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califano-lab / PISCES

R package for Protein activity analysis of single-cell RNAseq.
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How to extract target genes from each regulon #7

Open jdarmitage opened 3 years ago

jdarmitage commented 3 years ago

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 commented 3 years ago

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

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.

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jdarmitage commented 2 years ago

Hi Lukas,

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

Cheers, Jesse

lvlahos343 commented 2 years ago

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 commented 2 years ago

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