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 96

13 diseases · 50 shared-gene connections
13 Diseases
10 Unique genes
0.398 Avg. similarity score
Melnick-needles syndrome Most-connected disease (12 links)
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Disease Searched: Intestinal pseudoobstruction, neuronal 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 ⇵
Melnick-needles syndrome 12 12 1
Otopalatodigital spectrum disorder 12 12 1
Terminal osseous dysplasia with pigmentary defects 12 12 1
X-linked ehlers-danlos syndrome 12 12 1
X-linked keloid scarring syndrome 12 12 1
Cardiac valvular dysplasia 5 5 6
Congenital idiopathic intestinal pseudoobstruction 5 5 2
Congenital short bowel syndrome 5 5 2
Fg syndrome 2 5 5 1
Frontometaphyseal dysplasia 5 5 2
Intestinal pseudoobstruction, neuronal 5 5 1
Intestinal pseudoobstruction, neuronal, chronic idiopathic, x-linked 5 5 1
Otopalatodigital syndrome 5 5 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
FLNA 13 / 13 Cardiac valvular dysplasia, Congenital idiopathic intestinal pseudoobstruction, Congenital short bowel syndrome, Fg syndrome 2 and 9 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 ⇵
GP1b-IX-V activation signalling
FLNA, COL1A2
 Reactome 2 / 12 200× 4.10e-5 9.33e-4 ✓ sig.
NF-kappa B signaling pathway
ATM, MAP3K7
 KEGG 2 / 105 22.9× 3.25e-3 2.70e-2 ✓ sig.
L1CAM interactions
L1CAM
 Reactome 1 / 4 300× 3.33e-3 2.74e-2 ✓ sig.
Sensing of DNA Double Strand Breaks
ATM
 Reactome 1 / 6 200× 4.99e-3 3.64e-2 ✓ sig.
Platelet Aggregation (Plug Formation)
COL1A2
 Reactome 1 / 8 150× 6.64e-3 4.39e-2 ✓ sig.
OAS antiviral response
FLNA
 Reactome 1 / 9 133× 7.47e-3 4.73e-2 ✓ sig.
IRAK2 mediated activation of TAK1 complex
MAP3K7
 Reactome 1 / 10 120× 8.30e-3 5.06e-2
Pexophagy
ATM
 Reactome 1 / 10 120× 8.30e-3 5.06e-2
Stabilization of p53
ATM
 Reactome 1 / 11 109× 9.12e-3 5.37e-2
TICAM1,TRAF6-dependent induction of TAK1 complex
MAP3K7
 Reactome 1 / 11 109× 9.12e-3 5.37e-2
Alpha-protein kinase 1 signaling pathway
MAP3K7
 Reactome 1 / 11 109× 9.12e-3 5.37e-2
Platelet Adhesion to exposed collagen
COL1A2
 Reactome 1 / 11 109× 9.12e-3 5.37e-2
Cell-extracellular matrix interactions
FLNA
 Reactome 1 / 12 100× 9.95e-3 5.67e-2
TP53 Regulates Transcription of Caspase Activators and Caspases
ATM
 Reactome 1 / 12 100× 9.95e-3 5.67e-2
Interaction between L1 and Ankyrins
L1CAM
 Reactome 1 / 13 92.4× 1.08e-2 5.96e-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 ⇵
signal transduction in response to DNA damage
ATM, MAP3K7
 GO:0042770 2 / 21 178× 5.38e-5 1.95e-3 ✓ sig.
mitotic spindle assembly
FLNA, OFD1
 GO:0090307 2 / 46 81.2× 2.63e-4 6.19e-3 ✓ sig.
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
ATM, MAP3K7
 GO:0031146 2 / 61 61.3× 4.64e-4 9.05e-3 ✓ sig.
collagen fibril organization
ADAMTS19, COL1A2
 GO:0030199 2 / 65 57.5× 5.27e-4 9.87e-3 ✓ sig.
regulation of membrane repolarization during atrial cardiac muscle cell action potential
FLNA
 GO:1905000 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
regulation of membrane repolarization during cardiac muscle cell action potential
FLNA
 GO:1905031 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
protein heterotrimerization
COL1A2
 GO:0070208 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
10-formyltetrahydrofolate biosynthetic process
MTHFD1
 GO:0009257 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
establishment of RNA localization to telomere
ATM
 GO:0097694 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
establishment of protein-containing complex localization to telomere
ATM
 GO:0097695 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
positive regulation of telomerase catalytic core complex assembly
ATM
 GO:1904884 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
purine ribonucleotide biosynthetic process
MTHFD1
 GO:0009152 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation
OFD1
 GO:2000314 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
transforming growth factor beta receptor signaling pathway
COL1A2, MAP3K7
 GO:0007179 2 / 112 33.4× 1.55e-3 1.87e-2 ✓ sig.
cellular response to nitrosative stress
ATM
 GO:0071500 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Melnick-needles syndrome Otopalatodigital spectrum disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal Terminal osseous dysplasia with pigmentary defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal X-linked ehlers-danlos syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal X-linked keloid scarring syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal Melnick-needles syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal, chronic idiopathic, x-linked Otopalatodigital spectrum disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal, chronic idiopathic, x-linked Terminal osseous dysplasia with pigmentary defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal, chronic idiopathic, x-linked X-linked ehlers-danlos syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal, chronic idiopathic, x-linked X-linked keloid scarring syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal, chronic idiopathic, x-linked Melnick-needles syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intestinal pseudoobstruction, neuronal Otopalatodigital spectrum disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melnick-needles syndrome Terminal osseous dysplasia with pigmentary defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melnick-needles syndrome X-linked ehlers-danlos syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melnick-needles syndrome X-linked keloid scarring syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Otopalatodigital spectrum disorder Terminal osseous dysplasia with pigmentary defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Otopalatodigital spectrum disorder X-linked ehlers-danlos syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Otopalatodigital spectrum disorder X-linked keloid scarring syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Terminal osseous dysplasia with pigmentary defects X-linked ehlers-danlos syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Terminal osseous dysplasia with pigmentary defects X-linked keloid scarring syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
X-linked ehlers-danlos syndrome X-linked keloid scarring syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fg syndrome 2 Melnick-needles syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fg syndrome 2 X-linked keloid scarring syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fg syndrome 2 X-linked ehlers-danlos syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fg syndrome 2 Terminal osseous dysplasia with pigmentary defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fg syndrome 2 Otopalatodigital spectrum disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Frontometaphyseal dysplasia Terminal osseous dysplasia with pigmentary defects 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Melnick-needles syndrome Otopalatodigital syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Otopalatodigital syndrome X-linked keloid scarring syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Otopalatodigital syndrome X-linked ehlers-danlos syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Otopalatodigital syndrome Terminal osseous dysplasia with pigmentary defects 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Otopalatodigital spectrum disorder Otopalatodigital syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Otopalatodigital spectrum disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Terminal osseous dysplasia with pigmentary defects 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction X-linked ehlers-danlos syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction X-linked keloid scarring syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Melnick-needles syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital short bowel syndrome Otopalatodigital spectrum disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital short bowel syndrome Terminal osseous dysplasia with pigmentary defects 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital short bowel syndrome X-linked ehlers-danlos syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital short bowel syndrome X-linked keloid scarring syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital short bowel syndrome Melnick-needles syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Frontometaphyseal dysplasia Melnick-needles syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Frontometaphyseal dysplasia X-linked keloid scarring syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Frontometaphyseal dysplasia X-linked ehlers-danlos syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Frontometaphyseal dysplasia Otopalatodigital spectrum disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cardiac valvular dysplasia Melnick-needles syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cardiac valvular dysplasia Otopalatodigital spectrum disorder 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cardiac valvular dysplasia X-linked keloid scarring syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cardiac valvular dysplasia X-linked ehlers-danlos syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cardiac valvular dysplasia Terminal osseous dysplasia with pigmentary defects 0.143 1 3.87e-4 7.33e-4 ✓ sig.