Target genes of transcriptional factors from co-expression networks · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Target genes of transcriptional factors from co-expression networks

This might be a bit lame question. I have built a co-expression network from gene expression data. I observed that the network contains many transcription factors. If I consider a transcription factor, will any of its first-degree neighbour (which has a high correlation value with the transcription factor) give me any idea what are the target genes of that factor ? I have seen a few papers highlighting the first neighbours of TFs but I am not sure why they do this. Any view on this will be greatly appreciated.

co-expression network transcription factors

• 3,408 views • link

updated 12.0 years ago by Devon Ryan

• written 12.0 years ago by pixie@bioinfo

1 answer

Yeah, the most strongly correlated genes, which would presumably become first-degree neighbors if you did things correctly, are likely targets. This isn't definitive of course, but it'd be a smart starting place.

• 0 views • link

written 12.0 years ago by Devon Ryan

Thanks Devon !

• 0 views • link

written 12.0 years ago by pixie@bioinfo

Log in to answer this question.

More posts like this

Gene regulatory networks from expression data
written 7.9 years ago by pixie@bioinfo

Hello, I have RNA-seq data of a plant species. Is it possible to construct a gene-regulatory network, if I provide the transcription factor information ? …
RNA-seq Co-expression network construction from the output of DESeq2
written 8.7 years ago by pixie@bioinfo

Hello, I have generated a read count_matrix using DESeq2. I would like to construct co-expression network using WGCNA. For microarray data, they suggest to use …
Can we predict/quantify transcription factor activation using gene expression data?
written 9.7 years ago by Diwan

Hello, I am interested in analyzing transcription factor (TF) activity. Activation/activity of TF will be reflected in the altered gene expression of target genes. **Can …
co-expression between transcription factors and their targets
written 10.5 years ago by nazaninhoseinkhan

<p>Dear all,</p> <p>I have a basic question.</p> <p>I have constructed gene regulatory network for a bacterial pathogen based on expression data.</p> <p>In resulted network high …
Differential Network Analysis
written 10.6 years ago by pixie@bioinfo

<p>I have two sets of co-expression network, set 1 and 2. Set 1 has been built by combining a number of different microarray datasets corresponding …
transcription factor binding sites were not over represented in modules
written 11.1 years ago by beiki.h.m •

<p>Hello, my name is Hamid, I have constructed a condition independent gene co-expression network. There are some transcription factors in modules of this network. The …
Target Genes For Transcription Factors In Plants
written 12.4 years ago by pixie@bioinfo

<p>I am working on co-expression analysis of rice gene expression data using WGCNA approach. I have obtained a number of gene clusters. I am interested …
Calculating Expression Conservation Score Between Two Gene Co-Expression Networks
written 12.9 years ago by Bioinfo_2006

<p>Suppose these two matrices </p> <pre><code> set.seed(1) x <- matrix(rnorm(1000), nrow=100, ncol=10) y <- matrix(rnorm(1000), nrow=100, ncol=10) </code></pre> <p>represent the genes (as rows) and genotypes …
Microarray Expression Data For Network Analysis
written 14.9 years ago by pixie@bioinfo

<p>I have a couple of <strong>Microarray datasets</strong> belong to different experiments collected from ArrayExpress and GEO for a <strong>particular disease</strong>.</p> <p>I have analyzed them, built …
Basics Of Systems Biology...
written 16.0 years ago by pixie@bioinfo

<p>I have been entrusted with the job of planning some <strong>systems biology</strong> work. I have gone through numerous papers related to network biology where networks …