Association of copy number alterations with the immune transcriptomic landscape in cancer

This repository contains supplementary materials and data for the paper "Association of copy number alterations with the immune transcriptomic landscape in cancer". The materials are organized in the following folders:

00_code: code to reproduce the analysis

01_ica_datasets: transcriptional components, sample mixing matrix activities, and gene set enrichment analysis results of the GPL570, ARCHS4, and TCGA datasets

02_ica_cna_tc: identified CNA-TCs and their captured CNA regions, genomic plots of CNA-TCs

03_ica_immune_tc: identified immune-TCs, list of immune gene sets

04_ica_tc_dataset_overlap: reproducibility results of CNA-TCs and immune-TCs across datasets

05_immune_gene_occurences: frequency of genes with high gene weight in immune-TCs, list potential novel immune involved ORFs

06_projection_immune_tc_datasets: GPL570 and TCGA cancer samples corrected mixing matrix activitiy for CNA-TCs and immune-TCs of the other dataset

07_inferred_cna_profiles: TACNA profiles and CNA burden per cancer sample

08_cna_burden_immune_tc_association: cancer sample associations of CNA burden, individual CNAs, and single gene CNAs with immune-TCs

09_projection_single_cell: cell type activity of immune-TCs in a single-cell tumor immune atlas for precision oncology  

10_projection_spatial_transcriptomics: activity of immune-TCs and CNA-TCs for each spot in spatial transcriptomic datasets from 10x Genomics

11_immunotherapy_response: gene expression data, sample annotation, and mixing matrix of projected GPL570 immune- TCs and CNA-TCs for 13 immunotherapy response datasets with predictive performance