Gene

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Overview

The official gene sets of the IGVF Catalog are from the following GENCODE releases:

• Human: GENCODE v43
• Mouse: GENCODE vM36

Gene and Transcripts and Gene Structure (UTRs, Exons etc.) are loaded from the comprehensive annotation file as nodes. This includes all protein-coding, lncRNA and all other gene types annotated by GENCODE.

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Protein Function

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Coding Variant Effects

This table lists all coding variants in this gene with predictions or measurements. Predictions: MutPred2 and ESM-1v. Measurements: VAMP-seq and SGE.

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Gene Regulation

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Enhancer-Gene Prediction

This table reports predicted enhancers for this gene from the ENCODE-rE2G model and their relevant cell types. Each row reports one predicted enhancer and cell type. Score ranges from 0 (no prediction) to 1 (confident prediction). Currently, this table includes predictions from the ENCODE-rE2G model across 1700 ENCODE biosamples (see Gschwind et al. bioRxiv 2023) The table is initially sorted by Score in descending order, showing the strongest predictions first.

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Variants Table

Variants are linked to genes via both functional characterization experiments and QTLs. IGVFDS4359OODY shows the effect of 183 variants in the PPIF promoter measured via a CRISPR method called Variant-EFFECTS.
eQTLs and splice-QTLs are encoded as gene-variant edges. Datasets have been loaded from the EBI eQTL catalogue.
Additional QTLs have been loaded from the African Functional Genomics; AFGR resource.

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Molecular Networks

Perturb-seq and other CRISPR data coming soon!

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QTLs

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Related Variant

This table shows variants that are related to this gene through various evidence sources including eQTL, sQTL, and other regulatory mechanisms.

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Phenotypes

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Disease Associations (ClinGen, Orphanet)

This table displays diseases associated with this gene from ClinGen and Orphanet databases.

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Other Visualizations

The gene page includes several interactive visualization components that provide rich insights into gene function, variants, and relationships.

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Functional Score Distribution

An interactive histogram showing the distribution of functional/predictive scores for coding variants in this gene. Features:

• Displays score distributions across different data sources (REVEL, ClinVar, etc.)
• Hover over bars to see exact counts
• Automatically updates when selecting different data sources from the table above
• X-axis shows functional scores (typically 0-1 range)
• Y-axis shows count of variants

This visualization helps identify patterns in variant pathogenicity predictions and the overall functional landscape of the gene.

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Coding Variants Preview

An interactive, horizontally scrollable browser for exploring coding variants with functional scores. Features:

• Scrollable Interface: Navigate through variants using horizontal scroll
• Label Preferences: Choose between rsID, SPDI notation, or rsID-only filtering
• Auto-selection: Variants are automatically selected as you scroll
• Detailed View: Selected variant shows:
  • Complete variant details (chromosome, position, ref/alt alleles)
  • HGVS notation and SPDI format
  • rsID when available
  • Functional scores from multiple sources with visual score bars
• Score Visualization: Each score is displayed with a progress bar and numerical value

This component allows efficient exploration of the functional impact across all coding variants in the gene.

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Gene Interaction Network

An interactive network graph showing gene-gene interactions and co-expression relationships. Features:

• Interactive Navigation:
  • Pan by clicking and dragging
  • Zoom with mouse wheel or zoom buttons
  • Click nodes to navigate to related genes
• Visual Elements:
  • Central gene (query) shown in teal
  • Related genes shown in coral/orange
  • Edge thickness represents interaction strength
  • Node hover effects with black borders
• Data Integration: Combines multiple interaction databases (BioGRID, CoXPresdb, etc.)
• Force-Directed Layout: Nodes automatically arrange based on interaction strength
• Legend: Shows node type meanings

The network helps visualize the functional context and regulatory relationships of the gene.

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Pathway Enrichment Tree

A hierarchical tree visualization showing pathway associations organized by biological processes. Features:

• Interactive Navigation:
  • Horizontal panning with click-and-drag
  • Arrow button for quick navigation
  • Scroll bar at bottom for position reference
• Hierarchical Structure:
  • Root: “Pathways”
  • Groups: “Top-level pathways” and “GO biological processes”
  • Leaves: Individual pathways
• Visual Coding:
  • Different colors for pathway types
  • Rounded rectangles with connecting lines
  • Hover tooltips with detailed information
• Legend: Color-coded explanation of pathway types

This visualization helps understand the biological processes and pathways this gene participates in.