Table 1.

The top 20 enriched terms for demo list 2 by various traditional functional annotation tools

No.	GOMiner	DAVID Chart	GOstat	Ontologizer	topGO elim	ADGO
1	Inflammatory response	Response to pathogenic bacteria	Cell-cell signaling	Response to stimulus	Induction of positive chemotaxis	Inflammatory response/extracellular region
2	Clathrin coat of coated pit	Chemokine activity	Response to pest, pathogen or parasite	DNA repair	Positive regulation of vascular endothelium	Inflammatory response
3	Viral genome replication	Cell migration	Response to stress	Cell surface receptor linked signal transduction	Chemokine activity	Cell-cell signaling/extracellular space
4	Morphogenesis	Clathrin-coated vesicle	Response to external biotic stimulus	Positive regulation of protein metabolic process	Angiogenesis	Soluble fraction/chemokine activity
5	Cytokine activity	Clathrin vesicle coat	Response to wounding	Cytoskeleton organization and biogenesis	Vascular endothelial growth factor receptor	Extracellular space
6	Establishment of spindle localization	Clathrin coated vesicle membrane	Negative regulation of biological process	Molecular_function	Extracellular matrix binding	Sensory perception/chemokine activity
7	Cell communication	Receptor binding	Negative regulation of physiological process	Cell communication	Viral genome replication	Inflammatory response/chemokine activity
8	Establishment of mitotic spindle localization	Response to other organism	Cytoplasmic vesicle membrane	DNA binding	Extracellular space	Sensory perception/extracellular space
9	Regulation of cellular process	Kinase activity	Cytoplasmic vesicle membrane	Protein binding	Cell-cell signaling	Chemokine activity
10	Regulation of biological process	RNA polymerase II transcription factor activity	Negative regulation of cellular process	Cell cortex	Inflammatory response	Chemotaxis/extracellular space
11	Development	Clathrin coat	Regulation of biological process	Mitochondrial part	Vasculogenesis	G-protein coupled receptor protein signaling pathway/extracellular space
12	Signal transduction	Establishment of cellular localization	Cell proliferation	GTPase activity	Chemotaxis	Inflammatory response/extracellular space
13	Viral infectious cycle	Cell differentiation	Phagocytic vesicle	Chemotaxis	Neutrophil activation	Extracellular space/chemokine activity
14	Positive regulation of protein metabolism	Cell death	Calpain inhibitor activity	Anatomical structure formation	Ammonia ligase activity	G-protein coupled receptor protein signaling pathway/chemokine activity
15	Regulation of protein-nucleus import	Regulation of isotype switching	Cell adhesion	Lyase activity	Endothelin-converting enzyme 1 activity	Chemotaxis/soluble fraction
16	Immune cell migration	Membrane-bound vesicle	Negative regulation of cellular physiological process	Interleukin-12 production	U-plasminogen activator receptor activity	Cell-cell signaling/chemokine activity
17	Organ development	Cell cycle	Vesicle membrane	Nitrogen compound biosynthetic process	Cell adhesion	Cell proliferation/extracellular space
18	Organogenesis	Membrane fraction	Inflammatory response	DNA recombination	Fructose metabolism	Extracellular region/chemokine activity
19	Chemotaxis	Angiogenesis	Cell communication	Cytokine biosynthetic process	Response to pathogenic bacteria	G-protein coupled receptor protein signaling pathway/soluble fraction
20	Taxis	Cell communication	Cell differentiation	Immune system process	Hyaluronic acid binding	Sensory perception/extracellular region
	Total 380 terms (p < 0.05)	Total 157 terms (p < 0.05)	Total 119 terms (p < 0.05)	Total 31 terms (p < 0.05)	Total 160 terms (p < 0.05)	Total 67 terms (p < 0.05)

The example gene list was analyzed by GoMiner, DAVID, GOStat, Ontologizer, topGO, and ADGO. The annotation data coverage was set to GO terms of all levels, and all other parameters used were each tool's default settings. Only the top 20 terms from each tool are shown (see Additional data file 15 for all results). Many of the terms are redundant or found within the same hierarchy. We emphasize the top 20 terms for three reasons: first, the top ranked terms represent the overall quality of the tools in terms of sensitivity and specificity; second, it renders the amount of analytical effects equivalent and comparable throughout the comparisons, including the clustered results; and third, analysts usually spend more time and attention on the top ranked terms due to time and focus constraints.