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 220

8 diseases · 16 shared-gene connections
8 Diseases
22 Unique genes
0.238 Avg. similarity score
Intestinal pseudo-obstruction Most-connected disease (6 links)
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Disease Searched: Megacystis microcolon intestinal hypoperistalsis syndrome 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 ⇵
Intestinal pseudo-obstruction 6 6 4
Megacystis microcolon intestinal hypoperistalsis syndrome 6 6 7
Microhydranencephaly 5 5 1
microcephaly with lissencephaly and/or hydranencephaly 5 5 1
Visceral neuropathy 4 4 6
Microlissencephaly 2 2 3
Tricuspid valve disease 2 2 10
Visceral myopathy 2 2 5

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

Gene ⇵ Member diseases ⇵ Linked diseases
NDE1 7 / 8 Intestinal pseudo-obstruction, Megacystis microcolon intestinal hypoperistalsis syndrome, microcephaly with lissencephaly and/or hydranencephaly, Microhydranencephaly and 3 more
ACTG2 4 / 8 Intestinal pseudo-obstruction, Megacystis microcolon intestinal hypoperistalsis syndrome, Visceral myopathy, Visceral neuropathy
MYH11 4 / 8 Intestinal pseudo-obstruction, Megacystis microcolon intestinal hypoperistalsis syndrome, Tricuspid valve disease, Visceral myopathy
LMOD1 2 / 8 Megacystis microcolon intestinal hypoperistalsis syndrome, Visceral myopathy
MYL9 2 / 8 Megacystis microcolon intestinal hypoperistalsis syndrome, Visceral myopathy
MYLK 2 / 8 Megacystis microcolon intestinal hypoperistalsis syndrome, Visceral myopathy
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 ⇵
Smooth Muscle Contraction
ACTG2, MYH11, LMOD1, MYL9, MYLK
 Reactome 5 / 34 80.3× 3.40e-9 3.54e-7 ✓ sig.
Vascular smooth muscle contraction
ACTG2, MYH11, MYL9, MYLK, EDN3
 KEGG 5 / 134 20.4× 3.63e-6 1.57e-4 ✓ sig.
RHO GTPases activate PAKs
MYH11, MYL9, MYLK
 Reactome 3 / 23 71.2× 9.23e-6 3.33e-4 ✓ sig.
GRB7 events in ERBB2 signaling
ERBB3, ERBB2
 Reactome 2 / 5 218× 3.19e-5 9.25e-4 ✓ sig.
Tight junction
MYH11, MYL9, GATA4, ERBB2
 KEGG 4 / 170 12.8× 2.32e-4 4.50e-3 ✓ sig.
Downregulation of ERBB2:ERBB3 signaling
ERBB3, ERBB2
 Reactome 2 / 13 84.0× 2.47e-4 4.72e-3 ✓ sig.
ERBB2 Activates PTK6 Signaling
ERBB3, ERBB2
 Reactome 2 / 13 84.0× 2.47e-4 4.72e-3 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
PTPN11, ERBB3, ERBB2
 Reactome 3 / 75 21.8× 3.31e-4 5.99e-3 ✓ sig.
ERBB2 Regulates Cell Motility
ERBB3, ERBB2
 Reactome 2 / 15 72.8× 3.32e-4 6.00e-3 ✓ sig.
TFAP2 (AP-2) family regulates transcription of growth factors and their receptors
TFAP2B, ERBB2
 Reactome 2 / 15 72.8× 3.32e-4 6.00e-3 ✓ sig.
PI3K events in ERBB2 signaling
ERBB3, ERBB2
 Reactome 2 / 16 68.2× 3.78e-4 6.65e-3 ✓ sig.
Motor proteins
ACTG2, MYH11, MYL9, KIF26B
 KEGG 4 / 194 11.3× 3.84e-4 6.74e-3 ✓ sig.
SHC1 events in ERBB2 signaling
ERBB3, ERBB2
 Reactome 2 / 17 64.2× 4.28e-4 7.36e-3 ✓ sig.
Signaling by ERBB2
ERBB3, ERBB2
 Reactome 2 / 18 60.7× 4.81e-4 8.05e-3 ✓ sig.
PIP3 activates AKT signaling
PTPN11, ERBB3, ERBB2
 Reactome 3 / 93 17.6× 6.22e-4 9.79e-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 ⇵
ERBB2-ERBB3 signaling pathway
ERBB3, ERBB2
 GO:0038133 2 / 9 189× 4.74e-5 1.79e-3 ✓ sig.
epidermal growth factor receptor signaling pathway
PTPN11, ERBB3, ERBB2
 GO:0007173 3 / 64 39.8× 5.63e-5 2.03e-3 ✓ sig.
atrioventricular canal development
GATA4, PTPN11
 GO:0036302 2 / 11 154× 7.23e-5 2.46e-3 ✓ sig.
positive regulation of hormone secretion
EDN3, PTPN11
 GO:0046887 2 / 12 142× 8.67e-5 2.82e-3 ✓ sig.
wound healing
GATA4, ERBB3, ERBB2
 GO:0042060 3 / 76 33.5× 9.42e-5 3.00e-3 ✓ sig.
endocardial cushion development
GATA4, ERBB3
 GO:0003197 2 / 13 131× 1.02e-4 3.19e-3 ✓ sig.
myofibril assembly
LMOD1, MYL9
 GO:0030239 2 / 15 113× 1.38e-4 3.96e-3 ✓ sig.
Schwann cell development
ERBB3, ERBB2
 GO:0014044 2 / 20 84.9× 2.48e-4 6.07e-3 ✓ sig.
heart development
GATA4, PTPN11, ERBB3, ERBB2
 GO:0007507 4 / 273 12.4× 2.65e-4 6.36e-3 ✓ sig.
smooth muscle contraction
MYH11, MYLK
 GO:0006939 2 / 24 70.8× 3.59e-4 7.86e-3 ✓ sig.
peripheral nervous system development
ERBB3, ERBB2
 GO:0007422 2 / 26 65.3× 4.23e-4 8.84e-3 ✓ sig.
positive regulation of intracellular signal transduction
PTPN11, ERBB2
 GO:1902533 2 / 43 39.5× 1.16e-3 1.72e-2 ✓ sig.
phthalate metabolic process
SRD5A2
 GO:0018963 1 / 1 849× 1.18e-3 1.72e-2 ✓ sig.
tonic smooth muscle contraction
MYLK
 GO:0014820 1 / 1 849× 1.18e-3 1.72e-2 ✓ sig.
negative regulation of cortisol secretion
PTPN11
 GO:0051463 1 / 1 849× 1.18e-3 1.72e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Megacystis microcolon intestinal hypoperistalsis syndrome Visceral myopathy 0.625 5 2.91e-18 5.08e-17 ✓ sig.
Intestinal pseudo-obstruction Megacystis microcolon intestinal hypoperistalsis syndrome 0.333 3 2.30e-10 2.21e-9 ✓ sig.
Intestinal pseudo-obstruction Visceral myopathy 0.250 2 5.06e-7 3.14e-6 ✓ sig.
Intestinal pseudo-obstruction Visceral neuropathy 0.222 2 7.59e-7 4.54e-6 ✓ sig.
Intestinal pseudo-obstruction Tricuspid valve disease 0.154 2 2.28e-6 1.26e-5 ✓ sig.
Megacystis microcolon intestinal hypoperistalsis syndrome Visceral neuropathy 0.167 2 2.65e-6 1.44e-5 ✓ sig.
Megacystis microcolon intestinal hypoperistalsis syndrome Tricuspid valve disease 0.125 2 7.96e-6 3.99e-5 ✓ sig.
microcephaly with lissencephaly and/or hydranencephaly Microhydranencephaly 0.500 1 6.49e-5 2.33e-4 ✓ sig.
microcephaly with lissencephaly and/or hydranencephaly Microlissencephaly 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Microhydranencephaly Microlissencephaly 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Intestinal pseudo-obstruction Microhydranencephaly 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Intestinal pseudo-obstruction microcephaly with lissencephaly and/or hydranencephaly 0.200 1 2.60e-4 6.51e-4 ✓ sig.
microcephaly with lissencephaly and/or hydranencephaly Visceral neuropathy 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Microhydranencephaly Visceral neuropathy 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Megacystis microcolon intestinal hypoperistalsis syndrome microcephaly with lissencephaly and/or hydranencephaly 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Megacystis microcolon intestinal hypoperistalsis syndrome Microhydranencephaly 0.125 1 4.55e-4 9.73e-4 ✓ sig.