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 186

8 diseases · 12 shared-gene connections
8 Diseases
24 Unique genes
0.189 Avg. similarity score
Kleins syndrome Most-connected disease (6 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 ⇵
Kleins syndrome 6 6 5
Waardenburg-shah syndrome 4 4 4
Central precocious puberty 3 3 11
Craniofacial deafness hand syndrome 3 3 1
Waardenburg syndrome 3 3 13
Waardenburg syndrome type 2 2 2 1
Waardenburg syndrome type 4B 2 2 1
Temple syndrome 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
EDN3 4 / 8 Kleins syndrome, Waardenburg syndrome, Waardenburg syndrome type 4B, Waardenburg-shah syndrome
MITF 4 / 8 Kleins syndrome, Waardenburg syndrome, Waardenburg syndrome type 2, Waardenburg-shah syndrome
PAX3 4 / 8 Central precocious puberty, Craniofacial deafness hand syndrome, Kleins syndrome, Waardenburg syndrome
EDNRB 3 / 8 Kleins syndrome, Waardenburg syndrome, Waardenburg-shah syndrome
DLK1 2 / 8 Central precocious puberty, Temple syndrome
KITLG 2 / 8 Kleins syndrome, Waardenburg syndrome
SOX10 2 / 8 Waardenburg syndrome, Waardenburg-shah syndrome
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 ⇵
Melanogenesis
EDNRB, KITLG, MITF, TYR
 KEGG 4 / 101 19.8× 4.40e-5 1.15e-3 ✓ sig.
Peptide ligand-binding receptors
KISS1R, EDN3, EDNRB
 Reactome 3 / 106 14.2× 1.18e-3 1.54e-2 ✓ sig.
RNA Polymerase III Transcription Initiation From Type 2 Promoter
BDP1, POLR2F
 Reactome 2 / 27 37.1× 1.30e-3 1.65e-2 ✓ sig.
RNA Polymerase III Transcription Initiation From Type 3 Promoter
BDP1, POLR2F
 Reactome 2 / 28 35.7× 1.40e-3 1.75e-2 ✓ sig.
RNA Polymerase III Transcription Initiation From Type 1 Promoter
BDP1, POLR2F
 Reactome 2 / 28 35.7× 1.40e-3 1.75e-2 ✓ sig.
Pathways in cancer
ESR1, IL23R, EDNRB, KITLG, MITF
 KEGG 5 / 533 4.7× 3.56e-3 3.47e-2 ✓ sig.
G alpha (q) signalling events
KISS1R, EDN3, EDNRB
 Reactome 3 / 172 8.7× 4.68e-3 4.20e-2 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
ESR1, KITLG
 Reactome 2 / 75 13.3× 9.72e-3 6.74e-2
Melanin biosynthesis
TYR
 Reactome 1 / 5 100× 9.95e-3 6.82e-2
RUNX1 regulates estrogen receptor mediated transcription
ESR1
 Reactome 1 / 6 83.4× 1.19e-2 7.61e-2
RUNX1 regulates transcription of genes involved in WNT signaling
ESR1
 Reactome 1 / 6 83.4× 1.19e-2 7.61e-2
PIP3 activates AKT signaling
ESR1, KITLG
 Reactome 2 / 93 10.8× 1.47e-2 8.59e-2
Netrin-1 signaling
PRKCQ
 Reactome 1 / 8 62.6× 1.59e-2 9.02e-2
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
ESR1, KITLG
 Reactome 2 / 103 9.7× 1.78e-2 9.66e-2
Interleukin-23 signaling
IL23R
 Reactome 1 / 9 55.6× 1.78e-2 9.67e-2

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
melanocyte differentiation
EDN3, EDNRB, MITF, SOX10
 GO:0030318 4 / 21 148× 1.23e-8 2.05e-6 ✓ sig.
pigmentation
EDNRB, MITF, SNAI2, TYR
 GO:0043473 4 / 39 79.9× 1.67e-7 1.86e-5 ✓ sig.
neural crest cell migration
EDN3, EDNRB, KITLG, SOX10
 GO:0001755 4 / 47 66.3× 3.60e-7 3.54e-5 ✓ sig.
vein smooth muscle contraction
EDN3, EDNRB
 GO:0014826 2 / 4 389× 9.47e-6 5.01e-4 ✓ sig.
sensory perception of sound
PAX3, MYO6, SNAI2, TMPRSS3
 GO:0007605 4 / 162 19.2× 5.05e-5 1.81e-3 ✓ sig.
enteric nervous system development
EDNRB, SOX10
 GO:0048484 2 / 12 130× 1.04e-4 3.10e-3 ✓ sig.
positive regulation of hormone secretion
KISS1R, EDN3
 GO:0046887 2 / 12 130× 1.04e-4 3.10e-3 ✓ sig.
positive regulation of T-helper 17 type immune response
IL23R, PRKCQ
 GO:2000318 2 / 13 120× 1.22e-4 3.51e-3 ✓ sig.
vasoconstriction
EDN3, EDNRB
 GO:0042310 2 / 18 86.5× 2.39e-4 5.73e-3 ✓ sig.
negative regulation of apoptotic process
PRKCQ, EDNRB, KITLG, MITF, SOX10
 GO:0043066 5 / 524 7.4× 4.65e-4 9.11e-3 ✓ sig.
peripheral nervous system development
EDNRB, SOX10
 GO:0007422 2 / 26 59.9× 5.04e-4 9.63e-3 ✓ sig.
positive regulation of interleukin-17 production
IL23R, PRKCQ
 GO:0032740 2 / 27 57.7× 5.44e-4 1.01e-2 ✓ sig.
enteric smooth muscle cell differentiation
EDNRB
 GO:0035645 1 / 1 779× 1.28e-3 1.75e-2 ✓ sig.
response to endothelin
EDNRB
 GO:1990839 1 / 1 779× 1.28e-3 1.75e-2 ✓ sig.
positive regulation of T-helper 2 cell activation
PRKCQ
 GO:2000570 1 / 1 779× 1.28e-3 1.75e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Kleins syndrome Waardenburg syndrome 0.357 5 1.79e-16 2.98e-15 ✓ sig.
Waardenburg syndrome Waardenburg-shah syndrome 0.286 4 3.05e-13 4.09e-12 ✓ sig.
Kleins syndrome Waardenburg-shah syndrome 0.429 3 6.57e-11 7.05e-10 ✓ sig.
Waardenburg syndrome type 2 Waardenburg-shah syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Waardenburg syndrome type 4B Waardenburg-shah syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Craniofacial deafness hand syndrome Kleins syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Kleins syndrome Waardenburg syndrome type 2 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Kleins syndrome Waardenburg syndrome type 4B 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Central precocious puberty Craniofacial deafness hand syndrome 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Craniofacial deafness hand syndrome Waardenburg syndrome 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Central precocious puberty Temple syndrome 0.077 1 1.43e-3 2.21e-3 ✓ sig.
Central precocious puberty Kleins syndrome 0.063 1 3.57e-3 4.59e-3 ✓ sig.