Table 3 |
||||
|
Biological event and its frequency used in macrophage models and the number of warnings. |
||||
|
Biological event |
Freq. |
Warnings |
Reasons (freq.) |
|
|
|
||||
|
1 |
ME_Autocleavage |
2 |
2 |
# of input (2) |
|
ME Binding |
1898 |
253 |
TYPE (169), # of inputprocess (4), no inputprocess (80) |
|
|
ME_DNABinding |
29 |
0 |
(0) |
|
|
ME_DNAReplication |
6 |
0 |
(0) |
|
|
ME_Dissociation |
37 |
3 |
TYPE (3) |
|
|
ME_GDP-GTPExchange |
4 |
0 |
(0) |
|
|
ME_Isomerization |
1 |
0 |
(0) |
|
|
ME_MetabolicReaction |
40 |
7 |
TYPE (7) |
|
|
ME_ProteasomeDegradation |
34 |
0 |
(0) |
|
|
ME_ProteinCleavage |
5 |
0 |
(0) |
|
|
ME_UnknownDegradation |
45 |
1 |
TYPE (1) |
|
|
|
||||
|
2 |
ME_Acetylation |
3 |
7 |
(0) |
|
ME ADPRibosylation |
2 |
7 |
# of input (1) |
|
|
ME_Amidation |
1 |
1 |
no output (1) |
|
|
ME_Glycosylation |
1 |
3 |
(0) |
|
|
ME_Nitrosylation |
2 |
6 |
# of inputprocess (1) |
|
|
ME Oxidation |
12 |
28 |
(0) |
|
|
ME Phosphorylation |
448 |
967 |
no inputprocess(1), no output (1) |
|
|
ME_Reduction |
1 |
3 |
(0) |
|
|
ME_Sumoylation |
2 |
4 |
(0) |
|
|
ME_Ubiquitination |
67 |
166 |
(0) |
|
|
ME UnknownActivation |
793 |
1415 |
# of inputprocess (11), no inputprocess (3) |
|
|
ME_UnknownInactivation |
6 |
16 |
(0) |
|
|
ME_Autophosphorylation |
12 |
36 |
# of input (2) |
|
|
ME_Dephosphorylation |
9 |
19 |
(0) |
|
|
ME_Deubiquitination |
4 |
11 |
(0) |
|
|
|
||||
|
3 |
ME_Dimerization |
49 |
50 |
STOICHIOMETRY (49), |
|
# of inputprocess (1) |
||||
|
ME_Oligomerization |
7 |
7 |
STOICHIOMETRY (7) |
|
|
ME Polymerization |
5 |
5 |
STOICHIOMETRY (5) |
|
|
|
||||
|
4 |
ME Internalization |
9 |
22 |
CELLCOMPONENT (10) |
|
ME_NuclearExport |
4 |
3 |
CELLCOMPONENT (3) |
|
|
ME Translocation |
136 |
275 |
# of output (6), no inputprocess (2) |
|
|
CELLCOMPONENT (87) |
||||
|
|
||||
|
5 |
ME_GeneExpression |
721 |
262 |
CELLCOMPONENT (259), TYPE (3) |
|
ME_IonTransportThroughIonChannel |
2 |
4 |
TYPE (2) |
|
|
ME Transcription |
13 |
7 |
CELLCOMPONENT (4), TYPE (3) |
|
|
ME Translation |
364 |
393 |
# of input (1), TYPE (7),CELLCOMPONENT(385) |
|
|
|
||||
|
n/a |
no rules for 8 biological events |
136 |
- |
- |
|
|
||||
|
Total |
4910 |
3983 |
1121 |
|
|
|
||||
|
The biological events are grouped together along with the rules for criteria 2 in Methods. The biological events in the last group have no rules and are notified with n/a in the first column. |
||||
|
Jeong et al. BMC Bioinformatics 2011 12(Suppl 1):S8 doi:10.1186/1471-2105-12-S1-S8 |
||||
