Disease Clusters | GeDiPNet

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Cluster 426

5 diseases · 7 shared-gene connections

5 Diseases

20 Unique genes

0.268 Avg. similarity score

Intestinal pseudo-obstruction Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

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.

Intestinal pseudo-obstruction Megacystis microcolon intestinal hypoperistalsis syndrome Tricuspid valve disease Visceral myopathy Visceral neuropathy

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Intestinal pseudo-obstruction	4	4	4
Megacystis microcolon intestinal hypoperistalsis syndrome	4	4	7
Tricuspid valve disease	2	2	10
Visceral myopathy	2	2	5
Visceral neuropathy	2	2	6

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

Gene ⇵	Member diseases ⇵	Linked diseases
ACTG2	4 / 5	Intestinal pseudo-obstruction, Megacystis microcolon intestinal hypoperistalsis syndrome, Visceral myopathy, Visceral neuropathy
MYH11	4 / 5	Intestinal pseudo-obstruction, Megacystis microcolon intestinal hypoperistalsis syndrome, Tricuspid valve disease, Visceral myopathy
NDE1	4 / 5	Intestinal pseudo-obstruction, Megacystis microcolon intestinal hypoperistalsis syndrome, Tricuspid valve disease, Visceral neuropathy
LMOD1	2 / 5	Megacystis microcolon intestinal hypoperistalsis syndrome, Visceral myopathy
MYL9	2 / 5	Megacystis microcolon intestinal hypoperistalsis syndrome, Visceral myopathy
MYLK	2 / 5	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	88.3×	2.01e-9	2.06e-7 ✓ sig.
Vascular smooth muscle contraction ACTG2, MYH11, MYL9, MYLK, EDN3	KEGG	5 / 134	22.4×	2.17e-6	9.44e-5 ✓ sig.
RHO GTPases activate PAKs MYH11, MYL9, MYLK	Reactome	3 / 23	78.3×	6.85e-6	2.45e-4 ✓ sig.
GRB7 events in ERBB2 signaling ERBB3, ERBB2	Reactome	2 / 5	240×	2.63e-5	7.47e-4 ✓ sig.
Tight junction MYH11, MYL9, GATA4, ERBB2	KEGG	4 / 170	14.1×	1.57e-4	3.23e-3 ✓ sig.
Downregulation of ERBB2:ERBB3 signaling ERBB3, ERBB2	Reactome	2 / 13	92.4×	2.03e-4	3.95e-3 ✓ sig.
ERBB2 Activates PTK6 Signaling ERBB3, ERBB2	Reactome	2 / 13	92.4×	2.03e-4	3.95e-3 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer PTPN11, ERBB3, ERBB2	Reactome	3 / 75	24.0×	2.47e-4	4.60e-3 ✓ sig.
Motor proteins ACTG2, MYH11, MYL9, KIF26B	KEGG	4 / 194	12.4×	2.61e-4	4.81e-3 ✓ sig.
ERBB2 Regulates Cell Motility ERBB3, ERBB2	Reactome	2 / 15	80.1×	2.73e-4	4.98e-3 ✓ sig.
TFAP2 (AP-2) family regulates transcription of growth factors and their receptors TFAP2B, ERBB2	Reactome	2 / 15	80.1×	2.73e-4	4.98e-3 ✓ sig.
PI3K events in ERBB2 signaling ERBB3, ERBB2	Reactome	2 / 16	75.1×	3.12e-4	5.53e-3 ✓ sig.
SHC1 events in ERBB2 signaling ERBB3, ERBB2	Reactome	2 / 17	70.6×	3.53e-4	6.09e-3 ✓ sig.
Signaling by ERBB2 ERBB3, ERBB2	Reactome	2 / 18	66.7×	3.97e-4	6.66e-3 ✓ sig.
PIP3 activates AKT signaling PTPN11, ERBB3, ERBB2	Reactome	3 / 93	19.4×	4.66e-4	7.55e-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	208×	3.90e-5	1.49e-3 ✓ sig.
epidermal growth factor receptor signaling pathway PTPN11, ERBB3, ERBB2	GO:0007173	3 / 64	43.8×	4.19e-5	1.58e-3 ✓ sig.
atrioventricular canal development GATA4, PTPN11	GO:0036302	2 / 11	170×	5.95e-5	2.04e-3 ✓ sig.
wound healing GATA4, ERBB3, ERBB2	GO:0042060	3 / 76	36.9×	7.01e-5	2.32e-3 ✓ sig.
positive regulation of hormone secretion EDN3, PTPN11	GO:0046887	2 / 12	156×	7.14e-5	2.35e-3 ✓ sig.
endocardial cushion development GATA4, ERBB3	GO:0003197	2 / 13	144×	8.43e-5	2.66e-3 ✓ sig.
myofibril assembly LMOD1, MYL9	GO:0030239	2 / 15	125×	1.13e-4	3.32e-3 ✓ sig.
heart development GATA4, PTPN11, ERBB3, ERBB2	GO:0007507	4 / 273	13.7×	1.80e-4	4.68e-3 ✓ sig.
Schwann cell development ERBB3, ERBB2	GO:0014044	2 / 20	93.4×	2.04e-4	5.12e-3 ✓ sig.
smooth muscle contraction MYH11, MYLK	GO:0006939	2 / 24	77.9×	2.96e-4	6.65e-3 ✓ sig.
peripheral nervous system development ERBB3, ERBB2	GO:0007422	2 / 26	71.9×	3.48e-4	7.43e-3 ✓ sig.
positive regulation of intracellular signal transduction PTPN11, ERBB2	GO:1902533	2 / 43	43.5×	9.57e-4	1.47e-2 ✓ sig.
phthalate metabolic process SRD5A2	GO:0018963	1 / 1	934×	1.07e-3	1.57e-2 ✓ sig.
tonic smooth muscle contraction MYLK	GO:0014820	1 / 1	934×	1.07e-3	1.57e-2 ✓ sig.
negative regulation of cortisol secretion PTPN11	GO:0051463	1 / 1	934×	1.07e-3	1.57e-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	5.37e-17 ✓ sig.
Intestinal pseudo-obstruction	Megacystis microcolon intestinal hypoperistalsis syndrome	0.333	3	2.30e-10	2.34e-9 ✓ sig.
Intestinal pseudo-obstruction	Visceral myopathy	0.250	2	5.06e-7	3.32e-6 ✓ sig.
Intestinal pseudo-obstruction	Visceral neuropathy	0.222	2	7.59e-7	4.79e-6 ✓ sig.
Intestinal pseudo-obstruction	Tricuspid valve disease	0.154	2	2.28e-6	1.33e-5 ✓ sig.
Megacystis microcolon intestinal hypoperistalsis syndrome	Visceral neuropathy	0.167	2	2.65e-6	1.53e-5 ✓ sig.
Megacystis microcolon intestinal hypoperistalsis syndrome	Tricuspid valve disease	0.125	2	7.96e-6	4.23e-5 ✓ sig.

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