Comparing different time points

[Miha Tome]

Dear all,

first, thank you for the work you've done, it has been a good used experiance.

I've got a question regarding a setting, or more specific, how to analyze it.

Our experiment includes different generations/time points in a long sequential experiment (same strain, so same genetic makeup). Biolog data was obtained for several generations, and from laboratory and industrial setting.

I've managed to compare 2 or 3 generations/settings via "mutants" analysis - I've marked Generation_1 as the "WT", Generation_2 as "add" and Generation_3 as the "insert" mutant. (I've used the same genome/proteome mapping to the kegg for all three generations since they are genetically the same (or we don't know if any changed occurred)).

It worked, however, Is there any other way to analyze this type of experiment? Any specific way/mode to compare different time points, maybe even more than 3 "mutants"/time points?

Best,

Miha

[Marco Galardini]

Hi,

thanks! It's been a while (>5 years) since this software has been published and as such I have limited time to maintain it. So please forgive my brevity.

I believe you could do a "pangenome" analysis, pretending your different generations are different strains. You could provide the "pangenome" using the add-orth command, having a 1-to-1 genes relantionship between each generation. That might work, although it might be dependent on what you are interested in looking at.

Hope this helps,

Marco

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