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longmanz / Mixscale

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IFNG_program3_down means upregulated genes? #1

Closed funpys closed 1 month ago

funpys commented 7 months ago

Hi,

I am little bit confused because of the name of pathway gene list. For example, IFNG_program3_down. What is program3? And does down means down-regulated genes when IFNG signaling is activated or genes in IFNG singling is KO?

Thanks.

longmanz commented 7 months ago

Hi, The "program" stands for a group of correlated regulators in the IFNG pathway, returned by a MultiCCA-based decomposition method. program3 stands for the third program that was returned by this method. For each program, we provided the list of regulators at https://www.biorxiv.org/content/10.1101/2024.01.29.576933v1.supplementary-material?versioned=true.

As for "down", it means that these genes are down-regulated when the corresponding regulators are perturbed, compared to the non-targeting controls. Therefore, these genes should be "up-regulated" if the IFNG signaling is activated. In our paper, we mostly focused on the "down" gene lists for each pathway.

Thank you for bringing this up. I will leave this issue open just in case this might confuse other users as well.

funpys commented 6 months ago

@longmanz Thanks a lot!