How to compute Gene Regulatory Network on microarraay data
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shaheryar • 0
@shaheryar-8153
Last seen 4.8 years ago
Korea, Republic Of

Dear all,

I need a help. I have microarray data and i want to compute interaction graph so that it can be used for qualitative analysis. Can some one help me how i can do it. 

I want to compute gene gene interaction graph. Please help

microarray GRN gene interaction • 763 views
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chris86 ▴ 390
@chris86-8408
Last seen 22 months ago
UCL, United Kingdom

You have already asked this question. You can use ARACNE for this, for example. You want a tool that makes an adjacency matrix.

Margolin, A. A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Favera, R. D., & Califano, A. (2006). ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC bioinformatics, 7(Suppl 1), S7.

Basso, K., Margolin, A. A., Stolovitzky, G., Klein, U., Dalla-Favera, R., & Califano, A. (2005). Reverse engineering of regulatory networks in human B cells. Nature genetics, 37(4), 382-390.

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Thanks for your ans. I dnt want to use tool. Please tell me the logic behind it. I have only microarray human data with 24 samples and i want to made gene regulatory network. and put weights on it showing positve or negative edge.

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If you don't want to use a tool, you can at least read the references that Chris has provided, which is your gateway into learning about methodology behind how you might approach this.

Another tool people like to use is WGCNA. Again, you don't have to use the tool itself, but use the references under the "citation" section as an entry point into learning about the  methodology.

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