I have 1200 TFs. I should make a 1200 in 1200 matrices to compare them and get TF-TF interaction. How can I do it? What programming can I use? yes, I am trying to do is look for evidence of interaction (Y/N) between 1200 transcription factors by making a 1200 x 1200 matrix to look pairwise interactions between each of the 1200 TF. My data are human protein and were downloaded as file text. But I don’t know how to do it.
3 answers
Use a protein-protein interaction databases and use one of those to build your matrix, See other biostar threads for more info on PPI database. e.g. What Is Your Experience With The String (Interactions) Database?
•
written
by
Maximilian Haeussler
If you go to genecards link text and write your TF name and then in part of pathways&interactions you can observe interaction of your specific TF with the other proteins.But unfortunately I do not know to solve the problem by matrix... I am curious about it, good luck.
Pairwise interaction is not always a good approach to compute/establish interaction between such a huge list of TF's. I would suggest you to read the following article, " Scoring overlapping and adjacent signals from genome wide ChIP and DamID assays". This reviews gives an insight to the statistical methods which could be applied to study the interaction pattern between TF's. furthermore, you may also use Cooccur package from David huen.
Log in to answer this question.
-
Confusion of TF-gene interactions database
written by Batu
-
how can I extract group or modules from a huge number of intractions between gene-TF or gene-miRNA?
written by Calangoa •
-
Can we compare peaks of different transcription factors when they were obtained by different criter…
written by salamandra
-
extracting a file from a bigger file
written by zizigolu
-
transcrption factor analysis
written by flavia •
-
Tool: PlantTFDB and PlantRegMap: Plant Transcription Factor Database and Plant Regulation Data and …
written by jin •
-
removing and keeping some part of a matrix of genes interaction
written by zizigolu
-
removing gene-gene interaction from a correlation matrix
written by zizigolu
-
Is there a tool to retrive transcription factors (Tfs) which have the common binding site?or a tool…
written by mary99 •
-
is there any transcription factor and its target gene database?
written by Kurban
whar is TF ? a transcription factor ? What kind of data do you have ? What do you mean by "comparing" two TFs ?
and what would the data (numbers) you put in your 1200 x 1200 matrix represent?
I believe what shahram is trying to do is look for evidence of interaction (Y/N) between 1200 transcription factors by making a 1200 x 1200 matrix to look pairwise interactions between each of the 1200 TF in question. What I would suggest is a protein-protein interaction database but I dont know how accurate these are.