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 123

10 diseases · 19 shared-gene connections
10 Diseases
56 Unique genes
0.172 Avg. similarity score
Benign congenital myopathy Most-connected disease (6 links)
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Disease Searched: progressive muscular dystrophy 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 ⇵
Benign congenital myopathy 6 6 1
Dystrophinopathy 6 6 1
Leiomyosarcoma 6 6 7
progressive muscular dystrophy 6 6 1
Becker muscular dystrophy 4 4 3
Clinodactyly 4 4 18
Duchenne muscular dystrophy 3 3 29
Pseudo-torch syndrome 1 1 3
hereditary leiomyomatosis and renal cell cancer 1 1 1
thrombocytopenia-absent radius syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
DMD 7 / 10 Becker muscular dystrophy, Benign congenital myopathy, Clinodactyly, Duchenne muscular dystrophy and 3 more
FH 2 / 10 hereditary leiomyomatosis and renal cell cancer, Leiomyosarcoma
RBM8A 2 / 10 Clinodactyly, thrombocytopenia-absent radius syndrome
USP18 2 / 10 Leiomyosarcoma, Pseudo-torch 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 ⇵
Dilated cardiomyopathy
DMD, SNTA1, ADCY1, ADCY8, SLC8A1
 KEGG 5 / 105 10.2× 1.24e-4 2.70e-3 ✓ sig.
Regulation of IFNA signaling
PTPN1, USP18, STAT2
 Reactome 3 / 24 26.8× 1.81e-4 3.66e-3 ✓ sig.
Arrhythmogenic right ventricular cardiomyopathy
DMD, PKP2, SNTA1, SLC8A1
 KEGG 4 / 86 10.0× 6.78e-4 1.03e-2 ✓ sig.
WNT mediated activation of DVL
DVL3, CSNK2B
 Reactome 2 / 9 47.7× 7.53e-4 1.12e-2 ✓ sig.
Adenylate cyclase activating pathway
ADCY1, ADCY8
 Reactome 2 / 10 42.9× 9.38e-4 1.33e-2 ✓ sig.
Ovarian steroidogenesis
ADCY1, ADCY8, PTGS2
 KEGG 3 / 52 12.4× 1.81e-3 2.16e-2 ✓ sig.
Adenylate cyclase inhibitory pathway
ADCY1, ADCY8
 Reactome 2 / 14 30.6× 1.87e-3 2.22e-2 ✓ sig.
Hedgehog 'off' state
DYNC2H1, ADCY1, ADCY8
 Reactome 3 / 56 11.5× 2.23e-3 2.53e-2 ✓ sig.
Regulation of lipolysis in adipocytes
ADCY1, ADCY8, PTGS2
 KEGG 3 / 59 10.9× 2.59e-3 2.83e-2 ✓ sig.
PKA activation in glucagon signalling
ADCY1, ADCY8
 Reactome 2 / 17 25.2× 2.78e-3 2.97e-2 ✓ sig.
PKA activation
ADCY1, ADCY8
 Reactome 2 / 19 22.6× 3.47e-3 3.46e-2 ✓ sig.
Long-term potentiation
RPS6KA3, ADCY1, ADCY8
 KEGG 3 / 67 9.6× 3.72e-3 3.64e-2 ✓ sig.
SUMOylation of chromatin organization proteins
SATB2, NUP93, SATB1
 Reactome 3 / 70 9.2× 4.21e-3 3.96e-2 ✓ sig.
PTEN Loss of Function in Cancer
PTEN
 Reactome 1 / 1 214× 4.66e-3 4.24e-2 ✓ sig.
Biosynthesis of EPA-derived SPMs
PTGS2
 Reactome 1 / 1 214× 4.66e-3 4.24e-2 ✓ 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 ⇵
maintenance of blood-brain barrier
DMD, JAM2, OCLN
 GO:0035633 3 / 34 29.4× 1.43e-4 4.03e-3 ✓ sig.
regulation of heart rate
DMD, SNTA1, SLC8A1
 GO:0002027 3 / 39 25.7× 2.16e-4 5.43e-3 ✓ sig.
positive regulation of CREB transcription factor activity
ADCY1, ADCY8
 GO:0032793 2 / 10 66.7× 3.91e-4 8.28e-3 ✓ sig.
cAMP biosynthetic process
ADCY1, ADCY8
 GO:0006171 2 / 11 60.7× 4.77e-4 9.48e-3 ✓ sig.
intracellular signal transduction
RPS6KA3, DVL3, ADCY1, ADCY8, DGKB, RGS6, HMGA1
 GO:0035556 7 / 471 5.0× 4.93e-4 9.65e-3 ✓ sig.
regulation of cell differentiation
TFAP2B, UNCX, PTEN
 GO:0045595 3 / 54 18.5× 5.67e-4 1.06e-2 ✓ sig.
neuroinflammatory response
ADCY1, ADCY8
 GO:0150076 2 / 12 55.6× 5.71e-4 1.07e-2 ✓ sig.
cell communication by electrical coupling involved in cardiac conduction
PKP2, SLC8A1
 GO:0086064 2 / 12 55.6× 5.71e-4 1.07e-2 ✓ sig.
positive regulation of receptor recycling
RAMP3, SNCA
 GO:0001921 2 / 14 47.7× 7.84e-4 1.32e-2 ✓ sig.
cellular response to forskolin
ADCY1, ADCY8
 GO:1904322 2 / 16 41.7× 1.03e-3 1.57e-2 ✓ sig.
regulation of sodium ion transmembrane transport
DMD, SNTA1
 GO:1902305 2 / 16 41.7× 1.03e-3 1.57e-2 ✓ sig.
ventricular cardiac muscle cell action potential
PKP2, SNTA1
 GO:0086005 2 / 17 39.3× 1.17e-3 1.70e-2 ✓ sig.
cyclic nucleotide biosynthetic process
ADCY1, ADCY8
 GO:0009190 2 / 18 37.1× 1.31e-3 1.81e-2 ✓ sig.
positive regulation of synaptic transmission
CLSTN2, SNCA
 GO:0050806 2 / 18 37.1× 1.31e-3 1.81e-2 ✓ sig.
cellular response to glucose stimulus
SLC12A6, ZBTB20, ADCY8
 GO:0071333 3 / 74 13.5× 1.42e-3 1.90e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Benign congenital myopathy Dystrophinopathy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Benign congenital myopathy progressive muscular dystrophy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Dystrophinopathy progressive muscular dystrophy 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Becker muscular dystrophy Dystrophinopathy 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Becker muscular dystrophy progressive muscular dystrophy 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Becker muscular dystrophy Benign congenital myopathy 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Benign congenital myopathy Leiomyosarcoma 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Leiomyosarcoma progressive muscular dystrophy 0.125 1 4.55e-4 9.70e-4 ✓ sig.
hereditary leiomyomatosis and renal cell cancer Leiomyosarcoma 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Dystrophinopathy Leiomyosarcoma 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Clinodactyly thrombocytopenia-absent radius syndrome 0.053 1 1.17e-3 1.89e-3 ✓ sig.
Clinodactyly progressive muscular dystrophy 0.053 1 1.17e-3 1.89e-3 ✓ sig.
Clinodactyly Dystrophinopathy 0.053 1 1.17e-3 1.89e-3 ✓ sig.
Benign congenital myopathy Clinodactyly 0.053 1 1.17e-3 1.89e-3 ✓ sig.
Leiomyosarcoma Pseudo-torch syndrome 0.100 1 1.36e-3 2.15e-3 ✓ sig.
Becker muscular dystrophy Leiomyosarcoma 0.100 1 1.36e-3 2.15e-3 ✓ sig.
Duchenne muscular dystrophy progressive muscular dystrophy 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Duchenne muscular dystrophy Dystrophinopathy 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Benign congenital myopathy Duchenne muscular dystrophy 0.033 1 1.88e-3 2.76e-3 ✓ sig.