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marin-dna/zoonomia-v1-val_utr3

bolinas-dna/zoonomia-v1-val_utr3 Conservation pre-filtered, case-encoded human-genome validation set from the snakemake/zoonomia_projection_dataset pipeline (commit main). This is one of seven per-recipe validation parquets (val_cds, val_utr5, val_utr3, val_ncrna, val_promoter, val_enhancer, val_tss_pc) built from the same human-anchored phyloP_447m scoring used to create the cross-mammal training sets bolinas-dna/zoonomia-v1-v1 and bolinas-dna/zoonomia-v1-v2. Recipe… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-val_utr3.

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bolinas-dna/zoonomia-v1-val_utr3

Conservation pre-filtered, case-encoded human-genome validation set from the `snakemake/zoonomia_projection_dataset` pipeline (commit `main`).

This is one of seven per-recipe validation parquets (val_cds, val_utr5, val_utr3, val_ncrna, val_promoter, val_enhancer, val_tss_pc) built from the same human-anchored phyloP_447m scoring used to create the cross-mammal training sets `bolinas-dna/zoonomia-v1-v1` and `bolinas-dna/zoonomia-v1-v2`.

Recipe (val_utr3)

3' UTR (untranslated region downstream of CDS) from Ensembl release 115 proteincoding canonical transcripts (`tag "Ensemblcanonical"`). Each canonical 3' UTR region is extended by 20 bp on each side, then expanded to a minimum length of 255 bp.

Schema

ColumnTypeDescription
idstrchrom:start-end — 0-based half-open coordinates with bare Ensembl chrom names (e.g. 1:1234567-1234822, not chr1).
seqstr255 bp DNA sequence with case-encoded conservation (see below).

Sequence case encoding

For each base in seq:

  • —Uppercase (A / C / G / T / N): the phyloP447m score at this position is `>= 2.2162` (the calibrated conservation threshold for the 447-way Cactus alignment, set to match phyloP241m's passing-base proportion at 2.27).
  • —Lowercase (a / c / g / t / n): either the phyloP score is below the threshold, or there is no alignment at this position (NaN in the bigWig — NaN >= t is False in NumPy, so unaligned bases are encoded as lowercase).

Uppercase positions are confidently conserved across mammals; lowercase positions are either non-conserved or unaligned, and the encoding does not distinguish those two cases.

Construction

  1. 1.Build region BED from Ensembl release 115 (canonical transcripts, where applicable) or ENCODE cCRE V4 — see Recipe above.
  2. 2.Intersect with defined regions (genome minus N).
  3. 3.Tile into 255 bp non-overlapping windows (bedtools makewindows -w 255 -s 255).
  4. 4.Score each window against phyloP_447m (UCSC 447-way Cactus, Zoonomia + primates).
  5. 5.Conservation pre-filter: keep only windows with proportion_conserved >= 0.2 (i.e. at least 51 of the 255 bases pass the phyloP_447m threshold of 2.2162).
  6. 6.Deterministic subsample to ≤ 16,384 rows (seed 42).
  7. 7.Extract sequences from hg38 (Ensembl r115) via twoBitToFa -bedPos.
  8. 8.Case-encode each base by its per-position phyloP_447m value.

No reverse-complement augmentation — each genomic region appears exactly once. (RC augmentation is a training concern; for evaluation we want deterministic per-locus rows.)

Caveats

  • —Recipes are independent probes, not a partition. A small number of bases may appear in multiple recipes (e.g. a val_promoter PLS overlapping a val_utr5 5' UTR; an add_flank(20) on CDS extending into intronic splice signal that abuts a 3' UTR). Don't concatenate the seven parquets without dedup.
  • —Lowercase is ambiguous. Lowercase letters could mean either "phyloP score is below threshold" or "no alignment at this position". The encoding does not distinguish.
  • —Only autosomes + chrX + chrY are included; the mitochondrial contig is excluded.
  • —The val_promoter and val_enhancer cCRE recipes are not restricted to canonical transcripts — those classes are transcript-independent and come directly from ENCODE SCREEN cCRE V4.

Source code