data.RmdHere, we provide the download links of estimated tumor-specific total RNA expression proportion (\(\pi\)), TmS, and intrinsic signature genes for each cancer type from TCGA, EOPC, METABRIC and TRACERx cohorts, as described in our paper [1].
The links in the TmS summary column provide text files named TmS summary.csv; each file includes the following columns for the corresponding cancer type: - Sample ID - \(\pi\) estimate: estimated tumor-specific total RNA expression proportion - (1-\(\rho\))/(\(\rho\)*\(\psi\)): for TCGA, this is derived by consensus \(TmS / [2\pi/(1-\pi)]\). See Tutorial page for details about Consensus TmS estimation - TmS
The links in the Intrinsic tumor signature genes column provide text files named Intrinsic_signature_genes.txt; each includes the signature genes that are ranked by the gene selection scores for the corresponding cancer type [2, 3].
| Cohort | Cancer type | TmS summary | Intrinsic tumor signature genes |
|---|---|---|---|
| TCGA | BLCA | link | link |
| BRCA | link | link | |
| CRC | link | link | |
| HNSC | link | link | |
| KICH | link | link | |
| KIRC | link | link | |
| KIRP | link | link | |
| LIHC | link | link | |
| LUAD | link | link | |
| LUSC | link | link | |
| PAAD | link | link | |
| PRAD | link | link | |
| STAD | link | link | |
| THCA | link | link | |
| UCEC | link | link | |
| EOPC | link | link | |
| METABRIC | link | link | |
| TRACERx | link | link |
Note: EOPC, Early-Onset Prostate Cancer [4]; METABRIC, Molecular Taxonomy of Breast Cancer International Consortium [5]; TRACERx, Tracking Cancer Evolution through therapy [6].
[1] Cao, S. et al. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01342-x.
[2] Ahn, J. et al. DeMix: Deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics 29, 1865–1871 (2013).
[3] Wang, Z. et al. Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. iScience 9, 451–460 (2018).
[4] Gerhauser, C. et al. Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. Cancer Cell 34, 996–1011 (2018).
[5] Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346–352 (2012).
[6] Jamal-Hanjani, M. et al. Tracking the evolution of non-small-cell lung cancer. N. Engl. J. Med. 376, 2109–2121 (2017).