Question: How I interpret this plot from pathview
0
4 weeks ago by
Fereshteh20
Fereshteh20 wrote:

Hi

I have done differential expression in a treatment versus control and fed my differentially expressed genes to plot a KEGG pathway by pathview where I obtained this

![enter image description here][1]

I have selected for visualization because that was very significant. For example I knowCXCL1is being highly up regulated in my treated group;CXCL1 has been coloured by red here; What does that mean please? Actually I was not able to understand the colour scheme in this plot. Can you please help me?

Thanks a lot in advance

I

pathview R kegg pathway • 114 views
modified 11 days ago • written 4 weeks ago by Fereshteh20
Answer: How I interpret this plot from pathview
2
4 weeks ago by
Kevin Blighe390
Kevin Blighe390 wrote:

The red colour relates to precisely what you have said, i.e., the fact that CXCL1 has heightened expression levels in your data and is up-regulated in your treated group. Conversely, green, in this case, would indicate low expression / down-regulation.

However, the precise interpretation of the colour scale depends on the input data that you provide to pathview: If you provide a data-matrix of expression values, then the colour scale relates to high|low expression. If you supply fold-changes, then it relates to fold-change differences. You can technically supply any values that you want to pathview.

You can modify the limits of the scale to suit the input data that you provide. Please read the manual and vignette to see how to do this.

Kevin

Thank you Kevin, so could we say that CXCL1 is an important gene in IL-17 signalling pathway and a kind end product of this pathway?

1

Hey,

CXCL1 is an important gene in IL-17 signalling pathway

You need to be able to determine this based on the evidence that you are generating.

CXCL1 is ... a kind end product of this pathway

I am not sure how you can determine this.

1

Thank you , alright :)

ADD REPLYlink modified 29 days ago • written 29 days ago by Fereshteh20