Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 636

5 diseases · 10 shared-gene connections
5 Diseases
2 Unique genes
0.433 Avg. similarity score
Leukodystrophy, hypomyelinating with or without oligodontia and/or hypogonadotropic hypogonadism Most-connected disease (4 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Leukodystrophy, hypomyelinating with or without oligodontia and/or hypogonadotropic hypogonadism 4 4 1
Leukodystrophy, hypomyelinating, 8, with or without oligodontia and/or hypogonadotropic hypogonadism 4 4 1
Neurodevelopmental disorder with or without seizures, ataxia, spasticity, and demyelinating neuropathy 4 4 1
POLR3B-related disorder 4 4 1
Tremor-ataxia-central hypomyelination syndrome 4 4 2

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
POLR3B 5 / 5 Leukodystrophy, hypomyelinating with or without oligodontia and/or hypogonadotropic hypogonadism, Leukodystrophy, hypomyelinating, 8, with or without oligodontia and/or hypogonadotropic hypogonadism, Neurodevelopmental disorder with or without seizures, ataxia, spasticity, and demyelinating neuropathy, POLR3B-related disorder and 1 more
What do these columns mean?
Connections in cluster
How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
Significant partners
How many of those links are statistically significant (FDR q < 0.05).
Curated genes
Distinct curated genes linked to that disease in GeDiPNet.
Member diseases (Top shared genes)
How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
Overlap genes (x / y)
x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
Cluster gene count
Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
Fold enrichment
Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
P-value / FDR q-value
Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
Shared genes (Pairs within this cluster)
Number of curated genes the two diseases in that row have in common.
Similarity score (Pairs within this cluster)
Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.

Enriched Pathways (why this cluster is grouped, biologically)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Cytosolic sensors of pathogen-associated DNA
POLR3A, POLR3B
 Reactome 2 / 22 546× 3.20e-6 1.13e-4 ✓ sig.
RNA Polymerase III Transcription Initiation From Type 2 Promoter
POLR3A, POLR3B
 Reactome 2 / 27 445× 4.87e-6 1.61e-4 ✓ sig.
RNA Polymerase III Transcription Initiation From Type 3 Promoter
POLR3A, POLR3B
 Reactome 2 / 28 429× 5.24e-6 1.71e-4 ✓ sig.
RNA Polymerase III Transcription Initiation From Type 1 Promoter
POLR3A, POLR3B
 Reactome 2 / 28 429× 5.24e-6 1.71e-4 ✓ sig.
RNA polymerase
POLR3A, POLR3B
 KEGG 2 / 34 353× 7.78e-6 2.37e-4 ✓ sig.
Cytosolic DNA-sensing pathway
POLR3A, POLR3B
 KEGG 2 / 83 145× 4.72e-5 1.04e-3 ✓ sig.

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
positive regulation of interferon-beta production
POLR3A, POLR3B
 GO:0032728 2 / 41 456× 4.70e-6 3.02e-4 ✓ sig.
DNA-templated transcription
POLR3A, POLR3B
 GO:0006351 2 / 113 165× 3.62e-5 1.45e-3 ✓ sig.
defense response to virus
POLR3A, POLR3B
 GO:0051607 2 / 247 75.7× 1.74e-4 4.60e-3 ✓ sig.
snRNA transcription by RNA polymerase III
POLR3B
 GO:0042796 1 / 9 1,038× 9.63e-4 1.42e-2 ✓ sig.
innate immune response
POLR3A, POLR3B
 GO:0045087 2 / 605 30.9× 1.05e-3 1.51e-2 ✓ sig.
tRNA transcription by RNA polymerase III
POLR3A
 GO:0042797 1 / 11 849× 1.18e-3 1.59e-2 ✓ sig.
immune system process
POLR3A, POLR3B
 GO:0002376 2 / 943 19.8× 2.54e-3 2.40e-2 ✓ sig.
transcription by RNA polymerase III
POLR3B
 GO:0006383 1 / 24 389× 2.57e-3 2.40e-2 ✓ sig.
positive regulation of innate immune response
POLR3B
 GO:0045089 1 / 36 260× 3.85e-3 2.94e-2 ✓ sig.
positive regulation of gene expression
POLR3A
 GO:0010628 1 / 504 18.5× 5.32e-2 1.12e-1

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Leukodystrophy, hypomyelinating with or without oligodontia and/or hypogonadotropic hypogonadism POLR3B-related disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Leukodystrophy, hypomyelinating with or without oligodontia and/or hypogonadotropic hypogonadism Neurodevelopmental disorder with or without seizures, ataxia, spasticity, and demyelinating neuropathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Leukodystrophy, hypomyelinating with or without oligodontia and/or hypogonadotropic hypogonadism Leukodystrophy, hypomyelinating, 8, with or without oligodontia and/or hypogonadotropic hypogonadism 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Leukodystrophy, hypomyelinating, 8, with or without oligodontia and/or hypogonadotropic hypogonadism POLR3B-related disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Leukodystrophy, hypomyelinating, 8, with or without oligodontia and/or hypogonadotropic hypogonadism Neurodevelopmental disorder with or without seizures, ataxia, spasticity, and demyelinating neuropathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurodevelopmental disorder with or without seizures, ataxia, spasticity, and demyelinating neuropathy POLR3B-related disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Leukodystrophy, hypomyelinating with or without oligodontia and/or hypogonadotropic hypogonadism Tremor-ataxia-central hypomyelination syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Leukodystrophy, hypomyelinating, 8, with or without oligodontia and/or hypogonadotropic hypogonadism Tremor-ataxia-central hypomyelination syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neurodevelopmental disorder with or without seizures, ataxia, spasticity, and demyelinating neuropathy Tremor-ataxia-central hypomyelination syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
POLR3B-related disorder Tremor-ataxia-central hypomyelination syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.