Prediction Results
Class prediction with nominal gene set selected with the random variance t-test (P=0.001):
Number of classes: 2 (SSc vs normal)
Based on 5000 random permutations,
the compound covariate predictor has p-value of 0.002
the 1-nearest neighbor classifier has p-value of < 2e-04
the 3-nearest neighbors classifier has p-value of < 2e-04
the nearest centroid classifier has p-value of < 2e-04
the support vector machines classifier has p-value of < 2e-04
the linear discriminant analysis classifier has p-value of 0.003
Note: t-values used for the compound covariate predictor were truncated at abs(t)=10 level.
Performance of classifiers during cross-validation:
| Pair ID | Number of genes in classifier | Compound Covariate Predictor Correct? | Diagonal Linear Discriminant Analysis Correct? | 1-Nearest Neighbor Correct? | 3-Nearest Neighbors Correct? | Nearest Centroid Correct? | Support Vector Machines Correct? | |
|---|---|---|---|---|---|---|---|---|
| 1 | 1 | 22 | YES | YES | YES | YES | YES | YES |
| 2 | 10 | 18 | YES | YES | YES | YES | YES | YES |
| 3 | 11 | 23 | YES | YES | YES | YES | YES | YES |
| 4 | 12 | 23 | YES | YES | YES | YES | YES | YES |
| 5 | 13 | 23 | YES | YES | YES | YES | YES | YES |
| 6 | 14 | 15 | YES | YES | YES | YES | YES | YES |
| 7 | 15 | 19 | YES | YES | YES | YES | YES | YES |
| 8 | 16 | 25 | YES | YES | YES | YES | YES | YES |
| 9 | 17 | 22 | YES | YES | YES | YES | YES | YES |
| 10 | 18 | 24 | YES | YES | YES | YES | YES | YES |
| 11 | 19 | 19 | YES | YES | YES | YES | YES | YES |
| 12 | 2 | 19 | YES | YES | YES | YES | YES | YES |
| 13 | 20 | 25 | YES | YES | YES | YES | YES | YES |
| 14 | 21 | 29 | YES | YES | YES | YES | YES | YES |
| 15 | 22 | 22 | YES | YES | YES | YES | YES | YES |
| 16 | 23 | 19 | YES | YES | YES | YES | YES | YES |
| 17 | 24 | 25 | YES | YES | YES | YES | YES | YES |
| 18 | 25 | 23 | YES | YES | YES | YES | YES | YES |
| 19 | 3 | 24 | YES | YES | YES | YES | YES | YES |
| 20 | 4 | 27 | NO | NO | YES | YES | YES | YES |
| 21 | 5 | 18 | YES | YES | YES | YES | YES | YES |
| 22 | 6 | 18 | YES | YES | YES | YES | YES | YES |
| 23 | 7 | 17 | YES | YES | YES | YES | YES | YES |
| 24 | 8 | 18 | YES | YES | YES | YES | YES | YES |
| 25 | 9 | 28 | YES | YES | YES | YES | YES | YES |
| Percent correctly classified: | 96 | 96 | 100 | 100 | 100 | 100 |
Composition of classifier (26 genes significant at the 1e-04 level):
Table – Sorted by t -value:
| t-value | Parametric p-value | % CV support | Geometric mean of ratios (class Disease /class Normal) | Qiagen oligo ID | Description | GB acc | UG cluster | Gene symbol | |
|---|---|---|---|---|---|---|---|---|---|
| 1 | -6.61 | p < 0.000001 | 100 | 0.621 | H003528_01 | Decay accelerating factor for complement (CD55, Cromer blood group system) | M30142 (external link) | 1369 | DAF (external link) |
| 2 | -5.92 | 1e-06 | 100 | 0.548 | H003827_01 | Serum/glucocorticoid regulated kinase |
AJ000512 (external link) | 296323 | SGK (external link) |
| 3 | -5.91 | 2e-06 | 100 | 0.548 | H016371_01 | Hypothetical protein FLJ21212 | NM_024642 (external link) | 47099 | FLJ21212 (external link) |
| 4 | -5.48 | 5e-06 | 100 | 0.584 | H009347_01 | Neuronal cell adhesion molecule | AB002341 (external link) | 7912 | NRCAM (external link) |
| 5 | -4.86 | 3.1e-05 | 100 | 0.811 | H005438_01 | Homo sapiens mRNA; cDNA DKFZp434B1620 (from clone DKFZp434B1620) |
AL137548 (external link) | 43112 | |
| 6 | -4.86 | 3.1e-05 | 100 | 0.728 | H004078_01 | Heme-binding protein | NM_015987 (external link) | 108675 | HEBP (external link) |
| 7 | -4.85 | 3.2e-05 | 100 | 0.465 | H001509_01 | Aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II) |
D17793 (external link) | 78183 | AKR1C3 (external link) |
| 8 | -4.8 | 3.8e-05 | 100 | 0.708 | H002860_01 | Inositol polyphosphate-1-phosphatase |
L08488 (external link) | 32309 | INPP1 (external link) |
| 9 | -4.79 | 3.8e-05 | 100 | 0.62 | H010655_01 | Hypothetical protein FLJ20546 | AK000953 (external link) | 279896 | FLJ20546 (external link) |
| 10 | -4.78 | 3.9e-05 | 100 | 0.768 | H002574_01 | Alcohol dehydrogenase 5 (class III), chi polypeptide |
M81118 (external link) | 78989 | ADH5 (external link) |
| 11 | -4.78 | 3.9e-05 | 100 | 0.517 | H003858_01 | Aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-a |
U05598 (external link) | 201967 | AKR1C2 (external link) |
| 12 | -4.72 | 4.6e-05 | 76 | 0.751 | H004767_01 | Tetraspan 3 | AK001326 (external link) | 100090 | TSPAN-3 (external link) |
| 13 | -4.53 | 8e-05 | 24 | 0.771 | H016494_01 | Hypothetical protein FLJ12436 | NM_024661 (external link) | 69485 | FLJ12436 (external link) |
| 14 | -4.52 | 8.4e-05 | 36 | 0.721 | H003965_01 | Cellular repressor of E1A-stimulated genes |
AF084523 (external link) | 5710 | CREG (external link) |
| 15 | -4.51 | 8.4e-05 | 32 | 0.724 | H002462_01 | Receptor tyrosine kinase-like orphan receptor 1 |
M97675 (external link) | 274243 | ROR1 (external link) |
| 16 | -4.47 | 9.6e-05 | 32 | 0.689 | H000959_01 | Glycophorin C (Gerbich blood group) |
NM_002101 (external link) | 81994 | GYPC (external link) |
| 17 | -4.46 | 9.8e-05 | 36 | 0.742 | H008089_01 | KIAA0469 gene product | AB007938 (external link) | 7764 | KIAA0469 (external link) |
| 18 | 4.53 | 8.1e-05 | 36 | 1.689 | H016341_01 | Platelet derived growth factor C | NM_016205 (external link) | 43080 | PDGFC (external link) |
| 19 | 4.53 | 8.1e-05 | 40 | 1.757 | H002994_01 | Collagen, type XVIII, alpha 1 | AF018081 (external link) | 78409 | COL18A1 (external link) |
| 20 | 4.55 | 7.7e-05 | 36 | 1.314 | H003383_01 | Ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) |
Z82188 (external link) | 173466 | RAC2 (external link) |
| 21 | 4.6 | 6.6e-05 | 36 | 1.249 | H003776_01 | Aldehyde dehydrogenase 2 family (mitochondrial) |
X05409 (external link) | 195432 | ALDH2 (external link) |
| 22 | 4.64 | 5.9e-05 | 40 | 1.352 | H000498_01 | Desmoplakin (DPI, DPII) | AL031058 (external link) | 74316 | DSP (external link) |
| 23 | 4.69 | 5.1e-05 | 60 | 1.251 | H011854_01 | Heterogeneous nuclear ribonucleoprotein C (C1/C2) |
M16342 (external link) | 182447 | HNRPC (external link) |
| 24 | 4.71 | 4.8e-05 | 60 | 1.422 | H006183_01 | Metallothionein 1X | X65607 (external link) | 278462 | MT1X (external link) |
| 25 | 6.23 | p < 0.000001 | 100 | 1.453 | H007688_01 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 | AF109735 (external link) | 195471 | PFKFB3 (external link) |
| 26 | 7.26 | p < 0.000001 | 100 | 1.553 | H002655_01 | Collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive) |
L02870 (external link) | 1640 | COL7A1 (external link) |
Table – Sorted by mean difference:
| t-value | Parametric p-value | % CV support | Geometric mean of ratios (class Disease /class Normal ) | Qiagen oligo ID | Description | GB acc | UG cluster | Gene symbol | |
|---|---|---|---|---|---|---|---|---|---|
| 19 | 4.53 | 8.1e-05 | 40 | 1.757 | H002994_01 | Collagen, type XVIII, alpha 1 | AF018081 (external link) | 78409 | COL18A1 (external link) |
| 18 | 4.53 | 8.1e-05 | 36 | 1.689 | H016341_01 | Platelet derived growth factor C | NM_016205 (external link) | 43080 | PDGFC (external link) |
| 26 | 7.26 | p < 0.000001 | 100 | 1.553 | H002655_01 | Collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive) |
L02870 (external link) | 1640 | COL7A1 (external link) |
| 25 | 6.23 | p < 0.000001 | 100 | 1.453 | H007688_01 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 |
AF109735 (external link) | 195471 | PFKFB3 (external link) |
| 24 | 4.71 | 4.8e-05 | 60 | 1.422 | H006183_01 | Metallothionein 1X | X65607 (external link) | 278462 | MT1X (external link) |
| 22 | 4.64 | 5.9e-05 | 40 | 1.352 | H000498_01 | Desmoplakin (DPI, DPII) | AL031058 (external link) | 74316 | DSP (external link) |
| 20 | 4.55 | 7.7e-05 | 36 | 1.314 | H003383_01 | Ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) |
Z82188 (external link) | 173466 | RAC2 (external link) |
| 23 | 4.69 | 5.1e-05 | 60 | 1.251 | H011854_01 | Heterogeneous nuclear ribonucleoprotein C (C1/C2) |
M16342 (external link) | 182447 | HNRPC (external link) |
| 21 | 4.6 | 6.6e-05 | 36 | 1.249 | H003776_01 | Aldehyde dehydrogenase 2 family (mitochondrial) |
X05409 (external link) | 195432 | ALDH2 (external link) |
| 5 | -4.86 | 3.1e-05 | 100 | 0.811 | H005438_01 | Homo sapiens mRNA; cDNA DKFZp434B1620 (from clone DKFZp434B1620) |
AL137548 (external link) | 43112 | |
| 13 | -4.53 | 8e-05 | 24 | 0.771 | H016494_01 | Hypothetical protein FLJ12436 | NM_024661 (external link) | 69485 | FLJ12436 (external link) |
| 10 | -4.78 | 3.9e-05 | 100 | 0.768 | H002574_01 | Alcohol dehydrogenase 5 (class III), chi polypeptide |
M81118 (external link) | 78989 | ADH5 (external link) |
| 12 | -4.72 | 4.6e-05 | 76 | 0.751 | H004767_01 | Tetraspan 3 | AK001326 (external link) | 100090 | TSPAN-3 (external link) |
| 17 | -4.46 | 9.8e-05 | 36 | 0.742 | H008089_01 | KIAA0469 gene product | AB007938 (external link) | 7764 | KIAA0469 (external link) |
| 6 | -4.86 | 3.1e-05 | 100 | 0.728 | H004078_01 | Heme-binding protein | NM_015987 (external link) | 108675 | HEBP (external link) |
| 15 | -4.51 | 8.4e-05 | 32 | 0.724 | H002462_01 | Receptor tyrosine kinase-like orphan receptor 1 |
M97675 (external link) | 274243 | ROR1 (external link) |
| 14 | -4.52 | 8.4e-05 | 36 | 0.721 | H003965_01 | Cellular repressor of E1A-stimulated genes |
AF084523 (external link) | 5710 | CREG (external link) |
| 8 | -4.8 | 3.8e-05 | 100 | 0.708 | H002860_01 | Inositol polyphosphate-1-phosphatase | L08488 (external link) | 32309 | INPP1 (external link) |
| 16 | -4.47 | 9.6e-05 | 32 | 0.689 | H000959_01 | Glycophorin C (Gerbich blood group) | NM_002101 (external link) | 81994 | GYPC (external link) |
| 1 | -6.61 | p < 0.000001 | 100 | 0.621 | H003528_01 | Decay accelerating factor for complement (CD55, Cromer blood group system) |
M30142 (external link) | 1369 | DAF (external link) |
| 9 | -4.79 | 3.8e-05 | 100 | 0.62 | H010655_01 | Hypothetical protein FLJ20546 | AK000953 (external link) | 279896 | FLJ20546 (external link) |
| 4 | -5.48 | 5e-06 | 100 | 0.584 | H009347_01 | Neuronal cell adhesion molecule | AB002341 (external link) | 7912 | NRCAM (external link) |
| 3 | -5.91 | 2e-06 | 100 | 0.548 | H016371_01 | Hypothetical protein FLJ21212 | NM_024642 (external link) | 47099 | FLJ21212 (external link) |
| 2 | -5.92 | 1e-06 | 100 | 0.548 | H003827_01 | Serum/glucocorticoid regulated kinase | AJ000512 (external link) | 296323 | SGK (external link) |
| 11 | -4.78 | 3.9e-05 | 100 | 0.517 | H003858_01 | Aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-a |
U05598 (external link) | 201967 | AKR1C2 (external link) |
| 7 | -4.85 | 3.2e-05 | 100 | 0.465 | H001509_01 | Aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II) |
D17793 (external link) | 78183 | AKR1C3 (external link) |
‘Observed v. Expected’ table of GO classes and parent classes, in list of 26 genes shown above:
Only GO classes and parent classes with at least 5 observations in the selected subset and with an ‘Observed vs. Expected’ ratio of at least 2 are shown.
Biological Process
| GO id | GO classification | Observed in selected subset | Expected in selected subset | Observed/Expected |
|---|---|---|---|---|
| 0009887 | organogenesis | 5 | 1.24 | 4.02 |
| 0009653 | morphogenesis | 5 | 1.57 | 3.19 |
| 0007275 | development | 7 | 2.37 | 2.95 |