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GO analyses background genes

I analysed three microarrays includes lncRNAs from GEO. These are same platforms. After I found differentially expressed lncRNAs, I performed lncRNA:miRNA analyses using DIANA web tool. Then, I found mRNAs related to miRNAs using mirDB, miRTarBase and TargetScan tools. I found to be 354 overlapped mRNAs with "mirDB", "miRTarBase" and "TargetScan" databases.

According to these results, which background genes should I use in the GO analysis for the 354 overlapped mRNAs?

go microarray
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written by cagdas • cagdas

What's your goal with the GO analysis here? You seemingly have already narrowed down your list to a potential biological function of interest - interaction/regulation of miRNAs.

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written by jared.andrews07 jared.andrews07

To further understand the biological functions of the 354 mRNAs, I want to perform GO functional enrichment analysis and KEGG pathway analysis. Then, I will try to make a construct of lncRNA:miRNA:mRNA network.

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written by cagdas • cagdas

I'd likely just use all reasonably expressed genes in your dataset.

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written by jared.andrews07 jared.andrews07

Hi jared.andrews07, I understand that I can use all reasonably expressed mrnas obtained from mirDB, miRTarBase and TargetScan tools. Could you correct me if I am wrong, please. Thank you

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written by cagdas • cagdas

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