IntelliGO: a new vector-based semantic similarity measure including annotation origin

Benabderrahmane, Sidahmed; Smail-Tabbone, Malika; Poch, Olivier; Napoli, Amedeo; Devignes, Marie-Dominique

doi:10.1186/1471-2105-11-588

BMC Bioinformatics

Table 2 List of yeast and human pathways used in this study.

From: IntelliGO: a new vector-based semantic similarity measure including annotation origin

KEGG	KEGG	Yeast	Name	Nb genes	Human	Name	Nb genes
Category	Subcategory	Pathway			Pathway
01100 Metabolism	01101 Carbohydrate Metabolism	sce00562	Inositol phosphate metabolism	15	hsa00040	Pentose and glucuronate interconversions	26
	01102 Energy Metabolism	sce00920	Sulfur metabolism	13	hsa00920	Sulfur metabolism	13
	01103 Lipid Metabolism	sce00600	Sphingolipid metabolism	13	hsa00140	C21-Steroid homone metabolism	17
	01105 Amino Acid	sce00300	Lysine biosynthesis	13	hsa00290	Valine, leucine and isoleucine biosynthesis	11
	Metabolism	sce00410	Alanine biosynthesis	8
	01107 Glycan Biosynthesis and Metabolism	sce00514	O-Mannosyl glycan biosynthesis	13	hsa00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	23
	01109 Metabolism of Cofactors and Vitamins	sce00670	One carbon pool by folate	14	hsa00670	One carbon pool by folate	16
	01110 Biosynthesis of Secondary Metabolites	sce00903	Limonene and pinene degradation	7	hsa00232	Caffeine metabolism	7
01120 Genetic Information Processing	01121 Transcription	sce03022	Basal transcription factors	24	hsa03022	Basal transcription factors	38
					hsa03020	RNA polymerase	29
	01123 Folding, Sorting and Degradation	sce04130	SNARE interactionst in vesicular Transport	23	hsa04130	SNARE interactions in vesicular transport	38
	01124 Replication and Repair	sce03450	Non-homologous end-joining	10	hsa03450	Non-homologous end-joining	14
					hsa03430	Mismatch repair	23
01130 Environmental Information Processing	01132 Signal Transduction	sce04070	Phosphatidylinositol signaling system	15
01140 Cellular Processes	01151 Transport and Catabolism	sce04140	Regulation of autophagy	17
01160 Human Diseases	01164 Metabolic Disorders				hsa04950	Maturity onset diabetes of the young	25
Total genes number				185			280
Non-IEA:IEA ratio				572:435 (1.3)			560:620 (0.9)

Table 2: The KEGG categories and subcategories are indicated for each pathway as well as its name and the number of genes it contains (KEGG version Dec 2009). The non-IEA:IEA ratio refers to Biological Process GO annotation of the complete set of genes for each species.

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ISSN: 1471-2105

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