Table 3 Median (and maximum 1 ) of set sizes by organism and source
From: Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data
Gene ontology | KEGG2 | MO: Predicted Operons2 | SEED | |||||
|---|---|---|---|---|---|---|---|---|
BP2 | CC2 | MF2 | SS2 | Scen2 | Path2 | |||
Actinobacteria | ||||||||
Streptomyces coelicor A3(2) | 8 (3661) | 5 (1574) | 5 (4487) | 15 (192) | 3 (42) | 7 (57) | 5 (28) | 5 (28) |
Bacteroidetes | ||||||||
Bacteroidesthetaiotaomicron VPI-5482 | 7 (2141) | 7.5 (1037) | 5 (2580) | 13 (53) | 3 (32) | 5 (74) | 4 (17) | 4 (17) |
Cyanobacteria | ||||||||
Synechococcuselongatus PCC 7942 | 7 (1268) | 11 (580) | 4 (1498) | 10 (66) | 3 (18) | 6 (47) | 4 (13) | 5 (13) |
Deinococcus-Thermus | ||||||||
Thermusthermophilus | 6 (1039) | 6 (468) | 4 (1242) | 10 (63) | 2 (32) | 5 (39) | 3 (15) | 3 (15) |
Firmicutes | ||||||||
Staphylococcus aureus subsp. aureus Mu50 | 8 (1413) | 4.5 (711) | 5 (1596) | 11 (107) | 2 (23) | 5 (35) | 4 (12) | 4 (12) |
Streptococcus agalactiae | 6 (1064) | 16 (554) | 5 (1229) | 8 (97) | 4 (53) | 5 (32) | 3 (10) | 4 (10) |
Streptococcus pyogenes | 6 (965) | 11.5 (503) | 5 (1138) | 9 (66) | 4 (46) | 5 (34) | 4 (10) | 4(10) |
Mollicutes | ||||||||
Mycoplasma pneumoniae M129 | 5 (350) | 9 (196) | 5 (407) | 5 (52) | 5 (66) | 4 (32) | 4.5 (9) | 4.5 (9) |
Proteobacteria | ||||||||
Alpha | ||||||||
Bradyrhizobiumjaponicum | 7 (1578) | 3 (703) | 5 (2184) | 24 (354) | 3 (36) | 8 (66) | 4 (37) | 4 (37) |
Rhodobactersphaeroides | 7 (2076) | 4 (1054) | 4 (2480) | 15 (202) | 3 (52) | 6 (58) | 3 (14) | 3 (14) |
Rickettsia rickettsii str.Iowa | 7 (549) | 10 (315) | 4 (622) | 6 (53) | 3 (29) | 4 (32) | 3.5 (13) | 4 (13) |
Epsilon | ||||||||
Helicobacter pylori HPAG1 | 6 (815) | 11.5 (418) | 4.5 (932) | 10 (52) | 4 (29) | 5 (37) | 3 (9) | 3 (9) |
Gamma | ||||||||
Escherichia coli K12 | 7 (2370) | 4 (1308) | 4 (2665) | 14 (180) | 2 (28) | 6 (63) | 3.5 (18) | 3 (18) |
Pasteurella multocida subsp. multocida str. Pm70 | 7 (1207) | 10 (690) | 4 (1412) | 11 (124) | 4 (33) | 5 (33) | 3 (12) | 3 (12) |
Pseudomonas aeruginosa PA01 | 8 (2981) | 4 (1626) | 4 (3511) | 17 (200) | 2 (31) | 7 (58) | 4 (26) | 4 (26) |
Shewanellaoneidensis MR-1 | 7 (1959) | 5.5 (1024) | 5 (2237) | 14 (105) | 2 (28) | 7 (60) | 4 (15) | 4 (14) |
Vibrio parahaemolyticus RIMD 2210633 | 7 (1618) | 5 (896) | 4 (1771) | 12 (87) | 3 (46) | 6 (83) | 4 (15) | 4 (15) |
Total | 7 (3661) | 6.5 (1626) | 4 (4487) | 12 (354) | 3 (66) | 6 (83) | 4 (37) | 4 (37) |