Table 2:
Summary of the 28 predictive gene signatures evaluated in this study.
| Gene Signature Name |
Description | Number of Genes |
Reference |
|---|---|---|---|
| Angiogenesis | A signature is constructed from genes which are highly co-expressed in the angiogenesis pathway. | 16 | 34 |
| Chaurio | A set of genes that reflect T and B cell responses in human cancer. | 7 | 39 |
| Chemokine | Chemokine gene set. | 12 | 20,21 |
| Davoli | A signature based on scoring the immune infiltration based on gene expression profile. | 7 | 13 |
| effector_t | Effector T cell gene set | 6 | 24 |
| Glycolysis | This signature is related to the expression of glucose transporters and genes related to the metabolism of glucose. | 30 | 34 |
| gMDSC | The granulocytic myeloid-derived suppressor cell signature contains markers for neutrophils and chemokines which are ligands for the neutrophils. | 43 | 34 |
| Hypoxia | This signature was developed based on the transcriptional response of various cell types to hypoxia. | 20 | 34 |
| ifng-effector | IFNγ and T effector gene set | 8 | 23 |
| ifng18 | 18 gene IFNγ immune gene set | 18 | 19 |
| ifng6 | 6 gene IFNγ associated gene set | 6 | 19 |
| Impres | IMPRES score based on logical comparison of quantile-normalized expression of pre-defined checkpoint gene pairs. | 15 | 48 |
| Ipi-neo | A gene signature that reflects a proinflammatory tumor microenvironment and elements of T and B cell interplay. | 32 | 38 |
| MHC-I | 6 Major histocompatibility complex (MHC) class I genes. | 6 | 22 |
| MHC-II | 13 Major histocompatibility complex (MHC) class II genes. | 13 | 22 |
| mMDSC | The monocytic myeloid-derived suppressor cell signature contains markers of the monocytic morphology. | 209 | 34 |
| MYC | The Myc signature is an oncogenic signature focused on MYC pathway activation. | 32 | 34 |
| NRS | The neoadjuvant response signature (NRS) including genes involved in T cell activation, adaptive immune response, and T cell migration. | 68 | 49 |
| Ock | A gene signature predictor based around Bayesian compound covariate predictor algorithm. Stratifies patients into a responder/non-responder. | 105 | 50 |
| Pan | A gene panel of 18 DNA damage repair genes, developed to predict response to ICI. | 18 | 51 |
| Proliferation | A marker that emphasizes genes related to the cell cycle and proliferation rates in cell lines. | 227 | 34 |
| Ras | The Ras signature focuses on prediction of the response against PI3K and RAS inhibitors. | 11 | 34 |
| Roh | A gene signature that combines cytolytic markers, HLA molecules, IFNγ pathway genes, chemokines, and adhesions molecules. | 41 | 52 |
| Rooney | A gene signature based around the expression of two key cytolytic effectors. | 2 | 53 |
| Stroma | This signature is based on the infiltration of stromal cells into the tumor. | 51 | 34 |
| TIP Hot | Genes that serve as a marker of 'hot' (inflamed) tumors. | 12 | 54 |
| TLS | Tertiary lymphoid structures gene signature. | 9 | 55 |
| WNT | A signature developed to predict WNT mutations within human tumor datasets. | 13 | 34 |