Question: visualization of gene-miRNA interaction
1
gravatar for naodm2006awet4
3.9 years ago by
Finland
naodm2006awet420 wrote:

Hi All,

I have been trying to get miRNAs that are co-expressed with the genes. I computed the correlation matrix between the the two based on their expression. Now I would like to visualize their relationship. Is there any way to visualize the correlation matrix?  In addition to that, I also built a network in ARACNE algorithm with the rows of gene names and columns of miRNA names and I tried to use "Rgraphviz" package, but I got an error saying the column names and row names of the network should be the same. Can I also get some help regarding this? Thank you!

 

rna-seq R • 1.4k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by naodm2006awet420
1
gravatar for Biomonika (Noolean)
3.9 years ago by
State College, PA, USA
Biomonika (Noolean)3.0k wrote:

These are very nice correlation plots:

http://www.sthda.com/english/wiki/correlation-matrix-an-r-function-to-do-all-you-need#prerequisites

What are your exact commands for second problem?

ADD COMMENTlink written 3.9 years ago by Biomonika (Noolean)3.0k
1
gravatar for naodm2006awet4
3.9 years ago by
Finland
naodm2006awet420 wrote:

Thank you for your help. What I actually trying to do is, I have an a normalized read count for gene expression and miRNA expression. I computed a correlation between the genes and miRNAs based on their expression. I got a correlation matrix of rows with gene and columns with miRNAs. 

As I noticed from corrplot package, it helps to visualize the correlation within the dataset or within the genes in the gene expression dataset or within miRNAs in miRNA expression dataset.

My second question is similar to former one, Rgraphviz package is good enough to plot, for example, the gene networks. But I wanted to plot the gene-miRNA network. For example, I have a network in the form of matrix again with the genes in a row and miRNAs in the column. While I try to use Rgraphviz  package to plot the network, it says the column names and row names must be the same. And I was wondering if there is a way to visualize the gene-miRNA networks. Thanks again for your help.

 
 
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by naodm2006awet420
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