Biclustering Analysis

Research Use Only: This analysis is for exploratory research purposes. Biclusters identify co-occurring gene-phenotype patterns but do not imply causation.

About Biclustering

Spectral co-clustering identifies rectangular submatrices where subsets of genes share subsets of phenotypes. Unlike hierarchical clustering, this allows overlapping modules and reveals local patterns in the gene-phenotype matrix. Higher density indicates stronger within-bicluster associations.

Total Biclusters
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Gene-phenotype modules
Avg Genes/Bicluster
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Genes per module
Avg Traits/Bicluster
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Traits per module
Background Density
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Overall matrix density
Reordered Gene-Phenotype Matrix
Matrix reordered to show bicluster block structure. Darker = higher association density.
What you're seeing: Each row is a gene, each column is a phenotype (clinical feature). Blue cells indicate the gene is associated with that phenotype. The matrix has been rearranged so that genes and phenotypes belonging to the same bicluster appear next to each other, creating visible "blocks" of dense associations. What it means: If you see a dark rectangular block, those genes tend to share those specific phenotypes when mutated—suggesting they may affect similar biological processes.
What you're seeing: Each card represents one bicluster—a group of genes that share a common set of phenotypes. The "density" measures how consistently genes in this group share these traits (higher = more consistent). "Enrichment" compares this density to the overall background rate. What it means: A bicluster with high density and enrichment suggests these genes form a coherent functional group. For example, if 5 genes all cause seizures, intellectual disability, and hypotonia, they might all affect the same developmental pathway.
Bicluster Phenotype Similarity
Cosine similarity between average phenotype profiles of genes in each bicluster
What you're seeing: This matrix shows how similar the phenotype patterns are between different biclusters. Higher percentages (warmer colors) mean the genes in those two biclusters cause similar clinical features, even though they're in separate groups. What it means: Two biclusters with high similarity (e.g., 80%+) might represent related biological mechanisms or overlapping clinical presentations. Low similarity suggests distinct phenotypic profiles.
Bicluster Size Distribution
Number of genes and traits per bicluster
What you're seeing: A simple comparison of bicluster sizes. Blue bars show how many genes belong to each bicluster; purple bars show how many phenotypes. What it means: Smaller, denser biclusters often represent more specific gene-phenotype relationships. Larger biclusters may capture broader patterns but with more variability among members.