Question: representing pathways at different time points
0
gravatar for kanwarjag
9 weeks ago by
kanwarjag810
United States
kanwarjag810 wrote:

For an RNAseq time points data - control, 1, 2 , 4 days I separately did pathway analysis and has pathway enriched along with -log10 (p) in the form of bar diagrams. I have selected some pathways that are common in at least two time points while there are few pathways that are only in last time point and has biological significance. What should be the best way to show if there is any significant enrichment over time. CAn we perform some sort of statistical test like z score (like IPA does for canonical pathways) or we just show it bar diagrams at different time points with p value. Any suggestion.

rna-seq • 182 views
ADD COMMENTlink modified 9 weeks ago by Alex Reynolds21k • written 9 weeks ago by kanwarjag810
1
gravatar for Alex Reynolds
9 weeks ago by
Alex Reynolds21k
Seattle, WA USA
Alex Reynolds21k wrote:

Sankey plots are great for showing how sets and subsets of sets merge, diverge, grow and shrink over time.

http://sankeymatic.com/build/

https://github.com/d3/d3-sankey

etc.

You could use relative ribbon width and color attributes to communicate quantity and categorization of genes or other data that change over time.

ADD COMMENTlink written 9 weeks ago by Alex Reynolds21k

This looks very interesting and beautiful way of presentation.

ADD REPLYlink written 9 weeks ago by EagleEye4.8k
0
gravatar for EagleEye
9 weeks ago by
EagleEye4.8k
Sweden
EagleEye4.8k wrote:

Check out Fig. 2d from this article or to include the gene numbers along with it check my previous post.

ADD COMMENTlink written 9 weeks ago by EagleEye4.8k

Thanks for the suggestion. The figure with heatmap and bar diagram in your previous post @ C: Gene ontology comparsion between up- and down-regulated genes shows % of genes in particular pathway. This % is for each pathway enrichment. What I want to explain is e.g my data has 20 of 100 apoptosis pathway genes so that means % of genes that I will plot is 20%. Am I correct?

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by kanwarjag810

yes you are right.

ADD REPLYlink written 9 weeks ago by EagleEye4.8k
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