05/05/2020

Gene Ontology Analysis Options

Legend	Name	Description
A	Identifiers column	Column used to identify the genes used as input.
B	Identifier type	Type of identifier used as input. Currently, only Gene Symbol and Accession ID are available.
C	Included comparison results	One or more comparison results to peform the GO analysis
D	Filter genes	Filters the genes to be used as input.
E	Organism database option	Choose an organism from a predefined list of GO organism annotations.
F	Selected organism	List of available organisms. This list corresponds to the available organism packages in Bioconductor.
G	Ontology subset	Ontology subset to be taken into account. The options are Biological Process (BP), Molecular Function (MF), and Cellular Component (CC).
H	Custom annotation	Custom GO annotation used as input. It can be a GAF file available in the Gene Ontology Consortium.

Legend	Name	Description
A	Statistical test	Statistical test applied to the enrichment test. The options are: Fisher (default) Komogorov-Smirnov (KS) Student's t-test Goeman's globaltest Sum ^{(topGO-specific)} KS ties ^{(topGO-specific)}
B	Algorithm for statistical test	Defines the algorithm used to calculate the selected statistical test. The options are: Classic (Default) Weighted Weighted 01 type ^{topGO-specific} LEA ^{topGO-specific} Parent-child ^{topGO-specific}
C	Multiple testing correction	Method of p-value correction. The options are: FDR (Benjamini & Hochberg, 1995) (Default) BY (Benjamini & Yekutieli, 2001) Bonferroni correction Hommel (1988) Holm (1979) Hochberg (1988) None
D	Adjusted p-value cutoff	Maximum corrected p-value to consider significance.
E	Minimum required genes per GO term	Minimum required genes per GO to consider the GO entry significant for the current analysis.
F	Identifiers reference set	Choose between testing the genes against the selected genes or all genes in the dataset.
G	Generate plots for results	Check this if rendered plots must be included in the result.

The available organisms annotations are the same from those available in Bioconductor.

Below there's a list of these packages for each organism:

Consortium TGO (2019). The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Research. [LINK]

Alexa A, Rahnenfuhrer J (2020). topGO: Enrichment Analysis for Gene Ontology. Bioconductor. [LINK]

GEAP