Bioinformatics with Python Cookbook - Second Edition

See also

• As stated before, more so than Ensembl, the main resource for gene ontologies is http://geneontology.org.
• For visualization, we are using the pygraphviz library, which is a wrapper on top of Graphviz ( http://www.graphviz.org).
• There are very good user interfaces for GO data, for example, AmiGO (http://amigo.geneontology.org) and QuickGO (http://www.ebi.ac.uk/QuickGO/).
• One of the most common analyses performed with GO is the gene enrichment analysis to check whether some GO terms are overexpressed or underexpressed in a certain gene set. The geneontology.org server uses Panther (http://go.pantherdb.org/), but other alternatives are available (such as DAVID, at http://david.abcc.ncifcrf.gov/).