| Gene Symbol | Gene Name | Direction of Change in Class 2 Tumors |
| CDH1 | E-cadherin | Up |
| ECM1 | Extracellular matrix protein 1 | Up |
| E1F1B | Eukaryotic translation initiation factor 1B | Down |
| FXR1 | Fragile X mental retardation autosomal homolog 1 | Down |
| HTR2B | 5-hydroxytryptamine (serotonin) receptor 2B | Up |
| ID2 | Inhibitor of DNA binding 2 | Down |
| LMCD1 | LIM and cysteine-rich domains 1 | Down |
| LTA4H | Leukotriene A4 hydrolase | Down |
| MTUS1 | Microtubule-associated tumor suppressor 1 | Down |
| RAB31 | RAB31, member RAS oncogene family | Up |
| ROBO1 | Roundabout, axon guidance receptor 1 | Down |
| SATB1 | SATB homeobox 1 | Down |
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