Table 2 Overview of pairwise differential analysis of spatial transcriptomics (ST), bulk transcriptomics (BT) and bulk methylation (BM) data
Statistics | Data | Sample type | Variables | Group 1 | Group 2 |
|---|---|---|---|---|---|
Quasi-likelihood negative binomial generalized log-linear model | ST | Spot | 2436 | Normal stroma (n = 3186) | Cancer stroma (n = 4802) |
Quasi-likelihood negative binomial generalized log-linear model | ST | Spot | 2436 | LG Cancer stroma (n = 2620) | HG Cancer stroma (n = 2182) |
Quasi-likelihood negative binomial generalized log-linear model | ST | Spot | 2436 | Relapse-free cancer stroma (n = 1469) | Relapse cancer stroma (n = 3333) |
Quasi-likelihood negative binomial generalized log-linear model | ST | Spot | 2436 | Relapse-free LG cancer stroma (n = 1219) | Relapse LG cancer stroma (n = 1401) |
Quasi-likelihood negative binomial generalized log-linear model | ST | Spot | 2436 | Relapse-free HG cancer stroma (n = 250) | Relapse HG cancer stroma (n = 1932) |
Linear mixed models | BT | Bulk tissue | 1 | Non-cancer (n = 61) | Cancer (n = 115) |
Linear mixed models | BT | Bulk tissue | 1 | Relapse-free (n = 49) | Relapse (n = 127) |
Linear mixed models | BT | Bulk tissue | 1 | LG cancer (n = 61) | HG cancer (n = 54) |
Linear mixed models | BT | Bulk tissue | 1 | Relapse-free cancer (n = 29) | Relapse cancer (n = 86) |
Linear mixed models | BM | Bulk tissue | 20 | Non-cancer (n = 29) | Cancer (n = 35) |
Linear mixed models | BM | Bulk tissue | 20 | Relapse-free (n = 20) | Relapse (n = 44) |
Linear mixed models | BM | Bulk tissue | 20 | LG cancer (n = 17) | HG cancer (n = 10) |
Linear mixed models | BM | Bulk tissue | 20 | Relapse-free cancer (n = 14) | Relapse cancer (n = 32) |
