Question: representing pathways at different time points
0
gravatar for kanwarjag
11 days ago by
kanwarjag770
United States
kanwarjag770 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 • 132 views
ADD COMMENTlink modified 11 days ago by Alex Reynolds20k • written 11 days ago by kanwarjag770
1
gravatar for Alex Reynolds
11 days ago by
Alex Reynolds20k
Seattle, WA USA
Alex Reynolds20k 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 11 days ago by Alex Reynolds20k

This looks very interesting and beautiful way of presentation.

ADD REPLYlink written 11 days ago by EagleEye4.7k
0
gravatar for EagleEye
11 days ago by
EagleEye4.7k
Sweden
EagleEye4.7k wrote:

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

ADD COMMENTlink written 11 days ago by EagleEye4.7k

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 11 days ago • written 11 days ago by kanwarjag770

yes you are right.

ADD REPLYlink written 11 days ago by EagleEye4.7k
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