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Table 2 Summary of the GO terms used in this study.

From: Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell

GO term N (P)
DIP
N (P)
GOLD
GO term N (P)
DIP
N (P) GOLD
Developmental process (32502) 632 (16) 257 (8) Organelle envelope (31967) 230 (12) 69 (2)
   Reproductive developmental process (3006) 26 (0) 13 (0)    Organelle inner membrane (19866) 105 (8) 27 (2)
   Anatomical structure development (48856) 186 (15) 94 (8)    Organelle outer membrane (31968) 24 (0) ---
   Cellular developmental process (48869) 450 (1) 169 (0)    Organelle envelope lumen (31970) 25 (0) ---
   Aging (7568) 40 (0) 22 (0)    Nuclear envelope (5635) 86 (3) 35 (0)
       Mitochondrial envelope (5740) 148 (9) 34 (2)
Reproduction (3) 245 (7) 111 (4)    
   Sexual reproduction (19953) 95 (0) 41 (0)    Transcription regulator activity (30528) 276 (14) 107 (5)
   Asexual reproduction (19954) 74 (6) 44 (4)    Transcriptional activator activity (16563) 50 (0) 24 (0)
   Reproductive process (22414) 207 (7) 88 (4)    Transcriptional repressor activity (16564) 35 (2) 13 (1)
   Rep. of a single-celled organism (32505) 220 (7) 99 (4)    Transcription factor activity (3700) 45 (2) 13 (1)
       RNA polymerase II transcription factor activity (3702) 112 (4) 44 (1)
Establishment of cellular localization (51649) 452 (21) 188 (10)    Transcriptional elongation regulator activity (3711) 14 (6) ---
   Secretion by cell (32940) 206 (9) 84 (3)    Transcription cofactor activity (3712) 36 (1) 16 (0)
   Establishment of nucleus localization (40023) 17 (0) ---    
   Intracellular transport (46907) 409 (21) 175 (10)    Structural molecule activity (5198) 231 (29) 75 (18)
       Structural constituent of ribosome (3735) 115 (0) 21 (0)
Response to stimulus (50896) 514 (3) 207 (0)    Structural constituent of cytoskeleton (5200) 50 (29) 31 (18)
   Response to endogenous stimulus (9719) 197 (3) 101 (0)    
   Cellular response to stimulus (51716) 13 (0) ---    Transporter Activity (5215) 297 (8) 63 (1)
   Response to abiotic stimulus (9628) 83 (0) 32 (0)    Ion transport activity (15075) 111 (5) 16 (0)
   Response to external stimulus (9605) 27 (0) 13 (0)    Carbohydrate transporter activity (15144) 26 (0) ---
   Response to biotic stimulus (6907) 19 (0) ---    ATPase activity, coupled to movement of substances (43492) 41 (2) ---
   Response to chemical stimulus (42221) 212 (0) 65 (0)    Amine transporter activity (5275) 27 (0) ---
   Response to stress (6950) 370 (3) 159 (0)    Organic acid transporter activity (5342) 32 (0) ---
       Carrier activity (5386) 67 (0) 13 (0)
Ribonucleoprotein complex (30529) 318 (64) 96 (12)    Intracellular transporter activity (5478) 28 (0) 17 (0)
   Small nuclear ribonucleoprotein complex (30532) 58 (2) 24 (0)    Protein transporter activity (8565) 48 (1) 29 (1)
   Preribosome (30684) 12 (4) ---    Lipid transporter activity (5319) 11(2) ---
   Spliceosome (5681) 74 (12) 33 (2)    
   Small nucleolar ribonucleoprotein complex (5732) 49 (43) 10 (9)    
   Ribosome (5840) 156 (5) 45 (1)    
   Polysome (5844) 11 (0) ---    
  1. Results for both the DIP and GOLD datasets are indicated. Parent GO terms are indicated in bold and, below them, the child GO terms are detailed. The numbers in parentheses adjacent to the names refer to the numerical identifiers of the GO terms. N: number of proteins for which we obtained PPI data and whose genes were annotated to the GO term. (P): in parentheses, number of proteins among those N that are annotated with the GO term based exclusively on PPI evidence. The child GO terms with less than 10 proteins found when analyzing the GOLD dataset were not further examined (dashes).