How to decide which are the most pertinent overly-represented features during gene set enrichment analysis

BMC Bioinformatics

Table 4 Sets found similar to the MIPS '440.30.10 mRNA splicing' protein complex

GO Term	description	size	common
GO:0000398	nuclear mRNA splicing, via spliceosome	84	33
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	84	33
GO:0000375	RNA splicing, via transesterification reactions	88	33
GO:0008380	RNA splicing	99	33
GO:0006397	mRNA processing	108	33
GO:0016071	mRNA metabolism	132	33
GO:0006396	RNA processing	262	34
GO:0016070	RNA metabolism	360	34
GO:0043283	biopolymer metabolism	812	34
GO:0006139	nucleobase,...	1057	34
GO:0044238	primary metabolism	2191	34
GO:0044237	cellular metabolism	2407	34
GO:0008152	metabolism	2465	34
GO:0000245	spliceosome assembly	10	5
GO:0006461	protein complex assembly	61	5
GO:0006374	nuclear mRNA splicing via U2-type spliceosome	8	8
GO:0000391	U2-type spliceosome dissembly	2	2
GO:0000390	spliceosome dissembly	2	2
GO:0000370	U2-type nuclear mRNA branch site recognition	2	2
GO:0000348	nuclear mRNA branch site recognition	2	2
GO:0000393	spliceosomal conformational changes to generate catalytic conformation	3	3

Sets found similar to the MIPS '440.30.10 mRNA splicing' protein complex (36 proteins) in the neighborhood constructed on the biological processes branch of the Gene Ontology. Results are sorted to better illustrate pertinence definition application (i.e. not by similarity value). Pertinent target sets are in bold shape. Non pertinent target sets that violate Rule 2 are in normal shape (test of Rule 3 not performed). Non pertinent target sets that violate only Rule 3 are in italic.

ISSN: 1471-2105