Using Sirene in MATLAB for GRN inference
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Entering edit mode
8.8 years ago
Diana ▴ 900

Hi guys,

I am trying to use Sirene for Gene Regulatory Network Inference of expression data as it is a supervised inference program and seems simple and straightforward to understand. Also has good reviews. I seem to be having some trouble producing the Cytoscape file from Sirene and therefore I cannot view the network. I am new to MATLAB and there's no support for MATLAB here at my department and thus I'm incapable of identifying what could be causing this. I will really appreciate if someone could help me with this. I know this seems strange but I have been emailing the authors regarding this program and haven't heard from them and it's been quite a few months now.

I feel quite lost and am unable to get help from anywhere as few people seem to know about this program. But the reviews about this program are quite good as is indicated in this paper as well.

I will write everything in detail here:

I am using MATLAB 7.10.0 (R2010a), compiler: Microsoft Visual C++ 2010 Express, libsvm-3.18

The program comes with test data for E.Coli which has expression, gene_names, operongroups and regulation files in data>ecoli folder. Then in results folder, there is a folder called ecoli with a MATLAB code file called runexperiment_libsvm. In the first instance, I wanted to test the program on given dataset of ecoli. So I changed the file locations in this runexperimnet_libsvm file to where I had saved them and everything is on the path now. Then I simply run this file in matlab and it begins to compute and print like so a number of times:

optimization finished, #iter = 452
nu = 0.000074
obj = -28.403413, rho = 0.994572
nSV = 355, nBSV = 0
Total nSV = 355
Accuracy = 100% (393/393) (classification)


and at the end, it gives me

-3293 new predicted interactions in the known regulation matrix.


Along with this, during computation, it plots a number of graphs such as roc, auc, aup plots. It also writes a text file called cytofile60.txt but its always empty and another text file called nb_new_pred.txt which says one line only

---> Warning : level of precision  60 % not reached


I don't understand why that is. It might be my limited knowledge about MATLAB that's causing this but I was rather hoping, it would at least give me the cytoscape file for the test data that comes with the program because all the parameters would be optimized for this dataset. Do I need additional commands to write the network to the cytoscape file? because I thought everything was already written in runexperiment_libsvm.m file and all one had to do was give path to the data files and that's what I did.

I will be so grateful if someone could help me with this.

EDIT: It wouldn't take much time to run and is quite fast. If some MATLAB guru could quickly test run it on the given data (which you don't have to download from anywhere and everything is in the zip folder of Sirene already), it will really help me.

Thanks a lot!!!

MATLAB GRN • 2.5k views
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Entering edit mode

Hi Diana,

Thank you, Debashis