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 47

15 diseases · 47 shared-gene connections
15 Diseases
17 Unique genes
0.331 Avg. similarity score
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Most-connected disease (11 links)
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Disease Searched: obsolete lethal restrictive dermopathy 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 ⇵
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome 11 11 1
Emery dreifuss muscular dystrophy 11 11 1
Severe lipodystrophic laminopathy 11 11 1
Lipoatrophic diabetes mellitus 7 7 1
Mandibuloacral dysostosis 7 7 3
Mandibuloacral dysplasia 7 7 4
Restrictive dermopathy 7 7 2
Malouf syndrome 6 6 1
Emery-dreifuss muscular dystrophy 5 5 7
Werner syndrome 5 5 4
dilated cardiomyopathy 1A 5 5 1
Tight skin contracture syndrome 4 4 1
obsolete lethal restrictive dermopathy 4 4 1
Congenital small ears 3 3 5
arrhythmogenic right ventricular dysplasia 5 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LMNA 12 / 15 Congenital small ears, dilated cardiomyopathy 1A, Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome, Emery dreifuss muscular dystrophy and 8 more
ZMPSTE24 5 / 15 Mandibuloacral dysostosis, Mandibuloacral dysplasia, obsolete lethal restrictive dermopathy, Restrictive dermopathy and 1 more
MTX2 2 / 15 Mandibuloacral dysostosis, Mandibuloacral dysplasia
TMEM43 2 / 15 arrhythmogenic right ventricular dysplasia 5, Emery-dreifuss muscular dystrophy
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 ⇵
Cytoskeleton in muscle cells
LMNA, SYNE1, SYNE2, TMEM43, EMD, FHL1
 KEGG 6 / 232 18.3× 5.05e-7 2.70e-5 ✓ sig.
Nuclear Envelope Breakdown
LMNA, EMD
 Reactome 2 / 9 157× 6.75e-5 1.65e-3 ✓ sig.
Depolymerisation of the Nuclear Lamina
LMNA, EMD
 Reactome 2 / 15 94.2× 1.96e-4 3.89e-3 ✓ sig.
Initiation of Nuclear Envelope (NE) Reformation
LMNA, EMD
 Reactome 2 / 19 74.4× 3.18e-4 5.70e-3 ✓ sig.
Signaling by SCF-KIT
MMP9, PTPN11
 Reactome 2 / 37 38.2× 1.22e-3 1.62e-2 ✓ sig.
Proteoglycans in cancer
ESR1, MMP9, PTPN11
 KEGG 3 / 204 10.4× 2.75e-3 2.95e-2 ✓ sig.
Extra-nuclear estrogen signaling
ESR1, MMP9
 Reactome 2 / 58 24.4× 2.98e-3 3.11e-2 ✓ sig.
Breakdown of the nuclear lamina
LMNA
 Reactome 1 / 3 235× 4.24e-3 3.98e-2 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
ESR1, PTPN11
 Reactome 2 / 75 18.8× 4.93e-3 4.41e-2 ✓ sig.
Arrhythmogenic right ventricular cardiomyopathy
LMNA, EMD
 KEGG 2 / 86 16.4× 6.43e-3 5.28e-2
MET activates PTPN11
PTPN11
 Reactome 1 / 5 141× 7.06e-3 5.61e-2
PIP3 activates AKT signaling
ESR1, PTPN11
 Reactome 2 / 93 15.2× 7.48e-3 5.81e-2
Endocrine resistance
ESR1, MMP9
 KEGG 2 / 99 14.3× 8.44e-3 6.30e-2
Hypertrophic cardiomyopathy
LMNA, EMD
 KEGG 2 / 99 14.3× 8.44e-3 6.30e-2
RUNX1 regulates estrogen receptor mediated transcription
ESR1
 Reactome 1 / 6 118× 8.46e-3 6.31e-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 ⇵
nucleus organization
LMNA, SYNE1, ZMPSTE24
 GO:0006997 3 / 34 97.0× 3.68e-6 2.39e-4 ✓ sig.
nuclear membrane organization
TMEM43, EMD
 GO:0071763 2 / 7 314× 1.63e-5 7.76e-4 ✓ sig.
muscle organ development
LMNA, EMD, FHL1
 GO:0007517 3 / 114 28.9× 1.41e-4 4.00e-3 ✓ sig.
pharyngeal system development
BMP5, HOXA2
 GO:0060037 2 / 21 105× 1.62e-4 4.42e-3 ✓ sig.
nuclear migration
LMNA, SYNE2
 GO:0007097 2 / 22 99.9× 1.78e-4 4.75e-3 ✓ sig.
motor neuron axon guidance
HOXA2, PLXNA3
 GO:0008045 2 / 24 91.6× 2.12e-4 5.37e-3 ✓ sig.
nuclear envelope organization
LMNA, ZMPSTE24
 GO:0006998 2 / 24 91.6× 2.12e-4 5.37e-3 ✓ sig.
cellular response to gamma radiation
ZMPSTE24, WRN
 GO:0071480 2 / 28 78.5× 2.90e-4 6.68e-3 ✓ sig.
determination of adult lifespan
ZMPSTE24, WRN
 GO:0008340 2 / 38 57.9× 5.37e-4 1.02e-2 ✓ sig.
response to estrogen
KMT2D, ESR1
 GO:0043627 2 / 49 44.9× 8.93e-4 1.44e-2 ✓ sig.
beta-catenin-TCF complex assembly
KMT2D
 GO:1904837 1 / 1 1,099× 9.10e-4 1.46e-2 ✓ sig.
negative regulation of cation transmembrane transport
MMP9
 GO:1904063 1 / 1 1,099× 9.10e-4 1.46e-2 ✓ sig.
negative regulation of epithelial cell differentiation involved in kidney development
MMP9
 GO:2000697 1 / 1 1,099× 9.10e-4 1.46e-2 ✓ sig.
negative regulation of cortisol secretion
PTPN11
 GO:0051463 1 / 1 1,099× 9.10e-4 1.46e-2 ✓ sig.
negative regulation of growth hormone secretion
PTPN11
 GO:0060125 1 / 1 1,099× 9.10e-4 1.46e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Mandibuloacral dysostosis Mandibuloacral dysplasia 0.600 3 6.58e-12 7.34e-11 ✓ sig.
Mandibuloacral dysostosis Restrictive dermopathy 0.500 2 2.53e-8 1.93e-7 ✓ sig.
Mandibuloacral dysplasia Restrictive dermopathy 0.400 2 5.06e-8 3.72e-7 ✓ sig.
Lipoatrophic diabetes mellitus Severe lipodystrophic laminopathy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Lipoatrophic diabetes mellitus Malouf syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Malouf syndrome Severe lipodystrophic laminopathy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Emery dreifuss muscular dystrophy Malouf syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Emery dreifuss muscular dystrophy Lipoatrophic diabetes mellitus 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Emery dreifuss muscular dystrophy Severe lipodystrophic laminopathy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Malouf syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Lipoatrophic diabetes mellitus 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Severe lipodystrophic laminopathy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Emery dreifuss muscular dystrophy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
dilated cardiomyopathy 1A Malouf syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
dilated cardiomyopathy 1A Lipoatrophic diabetes mellitus 0.500 1 6.49e-5 2.32e-4 ✓ sig.
dilated cardiomyopathy 1A Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
dilated cardiomyopathy 1A Severe lipodystrophic laminopathy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
dilated cardiomyopathy 1A Emery dreifuss muscular dystrophy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
obsolete lethal restrictive dermopathy Tight skin contracture syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Restrictive dermopathy 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Restrictive dermopathy Tight skin contracture syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Restrictive dermopathy Severe lipodystrophic laminopathy 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Emery dreifuss muscular dystrophy Restrictive dermopathy 0.333 1 1.30e-4 3.91e-4 ✓ sig.
obsolete lethal restrictive dermopathy Restrictive dermopathy 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Mandibuloacral dysostosis Tight skin contracture syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Emery dreifuss muscular dystrophy Mandibuloacral dysostosis 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Mandibuloacral dysostosis Severe lipodystrophic laminopathy 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Mandibuloacral dysostosis 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Mandibuloacral dysostosis obsolete lethal restrictive dermopathy 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Mandibuloacral dysplasia Tight skin contracture syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Malouf syndrome Werner syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Emery dreifuss muscular dystrophy Werner syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Severe lipodystrophic laminopathy Werner syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Werner syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Lipoatrophic diabetes mellitus Werner syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Mandibuloacral dysplasia obsolete lethal restrictive dermopathy 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Mandibuloacral dysplasia 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Mandibuloacral dysplasia Severe lipodystrophic laminopathy 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Emery dreifuss muscular dystrophy Mandibuloacral dysplasia 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Congenital small ears Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome 0.167 1 3.25e-4 7.68e-4 ✓ sig.
Congenital small ears Severe lipodystrophic laminopathy 0.167 1 3.25e-4 7.68e-4 ✓ sig.
Congenital small ears Emery dreifuss muscular dystrophy 0.167 1 3.25e-4 7.68e-4 ✓ sig.
Emery-dreifuss muscular dystrophy Lipoatrophic diabetes mellitus 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Emery-dreifuss muscular dystrophy 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Emery-dreifuss muscular dystrophy Severe lipodystrophic laminopathy 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Emery dreifuss muscular dystrophy Emery-dreifuss muscular dystrophy 0.125 1 4.55e-4 9.70e-4 ✓ sig.
arrhythmogenic right ventricular dysplasia 5 Emery-dreifuss muscular dystrophy 0.125 1 4.55e-4 9.70e-4 ✓ sig.