Thanks for your answer Kevin, please let me know how to see in which module TP53 is assigned in WGCNA, I am new to this package, also using igraph, how can i filter the networks associated with TP53 in my gene expression data? What should I do after performing cor() and cor.test() - I ordered the correlations - I am not sure what should I do next.. Please help.
Find top genes that correlate with my gene of interest using WGCNA
HI
I want to know how to use WGCNA package to find gene expression networks related to your gene of interest. For example, If I want to know how p53 gene is correlated to all other genes in the expression matrix (RNA-Seq experiment), and find the top positively and negatively correlated genes, and then perform co-expression network analysis, gene ontology analysis for those highly positive and negative correlated genes with the P53 gene.
All the tutrials that I have seen in WGCNA from here: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/
The tutorials concentrate on analyzing the whole gene expression matrix , but I want to start with the correlation with my gene of interest with the rest of the genes, how can I perform this. If you know of any other tools, all the suggestions are welcome. Thanks.
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I do not see why WGCNA cannot be used in this situation. You would perform WGCNA and then check in which module TP53 is assigned, and then perform enrichment, etc. on the genes in that module.
If you instead just want a simple signed / unsigned correlation network, then try my own tutorial: Network plot from expression data in R using igraph
On the other hand, if you simply want to find genes statistically significantly correlated to TP53, then do you even need to do any 'network' analysis? You could instead just use cor() and cor.test().
Kevin
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please let me know how to see in which module TP53 is assigned in WGCNA
This should be apparent from the WGCNA vignettes, I think (?)
What should I do after performing cor() and cor.test() - I ordered the correlations - I am not sure what should I do next.. Please help.
If you have already done the correlation [to TP53] then I cannot really advise further. Please talk to your supervisor about the next step(s), as I do not know the broader picture of what you are aiming to do.
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I have performed cor() and cor.test(),
gene<-expr["gene_name",] cor<-apply(expr,1,function(x){cor(gene,x)}, gene)
I got the data like this:
I have ordered the correlations to see the top positive and negative ones, then I got this:
ABCD2 CCDC69 ESR2 FCRL2 FCRL5 IRF4 KCNA3 LAX1 NUGGC 0.5910211 0.5719230 .6686700 0.5685326 0.5819445 0.5857473 0.5744376 0.5685258 0.5964405 POU2AF1 0.5628753
Ignore the gene names here,
Then I do not know what should I do next, the graph I am getting is just one line (as it is in the matrix) I want scatter plot or correlation plot, which I am not getting.
Yes, it is one line because you have only generated correlations for a single gene, TP53. A correlation network is every gene correlated to every other gene; It seems that you may need to go back a step to fully understand what it is you are aiming to do with this work. If you just want to find genes that are correlated to TP53, then your work is already complete.