Table 1.
Elastic Net features selected using the gene signatures only model from CALGB 40601
| Feature | References | Coefficient |
|---|---|---|
| GS_HS_Green18 | PMID.21214954 | −0.07153 |
| GS_HS_Red19 | PMID.21214954 | −0.04255 |
| GS_Duke_Module17_PgR | PMID.20335537 | −0.03614 |
| GS_JANES_Oscillation_JUND_KRT5 | PMID.24658685 | −0.03246 |
| GS_MITO1 | PMID.21214954 | −0.02511 |
| GS_Scorr_LumA_Correlation | PMID.19204204 | −0.01563 |
| GS_MM_Green12 | PMID.21214954 | −0.01218 |
| GS_MUnknown_16 | PMID.21214954 | −0.0108 |
| GS_HS_Green1 | PMID.21214954 | −0.00953 |
| GS_Duke_Module14_p53 | PMID.20335537 | −0.00605 |
| GS_Scorr_P53_Wt_Correlation | PMID.17150101 | −0.00386 |
| GS_Pcorr_NKI70_Good_Correlation | PMID.11823860 | −0.00307 |
| GS_Lim2009_MatureLuminal | PMID.25575446 | −0.0014 |
| GS_Chromogramin | PMID.21214954 | −0.00022 |
| GS_Unknown_12 | PMID.21214954 | 5.94E-05 |
| GS_Duke_Module07_glucosedepletion | PMID.20335537 | 0.002937 |
| GS_GSEA_RB_PATHWAY_BIOCARTA | http.//www.broadinstitute.org/gsea/msigdb/cards | 0.00382 |
| GS_Scorr_P53_Mut_Correlation | PMID.17150101 | 0.004311 |
| GS_HER2_Amplicon | PMID.21214954 | 0.007577 |
| GS_ROR_S_Model | PMID.19204204 | 0.012094 |
| GS_IGG_Cluster | PMID.21214954 | 0.014302 |
| GS_HS_Red12 | PMID.21214954 | 0.018906 |
| GS_GHI_RS_Model | PMID.15591335 | 0.021864 |
| GS_Duke_Module08_her2 | PMID.20335537 | 0.028529 |
| GS_Bcells_Plasmablast | PMID.25800755 | 0.034936 |
| GS_S100A9_A8 | PMID.21214954 | 0.039593 |
| GS_XRTinducedgenes | PMID.24527691 | 0.043993 |
| GS_Scorr_Her2_Correlation | PMID.19204204 | 0.044143 |
Using Elastic Net feature selection, features that made the logistic regression model are shown in this table. All the selected features are weighted and show non-zero coefficient values where positive coefficients predict pCR and negative coefficients predict non-pCR. GS, gene signature; HS, homo sapiens; MM, mammary model; PgR, progesterone receptor; Wt, wild type; Mut, mutation