From: Factors affecting the accuracy of a class prediction model in gene expression data
Disease | ID+ | Medical question | Disease class | Cell/Tissue type | Affymetrix platform | Citation * | N | p | Ndeg | fc | cc |
---|---|---|---|---|---|---|---|---|---|---|---|
UC1 | E-GEOD-14580 | Response to treatment (non-/responder) | Inflammation | Colonic mucosal biopsies | HG U133 Plus 2.0 | yes | 24 (16,8) | 4650 | 623 | 1.551 | 0.162 |
UC2 | E-GEOD-21231 | Response to treatment (non-/responder) | Inflammation | Blood | HG 1.0 ST | yes | 40 (20,20) | 3388 | 0 | 0.207 | 0.112 |
UC3 | E-GEOD-36807 | Diagnostic (UC/CD) | Inflammation | Intestinal biopsy | HG U133 Plus 2.0 | no | 28 (15,13) | 6541 | 21 | 2.222 | 0.305 |
UC4 | E-GEOD-23597 | Response to treatment (non-/responder) | Inflammation | Colonic biopsy | HG U133 Plus 2.0 | yes | 14 (7,7) | 4793 | 0 | 1.119 | 0.298 |
UC5 | E-MTAB-331 | Diagnostic (UC/CD) | Inflammation | CD8+ T cell | HG 1.0 ST and HG 1.1 ST | yes | 59 (30,29) | 1402 | 312 | 0.714 | 0.164 |
UC6 | E-GEOD-9452 | Diagnostic (with/without inflammation) | Inflammation | Colon | HG U133 Plus 2.0 | yes | 17 (8,9) | 3702 | 2401 | 3.697 | 0.165 |
UC7 | E-GEOD-6731 | Diagnostic (UC/CD) | Inflammation | Colon | HG U95AV2 | yes | 30 (11,19) | 1055 | 0 | 0.485 | 0.228 |
AST1 | E-GEOD-27011 | Diagnostic (mild/severe) | Inflammation | Blood | HG 1.0 ST | no | 36 (19,17) | 1293 | 39 | 0.302 | 0.113 |
AST2 | E-GEOD-51392 | Diagnostic (asthma/rhinitis) | Inflammation | Bronchial epithelial cells | HG U133 Plus 2.0 | no | 11 (6,5) | 3969 | 0 | 1.805 | 0.171 |
AST3 | E-GEOD-31773 | Diagnostic (non/severe) | Inflammation | CD4 T cells | HG U133 Plus 2.0 | no | 12 (4,8) | 18321 | 14488 | 16.964 | 0.317 |
DYS | E-GEOD-19419 | Diagnosis (carrier/symp) | Infection | Blood | HG 1.0 ST | yes | 45 (22,23) | 2811 | 0 | 0.182 | 0.153 |
HIV1 | E-GEOD-35864 | Diagnostic (HIV/HIV with complication) | Infection | Basal ganglia | HG U133 Plus 2.0 | no | 18(6,12) | 8737 | 0 | 1.14 | 0.346 |
HIV2 | E-GEOD-14278 | Prognostic (resistant/susceptible) | Infection | Peripheral blood | HG U133 Plus 2.0 | no | 18 (9,9) | 11286 | 4 | 0.58 | 0.12 |
HIV3 | E-GEOD-6740 | Diagnostic (chronic/non chronic) | Infection | CD4 T cell | HG U133A | yes | 15 (10,5) | 865 | 5 | 0.74 | 0.168 |
PSO | E-GEOD-18948 | Response to treatment (non-/responder) | Immune | Blood | HG U95 | yes | 16 (7,9) | 1987 | 34 | 1.131 | 0.369 |
KD | E-GEOD-16797 | Response to treatment (IVIG responsive /non) | Immune | Blood | HG U133 Plus 2.0 | yes | 12 (6,6) | 11043 | 5 | 1.688 | 0.224 |
Dia1 | E-GEOD-18732 | Diagnostic (type 2 diabetes/intolerant) | Immune | Skeletal muscle | HG U133 Plus 2.0 | no | 71 (45,26) | 2038 | 10 | 0.279 | 0.16 |
Dia2 | E-CBIL-30 | Diagnostic (diabetes type 2/abnormal glucose) | Immune | Skeletal muscle | HG U133A | yes | 26 (18,8) | 1749 | 0 | 0.269 | 0.435 |
ALZ1 | E-GEOD-1297 | Diagnostic (severe/not severe) | Degenerative | Hippocampus | HG U133A | yes | 22 (7;15) | 2295 | 13 | 0.693 | 0.287 |
ALZ2 | E-MEXP-2280 | Diagnostic (Alz/Pick's disease) | Degenerative | Medial temporal lobe | HG U133 Plus 2.0 | yes | 19 (7,12) | 6899 | 1592 | 1.086 | 0.231 |
PARKI | E-GEOD-6613 | Diagnostic (Parkinson/non-Parkinson) | Degenerative | Blood | HG U133A | yes | 83 (50,33) | 638 | 0 | 0.192 | 0.361 |
HF | E-GEOD-26887 | Diagnostic (with/-out Diabetes) | Degenerative | Left ventricle cardiac biopsies | HG 1.0 ST | yes | 19 (7,12) | 2068 | 0 | 0.374 | 0.131 |
GAU | E-GEOD-21899 | Diagnostic (type 1/ 3) | Hereditary | Skin | HG U133A 2.0 | no | 10 (5,5) | 2017 | 4 | 1.807 | 0.143 |
CS | E-MEXP-2236 | Diagnostic (Apert/Muenke) | Hereditary | Skin | HG U133 Plus 2.0 | yes | 20 (10;10) | 5422 | 21 | 0.59 | 0.255 |
CF | E-GEOD-10406 | Diagnostic (Chronic rhinosinusitis/+Cystic fibrosis) | Hereditary | Sinus mucosa | HG U133 Plus 2.0 | no | 15 (9,6) | 7604 | 0 | 0.786 | 0.206 |