BC-Predict: Mining of signal biomarkers and multilevel validation of cascade classifier for early-stage breast cancer subtyping and prognosis -- Supplementary Information Systems Computational Biology Lab, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India.

Supplementary material to accompany the manuscript: BC-Predict: Mining of signal biomarkers and multilevel validation of cascade classifier for early-stage breast cancer subtyping and prognosis (2024). The files are:

S1 -- preprocessed gene vs sample expression dataset in cancers and controls (please see manuscript)

S2 -- Sorted linear model – Top 200 table

S3 -- Linear model genes – visualization of expression levels

S4 -- Stage-salient genes – visualization of expression levels

S5 -- Network analysis – GO

S6 -- Network analysis – KEGG

S7 -- Contra-regulation – patterns and analysis

S8 -- Nested model selection

S9 -- “Cancer vs normal” screening: extended results for the problem

S10 -- “Early-stage vs metastatic”: extended results for the problem

S11 -- "Molecular subtyping": extended results for the problem

S12 -- "Histological subtyping": extended results for the problem

S13 -- Validation with miRNA omics: extended results

S14 -- Validation with methylomics: extended results

S15 -- Significant monotonically expressed genes (MEG): discussion

S16 -- Consensus biomarkers – visualization of expression levels

S17 -- Cross-referencing of model biomarkers with human protein atlas

S18 -- Stage-salient genes: complete visualization of expression levels

S19 -- Validation with commercial panels: extended results