Alphagenome Atlas Website Links

AlphaGenome Atlas Deep-Linking & URL Configuration

Construct and validate deep-links for the AlphaGenome Atlas web application (https://deepmind.google.com/science/alphagenome/atlas).

Base URL: https://deepmind.google.com/science/alphagenome/atlas

[!IMPORTANT] Mandatory Atlas Deep-Linking with Variant Scores: Whenever presenting, discussing, or scoring genetic variants, you MUST always provide clickable deep-links to the AlphaGenome Atlas. Use scripts/alphagenome_atlas_links.py to automate link and table generation.

Prerequisites

# 1. Single Variant Exploration Link:
uv run scripts/alphagenome_atlas_links.py variant "chr9:128225994:G>A" \
  --biosample K562 \
  --modalities RNA_SEQ,DNASE,CHIP_TF

# 2. Genomic Locus / Interval Link:
uv run scripts/alphagenome_atlas_links.py locus "chr11:5288500-5290500" \
  --biosample K562 \
  --modalities RNA_SEQ,DNASE,CHIP_TF

# 3. Format Candidate Variant Records Table (with embedded clickable links):
uv run scripts/alphagenome_atlas_links.py table --input top_variants.json --biosample K562

# 4. Construct Ref vs. Alt Track Predictions Link (/atlas/track-predictions):
uv run scripts/alphagenome_atlas_links.py track-predictions \
  --variant "chr15:42387805:C>G" \
  --gene CAPN3 \
  --biosample "Muscle_Skeletal"

2. URL Query Parameters

• q (string, Required): Primary search target. Supports 1-based closed intervals (chr11:5288500-5290500), gene symbols (BRCA1), Ensembl IDs (ENSG00000012048), or 1-based variants (chr7:27170000:A>G).
• m (enum, Optional): View mode. Defaults to entity for genes/variants and locus for coordinate intervals. Use variant for variant queries. (Allowed: locus, entity, variant, motifs).
• i (string, Optional): Centered viewport zoom interval in 1-based closed chr:start-end format (e.g. chr11:5289310-5289690). Required for automatic motif rendering.
• f (string, Optional): Comma-separated filter predicates in KEY:VALUE format (e.g. BIOSAMPLE_NAME:K562,SCORER_MODALITY:RNA-seq,ASSAY_TRANSCRIPTOR_FACTOR:GATA1). Controls visible heatmap rows.
• lItems (string, Optional): Layout item sequence, AVI score track toggle (avi), section heatmaps, and pinned tracks list (e.g. avi,section:RNA_SEQ,section:DNASE,pinned:<TrackKey>).
• scores (string, Optional): Comma-separated list of ScoreId tokens for the /atlas/track-predictions page comparison (e.g. <ScoreId1>,<ScoreId2>).
• md (enum, Optional): Active modality tab selector on the track predictions view (RNA_SEQ, SPLICE_JUNCTIONS, SPLICE_SITE_USAGE, DNASE).
• tpRenames (string, Optional): Custom title overrides for specific score predictions (ScoreId:CustomTitle).
• tpLegendTitle (string, Optional): Custom legend title for the track predictions chart card (e.g. Predicted Gene Expression).

[!IMPORTANT] Variant Query Format: Variants in q must strictly use chr:pos_1_based:ref>alt format (e.g. chr7:27170000:A>G or URL-encoded chr7:27170000:A%3EG, where the position is 1-based). Do not use colon-separated alleles (A:G) or dbSNP rsIDs (rsIDs are unsupported).

3. Multi-Modality Filtering & The Assay Group Gotcha (f)

Filter Groups & Boolean Evaluation

Filters in f map to three primary evaluation groups:

• Biosample Group (BIOSAMPLE_NAME, BIOSAMPLE_TYPE): Evaluated with AND logic.
• Assay Group (SCORER_MODALITY, ASSAY_TRANSCRIPTOR_FACTOR, ASSAY_HISTONE_MARK): Evaluated with OR logic.
• Gene Group (GENE_NAME): Evaluated with OR logic.

⚠️ Mandatory Multi-Modality Filter Rule

RNA-seq and DNase tracks have no transcription factor code (transcriptionFactorCode === ""). If f contains only ASSAY_TRANSCRIPTOR_FACTOR filters under the Assay group, RNA-seq and DNase tracks fail the Assay evaluation and are hidden from the heatmap.

To display RNA-seq and DNase tracks alongside specific ChIP-seq transcription factors, explicitly include SCORER_MODALITY:RNA-seq and SCORER_MODALITY:DNase in f (handled automatically by scripts/alphagenome_atlas_links.py):

f=BIOSAMPLE_NAME:<CellLine>,SCORER_MODALITY:RNA-seq,SCORER_MODALITY:DNase,ASSAY_TRANSCRIPTOR_FACTOR:<TF1>,ASSAY_TRANSCRIPTOR_FACTOR:<TF2>

4. Layout Configuration, AVI Scores, & Pinned Tracks (lItems)

Plotting AVI Scores and Modality Sections

• AVI Variant Impact Track (avi): Including avi in lItems renders the top-level AlphaGenome Variant Impact score track for the interval or variant.
• Database Modality Sections (section:<MODALITY>): Sections render full unpinned heatmaps across all matching tracks for that modality (e.g. section:RNA_SEQ, section:DNASE, section:CHIP_TF, section:ATAC, section:CAGE).

Pinned Tracks & Motif Instances

[!NOTE] Track-Specific Motif Guideline: Pinned Active-ISM tracks with motif instances and Contribution Weight Matrix (CWM) logos should only be added when specifically requested for individual tracks. Only a limited subset of tracks (such as key ChIP-TF or RNA-seq tracks relevant to the locus) support and benefit from pinned motif overlays. For standard exploration links, default section heatmaps (avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF) without pinned tracks are preferred.

Motif instances and CWM logos render exclusively on pinned tracks at base-pair resolution. General section heatmaps do not trigger motif footprint rendering.

Pinned Track Key Schema

pinned:<TrackMetadataName>:<StrandNumber>:<ScorerShortName>:heatmap:HEATMAP_TILESET_SOURCE_ACTIVE_ISM_SCORES:<TilesetId>

• <TrackMetadataName>: Exact track name from production metadata proto, URL-encoded (%20 for spaces).
• <StrandNumber>: 1 (STRAND_POSITIVE), 2 (STRAND_NEGATIVE), 3 (STRAND_UNSTRANDED).
• <ScorerShortName>: RNA_SEQ, CHIP_TF, DNASE, ATAC, CAGE, PROCAP, CHIP_HISTONE.
• HEATMAP_TILESET_SOURCE_ACTIVE_ISM_SCORES: Required source identifier for Active-ISM motif layers.
• <TilesetId>: Server-assigned tileset identifier (17354278441953531756 for current production).