tools for GO analysis

Question

[biolab]

Hi everyone

Could you suggest me some good tools for Gene Ontology analysis? I only know DAVID online tool, but recently saw graphical output of GO analysis in a publication (hierarchy tree structure with some terms highlighted in yellow), but don't know how to draw that. THANKS A LOT.

[Ashutosh Pandey]

Some of the GO analysis tools can be found here. People generally use Cytoscape and Graphviz (Cytoscape is much better) to draw GO hierarchical trees.

[biolab]

Thank you very much.

Answer 1

[Chirag Nepal]

Alternatively, you can use Gostats (either from bioconductor or webserver). Get the p-value of enriched GOterms and plot the p-value as barplot. If you are comparing multiple stages/celllines/tissues, make a matrix for each Goterm and p-value. Then plot it a a heatmap.

You can follow this discussion: Tools To Find Gene Ontology Term Enrichment

Answer 2

[theblackbiologist]

I personally use Cytoscape with ClueGO, STRING and DAVID. I find that these usually cover my needs. Cytoscape has a fine grain control over the images with its visual styles, and I usually end up colouring the nodes as per the fold change.

Answer 3

[dariober]

After GO enrichment analysis (with DAVID or else), you can summarise and visualize the go terms with revigo. It's very easy to use and it returns also the R script used for the figures, in case you want some finer control of the output.