Using GOplot with data from Gene Ontology Resource

Question

[basch]

I have a list of differentially expressed genes that I have manually put into the GO Enrichment Analysis, using the web tool (http://geneontology.org/).

Now, I am trying to create a chord plot using the GOplot tool (https://wencke.github.io/). As input, GOplot expects results of the functional analysis formatted with at least four columns (category, term, genes, adjusted p-value). However, the output from GO Enrichment Analysis is not formatted like that, it only contains the following columns: GO biological process, REFLIST (22712), upload_1 (FDR), [and a couple of other metrics that I've removed for simplicity].

Is there any other tool that outputs the GO analysis in the format GOplot is expecting? Any other solutions to turn to?

Answer 1

[jkkbuddika]

You have to have do input data preparation to get the final version you need for GOplot tool. You can use the circle_dat function to do this. Import two files: results of the functional analysis (should at least have category, term, genes, adjusted p-value) [You can use gProfiler for GO analysis and provides an output with all these details] and results from a statistical analysis (DESeq2/edgeR) with gene names and log2FC values. Take a look at the Getting started section of the manual.

[basch]

gProfiler was what I needed, thanks!

[jkkbuddika]

Great! I love gProfiler.