Single Enrichment. Options

Fisher exact test

The user can choose between the three options for the Fisher exact test:

• Two-tailed: detects over and under-represented terms comparing both lists
• Over-represented terms in list 1 (recommended in genome comparison): detects over-represented terms in list 1 of genes. The best choice when list 2 of genes is the rest of the genome.
• Over-represented terms in list 2: detects over-represented terms in list 2 of genes compared to list 1 of genes.

See Methods section for details on the test.

Remove duplicates?

GO Enrichment gives the possibility of checking and removing duplicates existence in the lists of gene or protein identifiers. Four options are given:

• Never: list 1 and 2 are not checked for duplicate occurrences. Use this option only if you are sure that none of the references are duplicated.
• Remove on each list separately: each list is preprocessed for duplicates separately. One member of the duplicate pair is kept.
• Remove on each list and common ids: firstly each list is preprocessed for duplicates separately and one member of the duplicate pair is kept. Then both list are preprocessed for duplicates together and none of the pair is kept.
• Remove from list 2 those appearing in list 1 (complementary list).

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