heatmap for coding and noncoding genes

Question

[Rob]

Hi friends, I did differential expression for rna seq data: I did for coding genes also I did for all genes(coding+noncoding). I want to show significant genes in heatmap. Do you think heatmap is good for significant coding genes or all genes?

Answer 1

[Kevin Blighe]

It is your choice and it depends on the message that you want to convey in your work. You do not really need anybody else's verification for this task.

• All genes == unsupervised clustering
• Statistically significant genes == supervised clustering

Kevin

[Kevin Blighe]

I may have missed your point slightly in relation to non-coding versus protein coding genes. If you have conducted your entire analysis separately for protein coding genes and non-coding genes (that is, normalisation and differential expression analysis separately), then it is my view that they also should be shown separately in different heatmaps.

There is no problem conducting your analysis by just focusing on protein coding genes alone, and there is neither a problem focusing on protein coding + non-coding combined.

As you can see, there are no rules here... you can present your results in the way that helps to get the information best to the reader.

[Rob]

Thanks Kevin I have differentially expressed genes for coding genes alone and also all genes together(Coding+noncoding). I have volcano plot and now I want to plot heatmap for them.

[Kevin Blighe]

For the heatmap, you could try to follow this: A simple tutorial for a complex ComplexHeatmap

, or, at the most basic level, you just need:

heatmap(assay(vst)[sigGenes,])

, assuming here that you have used DESeq2 and that your normalsied+transformed data is contained in assay(vst) and that your vector of statistically significant genes, whose ID type should match that of the rownames of assay(vst), are held in sigGenes.

Answer 2

[cristopher.biotec]

You can show those results in the enhanced volcano plot using a different shape for coding and non-coding genes

[Kevin Blighe]

Good suggestion - I am also a developer of EnhancedVolcano.

[Rob]

Hi Cristopher Thanks good suggestion. I did volcano plot before just for significant genes all same shape. But how can I do this with different shape for coding and non-coding genes?

[Kevin Blighe]

Please see the vignette, which I personally wrote: https://bioconductor.org/packages/devel/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html#over-ride-colour-andor-shape-scheme-with-custom-key-value-pairs

[Rob]

Thanks Kevin I use your EnhancedVolcano a lot. This is really amazing. Appreciate that.

[Kevin Blighe]

Thank you Sir. You got it working?

[Rob]

Yes dear Kevin Your Enhancedvolcano is awesome and very useful. I wish you would do something like this for heatmap.

thanks