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Rudjer Boskovic Institute, Croatia

Rudjer Boskovic Institute,
Croatia

Welcome to REVIGO!

REViGO is a web server that can take long lists of Gene Ontology 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. More about REViGO...In Croatian
Please enter a list of Gene Ontology IDs below, each on its own line. The GO IDs may be followed by a numeric value which describes it in a way meaningful to you. For instance, you may provide a p-value
        (statistical significance), a fold change, enrichment, or some
        directly measured quantity such as average signal intensity from
        microarrays, ion count from mass spec, or read count from RNA-seq.
        You may also provide more than one value per line, although only the
        first value will be used in GO term selection/clustering.
Examples: #1 #2 #3

Allowed similarity:  How large would you like the resulting list to be?
Large (allowed similarity=0.9) Medium (0.7) Small (0.5) Tiny (0.4) Warning

If provided, the numbers associated to GO categories are...
p-values
some other quantity, where

Advanced options:

Select a database with GO term sizes:   

Select a semantic similarity measure to use:    The default is normally a sensible choice. Click the icon to
            view a web page with detailed information on how these measures are
            computed.

The version of the Gene Ontology used is monthly release of Apr 2013 "go_201304-termdb.obo-xml.gz". The UniProt-to-GO mapping file "gene_association.goa_uniprot.gz" is dated 30th Apr 2013, downloaded from the EBI GOA project.
If you found REVIGO useful in your work, please cite the following reference:
Supek F, Bošnjak M, Škunca N, Šmuc T.
"REVIGO summarizes and visualizes long lists of Gene Ontology terms"
PLoS ONE 2011. doi:10.1371/journal.pone.0021800

Q + A

Q: I have a list of interesting genes, but not a list of GO terms.

A: You can use one of the following web servers to search for GO terms that are overrepresented in your list of genes:

After that, return here with the list of GO terms and p-values (or enrichments).


Q: I still don't have a list of interesting genes, but I'd like to try out my favourite GO enrichment tool and then bring the output to REVIGO to summarize and visualize.

A: Here are the links to two example gene sets, one from agriGO (click "Example") and another one from DAVID (click "Demolist_1").


Q: The organism I work on is not listed in the "GO term sizes" box in Advanced options.

A: The chosen database is used to find the size of each GO term i.e. the percentage of genes annotated with the term. This quantity determines the size of bubbles in the vizualizations, thus indicating a more general GO term (larger) or a more specific one (smaller). The choice of database also has some influence on the GO term clustering/selection process, and on the bubble placement in the visualizations. If your organism is not available, select the closest relative, e.g. human or mouse should work for any mammal. The default choice (whole UniProt) should also suffice in most cases.


Q: I have made a Web server/software which produces lists of GO categories. Can its output be fed into REVIGO?

A: Yes! REVIGO can be used to summarize and visualize the results of your server. Please see instructions on this page, or email for more information.

REViGO is an iProject funded by the Minstry of Science, Education and Sport of Croatia (2008-057) implemented at the Laboratory for information systems, at the Rudjer Boskovic Institute, Croatia.

Other iProjects at the Rudjer Boskovic Institute:

GORBI - function predictions for thousands of poorly characterized bacterial proteins using phylogenetic profiling.

wGMDH - a Java implementation of the powerful "group method of data handling" regression algorithm. Integrates into Weka.