sigmutselcovs covariate matrices: TCGA-UCEC

Pre-built per-gene covariate matrices for TCGA-UCEC (Uterine Corpus Endometrial Carcinoma. encode_chromatin added 2026-09-03 (expanded-covariate-sources task): ENCODE has adult primary uterus tissue for 5 of our 7 default marks plus DNase -- H3K4me1, H3K9me3, H3K36me3, H3K27ac, H3K27me3 and DNase (one of two available adult uterus DNase experiments used). H3K9ac is not released for this biosample. H3K4me3 added 2026-10-04: ENCFF181HLF (ENCSR743GCE, released 2018), from the 51-year-old donor behind four of the other marks; it was wrongly recorded here as unreleased. encode_chromatin cell line added 2026-09-07: Ishikawa (DNase-seq, native GRCh38; since 2026-10-04 the vehicle-control experiment ENCFF926OUY, replacing the tamoxifen-treated ENCFF251BFP) is a genuine endometrial adenocarcinoma cell line -- a disease-matched complement to the adult primary uterus tissue tracks above, not just an organ-level proxy. Found via Martincorena et al. 2017's STAR Methods confirming dNdScv's matrix is cell-line-based.), built with sigmutselcovs: GTEx tissue-matched gene expression, TCGA per-sample gene expression, replication timing (mean replication time and CLR-transformed S-phase fractions), Roadmap Epigenomics histone marks, and TCGA ATAC-seq accessibility, indexed by Ensembl gene ID. Files: cov_matrix_full.parquet — the full matrix (all covariate columns) cov_matrix_pca.parquet — PCA-reduced to 1213 components, the smallest number reaching 99% cumulative explained variance (see pca_manifest.json) cov_matrix_columns.csv — a data dictionary: one row per column of the full matrix, with source, description, assembly, and units build_manifest.json, pca_manifest.json — build provenance and PCA parameters Full source citations and methodology: SOURCES.md. Release of 2026-10-26. Every chromatin and ATAC column is one track, summarized as log1p of the mean signal over the gene's CDS span (first to last coding base); replication timing covers chrX. cov_matrix_pca.parquet now reduces the combined matrix: this cohort's own covariates plus the tissue-agnostic GENERIC pool (GENERIC record), with the pool's columns for chromatin tracks this cohort already has left out. That is the matrix the sigmutsel covariate model is fitted on; it predicts held-out mutation counts better than the cohort's own matrix alone in the cohorts tested, so the first components of this artifact are the ones a model should use. Versions before 2026-10-26 reduced the own matrix alone. cov_matrix_full.parquet is still the cohort's own matrix; GENERIC's is in its record. pca_manifest.json records which matrix was reduced (matrix) and the column counts. To rebuild: sigmutselcovs pca-artifact UCEC --data-dir DIR --generic-dir GENERIC_DIR.