Question: R: Heatmap Of Rna-Seq Count Table With Functional Gene Clustering
2
gravatar for mtw
6.9 years ago by
mtw20
Vienna, Austria
mtw20 wrote:

I would like to prepare a heatmap of differentially expressed genes from an RNA-seq experiment with some sort of functional gene clustering in R. Starting from standard read counts (as obtained by htseq-count), the DESeq manual illustrates how to create a heatmap for the most differentially expressed genes, however I would like to have a clustering based on GO terms.

Is there any R package available?

Thanks, Michael

htseq R rna-seq heatmap • 5.3k views
ADD COMMENTlink modified 6.3 years ago by vj410 • written 6.9 years ago by mtw20

Is that boils down to some sort of metrics based on the product of GO group assignment score (similarity) and observed expression variance? It is quite interesting to see!

ADD REPLYlink written 6.9 years ago by Pavel Senin1.9k

I am not sure if any R packages are available for this. Closest service I can think of is Revigo: http://revigo.irb.hr/

It probably isn't what you want, but they provide some resources on how you can cluster GO terms based on semantic distance calculated from the GO graph.

ADD REPLYlink written 6.9 years ago by Damian Kao15k

Depending on how you annotate your DEseq results, you can add GO annotations (for example using biomaRt), then filter those rows for whichever GO id you are interested in. After you have the filtered dataset, the heatmap should be the same as for differentially expressed genes.

ADD REPLYlink written 6.9 years ago by Dave Bridges1.3k
2
gravatar for vj
6.3 years ago by
vj410
UK
vj410 wrote:

Try using http://bioconductor.org/packages/2.12/bioc/html/GOSemSim.html The function mgeneSim may be what you are looking for.

ADD COMMENTlink written 6.3 years ago by vj410
0
gravatar for Wrf
6.3 years ago by
Wrf210
Wrf210 wrote:

maybe check out edgeR. if you have numbers already, i think the image() command can generate heatmap graphs.

ADD COMMENTlink written 6.3 years ago by Wrf210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1695 users visited in the last hour