How to extract target genes from each regulon

[jdarmitage]

Hi,

Thank you for this brilliant package. Using the PISCES method, I had generated 7 cell-type specific networks which I have then projected onto my single cell dataset to calculate the activity for 850 transcription factors. I am specifically interested in regulons that are differentially expressed within my CD8+ T cell cluster (between treatment and control) and have identified a number of candidates I wish to investigate further. To dissect the pathways in this regulon how I can extract the target genes within the regulon that is differentially expressed in cluster of interest?

Thanks again.

[lvlahos343]

Hey there, thanks for using PISCES. I'm currently on vacation and out of town until Saturday. I'll take a look at your question in more detail when I'm back in the office. Lukas

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On Sun, Jul 11, 2021 at 11:08 PM jdarmitage ***@***.***> wrote: Hi, Thank you for this brilliant package. Using the PISCES method, I had generated 7 cell-type specific networks which I have then projected onto my single cell dataset to calculate the activity for 850 transcription factors. I am specifically interested in regulons that are differentially expressed within my CD8+ T cell cluster (between treatment and control) and have identified a number of candidates I wish to investigate further. To dissect the pathways in this regulon how I can extract the target genes within the regulon that is differentially expressed in cluster of interest? Thanks again. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACRKT6QWHQIMKEEQ43BP6HLTXJMCPANCNFSM5AF6UASA> .

[jdarmitage]

Hi Lukas,

Thanks for the response. Have you managed to identify a solution to this issue?

Cheers,
Jesse

[lvlahos343]

Hi, you can do this by indexing into your network objects. For instance, if you had a network titled pdac.net, you could look at the targets of KRAS using pdac.net$KRAS. You could replace KRAS with whatever protein is showing differential activity in the cluster that you're investigating.

[jdarmitage]

Thanks for the reply Lukas. I have used this strategy to interrogate specific regulons from a single network, however if multiple networks are used to estimate protein activity, how does one create a consensus network that can be visualised in something like cytoscape?

In my example, i have 7 celltype-specific networks and when looking at a specific regulator such as IRF7, each network has vastly different targets. Is there a way to plot a single network from this?

Cheers,
Jesse