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.

Huang et al. Genome Biology 2007 8:R183   doi:10.1186/gb-2007-8-9-r183

Open Data