Comparing Duplicates in two transcriptome data sets

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9.3 years ago

kevluv93 ▴ 170

Lets say you have three transcriptomes taken from the same plant in three different conditions. You then got a list of differentially expressed genes for each of these conditions. You want to compare these lists to see how many genes are unique to one condition and how many genes are differentially expressed between condition AB, condition AC, BC and ABC. Something like figure 2 from this paper.

Is there a good program or way to do this? I've been googling excel tutorials for a while, and my experience with programming is minimal. Any advice? Thank you!

gene-expression • 2.1k views

ADD COMMENT • link updated 2.0 years ago by Ram 44k • written 9.3 years ago by kevluv93 ▴ 170

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I think in venny you can find four parts to paste your conditions separately, then you can select the common parts as genes differentially expressed between conditions

ADD REPLY • link updated 2.0 years ago by Ram 44k • written 9.3 years ago by zizigolu ★ 4.3k

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Have you googled "venn diagram R"?

BTW, don't use Excel.

ADD REPLY • link updated 2.0 years ago by Ram 44k • written 9.3 years ago by Devon Ryan 104k

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I have not, I'll go and do that right now. I try and avoid excel when I do transcriptome analysis, but I'm completely new to this so I end up constantly going back to it. Thanks for the help. Updates will come once I figure out how to do this

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by kevluv93 ▴ 170

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I'll save you some of the googling: Vennerable

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by Asaf 10k

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