematopoietic, especially myeloid cells, whereas its "target" BGLAP is a gene mainly found in brain and GI tract tissue. I think it is really celltype-dependent whether there is a regulation between these two, and whether both are even expressed in the same cells at a given time.

[gglim]

Hi ATpoint, thank you for your insights. You are right, I should think more carefully about the biological part. The package was utilized in this article I referenced to learn specific analysis methods.

Answer 2

[massa.kassa.sc3na]

Hi, generally speaking, even getting the list of genes that are TFs is non-trivial for some organisms and usually such a list is incomplete.

• One of the most comprehensive resources about what protein is transcription factor, that I've found, is here: https://zenodo.org/records/4264963 (prediction only).

Deriving whether the TF of interest actually binds in regulatory region and influence your gene of interest is another matter. For some organisms and for some TFs this was studied and some of this knowledge was transferred to one of the databases (such is TRANSFAC). These can be list of influenced genes, possibly with binding motifs (which you than can try to use to derive new binding sites).

As you can see, previous paragraph contains lot of "some". To my knowledge, there is very few databases, updated with recent literature, especially for bacteria. The situational appears to be better in human and other model eukaryote (please correct me if I'm wrong). Depending of your organism of interest, you might need to make literature review yourself. (Possibly compiling list of binding motifs and searching regulatory regions yourself; also Chip-seq, perturb-seq and other experiments are sometimes already available, and you can try to compile the results.)

Answer 3

[jared.andrews07]

See this answer to a previous question with some options. I presume you want TFs that bind/regulate your genes of interest.