Gene Interactions

Research Use Only: Gene interactions shown here are based on phenotype co-occurrence patterns, not direct molecular interactions. High Jaccard similarity indicates genes share many phenotype associations but does not confirm epistasis.

About Gene Pair Analysis

This analysis identifies gene pairs that share phenotype patterns, suggesting possible functional relationships. Within-pathway pairs share a biological pathway; cross-pathway pairs may indicate convergent mechanisms. Jaccard similarity measures the overlap of phenotype profiles.

Within-Pathway Pairs

Same pathway

Cross-Pathway Pairs

Different pathways

Avg Shared Traits

Per gene pair

Avg Jaccard

Phenotype overlap

What you're seeing: A network graph where each node (circle) is a gene and each line (edge) connects genes that share phenotypes. Node colors indicate biological pathways. Thicker lines mean higher Jaccard similarity (more phenotype overlap). What it means: Genes clustered together share similar phenotype profiles. If two genes from the same pathway are connected, they cause similar clinical features. Connections between genes from different pathways suggest convergent biological mechanisms—different pathways leading to similar outcomes.

Gene Interaction Network

Nodes are genes, edges connect pairs with shared phenotypes. Node color = pathway, edge width = Jaccard similarity.

What you're seeing: A circular layout showing genes arranged by pathway around the ring. Lines connect genes that share phenotypes—thicker lines indicate stronger similarity. Genes are grouped by color (pathway). What it means: This view emphasizes which pathways have the most internal connections (within-pathway) vs cross-pathway bridges. Dense clusters within a pathway segment suggest highly conserved phenotypes. Lines crossing the circle reveal convergent mechanisms.

Gene Interaction Chord Diagram

Genes arranged by pathway, connected by phenotype similarity

What you're seeing: Gene pairs from the same biological pathway that share phenotypes. "Shared traits" lists the clinical features both genes cause when mutated. "Jaccard similarity" measures overlap (higher = more similar phenotype profiles). What it means: High similarity between genes in the same pathway confirms they affect the same biological processes. For example, if two chromatin remodeling genes both cause ID, macrocephaly, and seizures, this suggests chromatin dysfunction produces a characteristic phenotype pattern.

Within-Pathway Gene Pairs

Showing pairs

What you're seeing: Gene pairs from different biological pathways that nonetheless share phenotypes. These are genes that work in different molecular mechanisms but produce similar clinical outcomes. What it means: Cross-pathway similarity suggests convergent biology—different roads leading to the same destination. For example, a synaptic gene and a chromatin gene both causing seizures might indicate seizures can arise from multiple biological disruptions, or that these pathways interact.

Cross-Pathway Gene Pairs

Showing pairs

Pathway Similarity Matrix

Average Jaccard similarity between genes in different pathways

What you're seeing: Each cell shows the average phenotype similarity between all gene pairs from two pathways. Diagonal values show within-pathway similarity (how similar genes within the same pathway are); off-diagonal values show cross-pathway similarity. What it means: Pathways with high within-pathway similarity have genes that cause consistent phenotypes. Pathways with high cross-pathway similarity may represent related biological functions or convergent clinical outcomes, even though they involve different molecular mechanisms.