REVIGO #

REVIGO is a web server that can take long lists of Gene Ontology (GO) terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds.

It simply collapsing GO with semantic similarity. It visualize it together with nice coloring according to p-value (or other metric) assigned to each GO. Following calculation of enrichment of GO terms, it will display the results mapped to on the GO hierarchical clustering methods, so we can clearly see all the overlaps and relationships.

The other web servers exist to test the GO term includes WeGO, L2L, FatiGO, GOrilla and agriGO. REVIGO is freely available from http://revigo.irb.hr/.

Input File #

Input file (tab-delimited) must contains GO id in one column and its representative p-value in another column.

Scatterplot & Table view #

The visualization can adjusted based on p-value, log10 ratio and colour.

Interactive graph #

Highly similar GO terms are linked by edges in the graph, where the line width indicates the degree of similarity.

Tree Map #

Each rectangle in the tree map is single cluster representative. The representatives are joined into ‘superclusters’ of loosely related terms, visualized with different colors. Size of the rectangles may be adjusted based on its p-value.

Tag Cloud #

Larger and darker letters signifying stronger overrepresentation whereas underrepresented keywords are not displayed in the Tag Cloud.

References #

• REVIGO (http://revigo.irb.hr/ "REVIGO")

• Supek F, Bosnjak M, Skunca N, Smuc T (2011) REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms. PLoS ONE 6(7): e21800. doi:10.1371/journal.pone.0021800