converting mutual information matrix to gene regulatory network

> head(MI[,1:4]) hsa-let-7a-1 hsa-let-7a-2 hsa-let-7a-3 hsa-let-7b ACTB 0.012524427 0.026290733 0.012733996 -0.0006921249 ACTG1 -0.019429116 -0.010771804 -0.002583545 0.0072491626 ACTN4 -0.014522811 0.001822348 -0.005929466 -0.0138257202 AGR2 0.010171113 0.024482873 0.018627891 -0.0141422661 ALDOA 0.007940716 -0.007355786 -0.005625332 0.0027172067 ANXA2 -0.005766246 -0.003621098 0.011360110 -0.0636632984 >

> grn <- aracne.a(MI, 0.05) > head(grn[,1:4]) ACTB ACTG1 ACTN4 AGR2 ACTB 0.0125244268 0.000000000 0.000000000 0.010171113 ACTG1 0.0000000000 -0.010771804 0.000000000 0.024482873 ACTN4 0.0000000000 0.000000000 -0.005929466 0.018627891 AGR2 -0.0006921249 0.007249163 -0.013825720 -0.014142266 ALDOA 0.0000000000 0.000000000 0.000000000 0.008910742 ANXA2 0.0000000000 0.000000000 0.000000000 0.000000000 >

2.8 years ago by

theobroma22 • 1.1k

theobroma22 • 1.1k wrote:

I don't follow, miRNAs disappeared?...isn't the grn object the matrix needed to plot the network?

ADD COMMENT • link written 2.8 years ago by theobroma22 • 1.1k

I mean grn created by MI dose not contain any miRNAs and there only mRNA in rows and columns while I was going to plot network by bith of them. whathappened for miRNA?

ADD REPLY • link written 2.8 years ago by A • 3.7k

Ok, but your tables do not show the error you are asking for help on in your post. So, it is a bit disconnected. Can you please show how the miRNAs are not in the co-expression or correlation matrix? Before you do this, first I think it is at least due to the eps value you used (0.05) for the arcane.a algorithm, a positive numeric value used to remove the weakest edge of each triple of nodes. Second, are you certain this is the algorithm you should use?? Can you tell me why you didn't choose the knnmi.cross algo in the parmigene package? I only looked at the reference manual and didn't search for any workflow/vignette, so sorry for my ignorance if I am wrong. Also, I think there may be other (perhaps better) ways to demonstrate miRNA-mRNA interactions such as by the sequence nucleotides, or using the http://mircomb.sourceforge.net/docs/miRComb-vignette.pdf package. Skimming this package vignette workflow there are two separate datasets, one for the mrna and the other for the mirna, then a correlation matrix is made this way. As such, as stated above this made me think you are using the incorrect algo for starters.

ADD REPLY • link written 2.8 years ago by theobroma22 • 1.1k

thank you I built MI matrix by knnmi.cross(mat1, mat2) function

ADD REPLY • link written 2.8 years ago by A • 3.7k

Ok, thanks. I read https://academic.oup.com/bioinformatics/article/27/13/1876/184634/parmigene-a-parallel-R-package-for-mutual

Your miRNA may be removed because they may be consider as indirect edges. I would recommend to use a package that is specific to miRNA-mRNA interactions. This parmigene method or aracane.a() function doesn't seem to do what you want to do, per se. This being said, what happens when you use the multiplicative algo, aracane.m()? Are the miRNAs removed?

ADD REPLY • link written 2.8 years ago by theobroma22 • 1.1k

Also, what happen when you use eps = 0.15 in the additive method, and what happens when you use a tau = 0.05 and 0.15 in the multiplicative method? Thanks.

ADD REPLY • link written 2.8 years ago by theobroma22 • 1.1k

Sorry...also try the mrnet function. This may be what you need to use. Thanks.

ADD REPLY • link written 2.8 years ago by theobroma22 • 1.1k

I think I should try miRComb might work. miRComb needs many packages as dependencies I am still downloading them.

ADD REPLY • link written 2.8 years ago by A • 3.7k

thank you for your kindly helps. actually grn inferred by clr, ARACNE or whatever in this package give a grn depends on miRNAs or mRNAs placed in row the same as the result. for example if in MI matrix miRNAs are in rows whole of grn is only miRNA.. vice versa

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by A • 3.7k

Ok, then the aracane.a function removes the miRNA due to how it computes the adjacency matrix. What happens when you do grn =mrnet(MI) ?

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by theobroma22 • 1.1k

I shared screen shots of MI and grn in R

as you consider MI contains both miRNAs and mRNAs but grn only mRNAs :(

MI https://y10i.imgup.net/MIde38.jpg

grn

https://u14i.imgup.net/grnc539.jpg

ADD REPLY • link written 2.8 years ago by A • 3.7k

What value did you use for the k argument in knnmi.cross(mat1, mat2) ? This is important.

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by theobroma22 • 1.1k

knnmi.cross(mat1, mat2, 5) as default

ADD REPLY • link written 2.8 years ago by A • 3.7k

sorry miRComb needs miRData R package as dependency but whatever I am trying to install that telling

install.packages("miRData")

Installing package into ‘C:/Users/Lenovo/Documents/R/win-library/3.2’

as ‘lib’ is unspecified)

Warning in install.packages :

package ‘miRComb’ is not available (for R version 3.2.5)

how I can download that please?

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by A • 3.7k

Are you using Linux, Mac or windows? It states that you need to use install.packages("miRComb_x.x.zip") for windows and "miRComb_x.x.tar.gz" for Linux and Mac. And x.x is the package version number. See https://sourceforge.net/projects/mircomb/files/?source=navbar

When you post, please put as much info as possible to help you in the least amount of back and forth. Thanks.

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by theobroma22 • 1.1k

First you need to download the file to the local folder, then in R use the above command.

ADD REPLY • link written 2.8 years ago by theobroma22 • 1.1k

yes you all right I am in windows

ADD REPLY • link written 2.8 years ago by A • 3.7k

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