About ISHMap

Calling intervals

• High: alphagenome_splicing ≥ 1.0
• Moderate: 0.56 ≤ alphagenome_splicing < 1.0
• Sliding window 15 nt, step 1; one-sided binomial enrichment vs the intron-wide spliceogenic fraction
• Benjamini–Hochberg FDR 0.05 within each intron
• Deep-intronic filter: drop 100 nt from each intron end; keep intervals whose centre lies in that interior

The browser lists every interior significant interval, sorted by lowest BH q-value. A top mark is the best-q interval in that intron. Concentration = spliceogenic variants in the interval / spliceogenic variants in the intron interior.

Transcripts

Each gene uses the RefSeq transcript chosen for the screen (primary assembly, NM_ preferred over NR_/XM_, then most exons, then longest span). Exon maps on the gene page come from that same transcript, not necessarily MANE Select.

What is not scored

Single-exon disease genes and a small set of multi-exon genes with no Atlas coverage (including some noncoding loci) are omitted from the browser. They will be listed in not_scored.tsv of the Zenodo release.

Downloads

Gene pages offer a compact intervals CSV for that gene only. The full atlas (result tables, OMIM gene list, merged intron BED/TSV, per-gene tables, and PNG plots as chromosome archives) is on Zenodo: 10.5281/zenodo.24167125.

Code

Analysis repository: github.com/hassansaei/Saei_deep_intronic_hotspots