Q : BiNGO aborts without any error message.

A : Cytoscape’s default memory settings (particularly in version 2.7) are probably not sufficient. Try running Cytoscape from cytoscape.bat (Windows) or (Linux, Mac), or see here to increase Cytoscape’s default memory settings.

Q : The number of genes in my test set according to  the BiNGO output window does not match with the number of nodes I pasted into the text field or selected in the graph. Is this a bug ?

A : No, it's not. Given the current status of GO annotation efforts, a lot of genes haven't actually been looked at by a curator and annotated in the GO hierarchy. The genes for which there is no annotation available are not taken into account in the over-representation analysis, and they're not counted as genes belonging to the test or reference set. There is however a difference with genes that are annotated to categories such as Biological_Process unknown. This means that some curator has actually looked at them and had to conclude that there is as yet no clear-cut functional classification. However, these genes do have an annotation and they are taken into account.

Q : The default annotations/ontologies in BiNGO are already several months old. I would like to use more recent annotations.

A : Download the most recent annotation and ontology files from the GO website. You can use these as custom annotation/ontology files.

Q : I would like to change the default settings in the BiNGO Settings Panel. Can I do that ?

(BiNGO versions before 2.4)

A : Yes, you can modify most of BiNGO's default settings by modifying the file in the BiNGO.jar archive. E.g. if you want to change the default organism to A. thaliana, change

species_def = Saccharomyces cerevisiae


species_def = Arabidopsis thaliana

Q : BiNGO stalls at 0% while parsing annotations. What is going on ?

(only for BiNGO 1.0 and 1.1)

A : The fact that BiNGO specifically stalls at 0% indicates that the program can't find the annotation and ontology files in the proper directory. Apparently this exception is not properly handled by BiNGO (it will be fixed in a later version). BiNGO assumes the following directory structure : there should be a file called BiNGO.jar and a folder called BiNGO (containing the annotation files) in the /plugins directory of Cytoscape (produced by unzipping the BiNGO zip file in the plugins folder). Please check if this is the case. If it is not, remove the existing BiNGO files and unzip the BiNGO zip file again, directly into the /plugins directory, not into /plugins/bingo or such. This should solve the problem.


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