Nteworks in Cytoscape, time-series gene-expression

Question

[Malgorzata.Wieteska]

Dear All,

I'm new to Cytoscape. I'm trying to input my experimental gene expression time-series into the network. I've created the network based on the interactions (IMEX, INtact, Mint) and input microarray gene expression publicly available dataset.

Now, I would like to input my own data (time-series gene expression) to visualise how the data corresponds to the uploaded microarray dataset. I have 8 different treatments and few time intervals, so I would like to also visualise the effect of the treatment on the gene expression and relate that to the pathway enrichment by a given treatment.

I would like to ask you about any useful tutorial related to that problem or advice on how I can do it.

Thank you in advance for your help.

Malgosia

Answer 1

[scooter]

Hi Malgosia, Importing the data shouldn't be a problem. Each of your conditions would be a separate column, and you can color the nodes by the expression value in that column. Pathway enrichment would be a little trickier, but fundamentally just the same basic steps repeated over and over:

1. Select the genes of interest based on your criteria (over/under expressed, p-Value, etc.)
2. Do enrichment analysis on those genes

(Note: A shortcut to this might be to use the StringApp to create your initial network since it's got built-in enrichment analysis.)

If you use clusterMaker to bring up a heatmap of your time-series data, you should also be able to run an animation to show how your network changes through each step.

Hope this helps!

-- scooter

Answer 2

[Malgorzata.Wieteska]

Hi Scooter, Thank you for your answer. I didn't think about the possibility of splitting the times and treat them as separate conditions. Thank you once again.