Background
Results
Data Selection
Pre-processing
Pre-processed Data Set | Inflammatory | Not Inflammatory |
---|---|---|
Learning | 106 | 49 |
Validation | 32 | 17 |
Feature Selection
Feature Name | Chromosome | Gene Symbol | Gene Title | Entrez Gene ID |
---|---|---|---|---|
101481_at1415791_at | 5 | Rnf34 | ring finger protein 34 | 80751 |
92232_at-1416576_at | 11 | Socs3 | suppressor of cytokine signaling 3 | 12702 |
97409_at-1418825_at | 11 | Irgm1 | immunity-related GTPase family M member 1 | 15944 |
100779_at-1419530_at | 11 | Il12b | interleukin 12b | 16160 |
93347_at-1421873_s_at | 13 | Rab24 | RAB24, member RAS oncogene family | 19336 |
102062_at-1423416_at | 9 | Smarcc1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 | 20588 |
103260_at-1430291_at | 14 | Dock5 | dedicator of cytokinesis 5 | 68813 |
98589_at-1448318_at | 4 | Plin2 | perilipin 2 | 11520 |
97507_at-1448380_at | 11 | Lgals3bp | lectin, galactoside-binding, soluble, 3 binding protein | 19039 |
92962_at-1449473_s_at | 2 | Cd40 | CD40 antigen | 21939 |
Model Training and Performance Estimation
Precision | Recall | F-measure | ROC | Accuracy | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
min |
mid
| max | min |
mid
| max | min |
mid
| max | min |
mid
| max | min |
mid
| max | |
ZeroR | 46.8 |
46.8
| 46.8 | 68.4 |
68.4
| 68.4 | 55.5 |
55.5
| 55.5 | 47.9 |
47.9
| 47.9 | 68.4 |
68.4
| 68.4 |
IB-3 | 97.4 |
98.1
| 98.7 | 97.4 |
98.1
| 98.7 | 97.4 |
98.1
| 98.7 | 99.9 |
99.9
| 100.0 | 97.4 |
98.1
| 98.7 |
C4.5 | 94.2 |
96.3
| 98.1 | 94.2 |
96.3
| 98.1 | 94.1 |
96.3
| 98.1 | 92.9 |
97.5
| 98.9 | 94.2 |
96.3
| 98.1 |
Logistic | 94.4 |
95.6
| 96.9 | 94.2 |
95.5
| 96.8 | 94.2 |
95.5
| 96.8 | 98.3 |
98.6
| 98.9 | 94.2 |
95.5
| 96.8 |
MLP | 98.2 |
98.7
| 98.8 | 98.1 |
98.6
| 98.7 | 98.1 |
98.6
| 98.7 | 99.9 |
100.0
| 100.0 | 98.1 |
98.6
| 98.7 |
NB | 93.7 |
94.4
| 95.1 | 93.5 |
94.2
| 94.8 | 93.6 |
94.2
| 94.9 | 98.3 |
98.6
| 98.9 | 93.6 |
94.2
| 94.8 |
RF | 96.8 |
99.1
| 100.0 | 96.8 |
99.1
| 100.0 | 96.7 |
99.1
| 100.0 | 98.5 |
99.8
| 100.0 | 96.8 |
99.1
| 100.0 |
SMO-puk | 98.2 |
98.7
| 98.8 | 98.1 |
98.6
| 98.7 | 98.1 |
98.6
| 98.7 | 98.6 |
99.0
| 99.1 | 98.1 |
98.6
| 98.7 |
TAN | 94.9 |
96.3
| 98.1 | 94.8 |
96.3
| 98.1 | 94.8 |
96.2
| 98.1 | 98.9 |
99.2
| 99.4 | 94.8 |
96.3
| 98.1 |
Validation
Precision | Recall | F-measure | ROC | Accuracy | Errors | |
---|---|---|---|---|---|---|
ZeroR | 42.6 | 65.3 | 51.6 | 50.0 | 65.3 | 17/49 |
IB-3 | 85.6 | 85.7 | 85.6 | 92.6 | 85.7 | 07/49 |
C4.5 | 94.4 | 93.9 | 93.7 | 91.2 | 93.9 | 03/49 |
Logistic | 81.9 | 81.6 | 80.7 | 86.6 | 81.6 | 09/49 |
MLP | 77.2 | 77.6 | 76.4 | 88.1 | 77.6 | 11/49 |
NB | 87.7 | 87.8 | 87.6 | 93.0 | 87.8 | 06/49 |
RF | 93.9 | 93.9 | 93.8 | 89.6 | 93.9 | 03/49 |
SMO-puk | 90.1 | 89.8 | 89.5 | 86.7 | 89.8 | 05/49 |
TAN | 91.9 | 91.8 | 91.7 | 92.8 | 91.8 | 04/49 |
Functional Gene Selection
Diseases and Disorders
| ||
---|---|---|
Name | p-value | # Molecules |
Infection Mechanism | 4.32E-07 - 4.79E-02 | 4 |
Genetic Disorder | 1.30E-06 - 4.33E-02 | 4 |
Hematological Disease | 1.30E-06 - 1.91E-02 | 5 |
Immunological Disease | 1.30E-06 - 4.27E-02 | 5 |
Gastrointestinal Disease | 1.33E-06 - 3.80E-02 | 4 |
Molecular and Cellular Functions
| ||
Name
|
p-value
|
# Molecules
|
Cellular Growth and Proliferation | 1.23E-07 - 4.72E-02 | 5 |
Lipid Metabolism | 4.32E-06 - 2.05E-02 | 4 |
Small Molecule Biochemistry | 4.32E-06 - 4.13E-02 | 5 |
Cell Signaling | 4.35E-06 - 4.13E-02 | 4 |
Cellular Development | 6.63E-06 - 4.86E-02 | 5 |
Physiological System Development and Function
| ||
Name
|
p-value
|
# Molecules
|
Hematological System Development and Function | 1.23E-07 - 4.86E-02 | 6 |
Tissue Development | 1.23E-07 - 3.93E-02 | 6 |
Humoral Immune Response | 4.32E-07 - 2.99E-02 | 2 |
Organismal Survival | 6.36E-06 - 4.67E-04 | 5 |
Cell-mediated Immune Response | 6.63E-06 - 3.86E-02 | 5 |
Feature Name | Chromosome | Gene Symbol | Gene Title | Entrez Gene ID |
---|---|---|---|---|
92232_at-1416576_at | 11 | Socs3 | suppressor of cytokine signaling 3 | 12702 |
97409_at-1418825_at | 11 | Irgm1 | immunity-related GTPase family M member 1 | 15944 |
100779_at-1419530_at | 11 | Il12b | interleukin 12 b | 16160 |
98589_at-1448318_at | 4 | Plin2 | perilipin 2 | 11520 |
97507_at-1448380_at | 11 | Lgals3bp | lectin, galactoside-binding, soluble, 3 binding protein | 19039 |
92962_at-1449473_s_at | 2 | Cd40 | CD40 antigen | 21939 |
Precision | Recall | F-measure | ROC | Accuracy | Errors | |
---|---|---|---|---|---|---|
ZeroR | 42.6 | 65.3 | 51.6 | 50.0 | 65.3 | 17/49 |
IB-3 | 91.8 | 91.8 | 91.8 | 90.8 | 91.8 | 04/49 |
C4.5 | 86.8 | 85.7 | 85.9 | 86.3 | 85.7 | 07/49 |
Logistic | 84.3 | 83.7 | 83.9 | 91.5 | 83.7 | 08/49 |
MLP | 82.8 | 81.6 | 81.9 | 86.8 | 81.6 | 09/49 |
NB | 87.8 | 87.8 | 87.8 | 89.9 | 87.8 | 06/49 |
RF | 86.8 | 85.7 | 85.9 | 90.1 | 85.7 | 07/49 |
SMO-puk | 89.7 | 89.8 | 89.7 | 88.1 | 89.8 | 05/49 |
TAN | 91.9 | 91.8 | 91.7 | 90.1 | 91.8 | 04/49 |
Precision | Recall | F-measure | ROC | Accuracy | Errors | |
---|---|---|---|---|---|---|
ZeroR | 42.6 | 65.3 | 51.6 | 50.0 | 65.3 | 17/49 |
IB-3 | 91.9 | 91.8 | 91.7 | 93.5 | 91.8 | 04/49 |
C4.5 | 85.6 | 85.7 | 85.6 | 83.5 | 85.7 | 07/49 |
Logistic | 89.7 | 89.8 | 89.7 | 91.5 | 89.8 | 05/49 |
MLP | 88.3 | 87.8 | 87.9 | 92.5 | 87.8 | 06/49 |
NB | 91.8 | 91.8 | 91.8 | 93.2 | 91.8 | 04/49 |
RF | 85.6 | 85.7 | 85.6 | 84.7 | 85.7 | 07/49 |
SMO-puk | 96.2 | 95.9 | 95.9 | 94.1 | 95.9 | 02/49 |
TAN | 90.0 | 89.8 | 89.9 | 89.3 | 89.8 | 05/49 |
A 3-gene signature associated with inflammation in Human Dendritic Cells
Accuracy | Errors | |
---|---|---|
IB-3 | 92.6 | 2/27 |
C4.5 | 100.0 | 0/27 |
Logistic | 100.0 | 0/27 |
MLP | 100.0 | 0/27 |
NB | 100.0 | 0/27 |
RF | 100.0 | 0/27 |
SMO-puk | 71.4 | 8/27 |
TAN | 100.0 | 0/27 |