Table 3  Ontological classification of 22,339 human gene products
Biological function  Number of transcripts  Biological process  Number of transcripts
Transcription factor  958 (306)  Carbohydrate metabolism  281 (84)
Translation factor  62 (27)  Nucleotide and nucleic acid metabolism  173 (51)
RNA binding  142 (41)  DNA replication  240 (126)
Ribosomal protein  232 (130)  Transcription  1,059 (651)
Cell cycle regulator  42 (16)  RNA processing  204 (59)
Structural protein  145 (48)  Amino acid and derivative metabolism  87 (29)
Cytoskeleton structural protein  329 (181)  Protein biosynthesis  264 (162)
Extracellular matrix  361 (87)  Protein modification  235 (88)
Actin binding  66 (25)  Protein targeting  26 (5)
Motor protein  245 (77)  Protein degradation  136 (45)
Chaperone  87 (27)  Proteolysis and peptidolysis  96 (36)
Enzyme  2,664 (1,404)  Lipid metabolism  424 (187)
Protein kinase  895 (484)  Monocarbon compound metabolism  9 (3)
Protein kinase inhibitor  19 (12)  Coenzyme and prosthetic group metabolism  92 (29)
Protein phosphatase  43 (7)  Steroid compound metabolism  40 (10)
Protein phosphatase inhibitor  17 (3)  Prostaglandin metabolism  12 (3)
Protease  441 (255)  Transport  549 (288)
Protease inhibitor  92 (37)  Electron transport  491 (273)
Enzyme activator  18 (3)  Ion transport  302 (90)
Enzyme inhibitor  14 (4)  Small molecular transport  19 (9)
Alkyl transfer  17 (3)  Neurotransmitter transport  9 (3)
Amide transfer  15 (3)  Ion homeostasis  201 (57)
Carbonyl transfer  191 (38)  Organelle organization and biogenesis  408 (254)
Hydroxyl transfer  13 (6)  Nuclear organization and biogenesis  1,380 (647)
Phosphoryl transfer  823 (281)  Cytoplasm organization and biogenesis  42 (20)
Oxireduction  148 (76)  Meiosis  15 (2)
Transmembrane protein  184 (48)  Mitosis  25 (6)
Receptor  921 (478)  Cell cycle  271 (100)
G protein-linked receptor  164 (106)  DNA packaging  15 (6)
Defense/immunity protein  353 (164)  DNA repair  132 (41)
Ligand binding or carrier  691 (331)  DNA recombination  31 (3)
Ion channel  245 (141)  Methylation  185 (53)
Oncogene  128 (42)  Signal transduction  1,231 (383)
Tumor suppressor  8 (6)  Growth regulation  15 (4)
Growth factor  95 (40)  Differentiation  24 (6)
Hormone  42 (14)  Apoptosis  160 (49)
Cell communication  247 (84)  Angiogenesis  11 (4)
Cell adhesion  433 (252)  Defense/immunity  112 (49)
Detoxification  33 (15)
Stress response  90 (41)
Developmental process  278 (99)
Neurogenesis and regeneration  147 (43)
Physiological process  159 (43)
Sensory perception  292 (65)
Functionally classified  12,334 (5,204)  Process classified  10,005 (4,225)
Each transcriptional unit and HINT transcript (in parentheses) was assigned to a unique biological function or process.