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Cluster 543

5 diseases · 7 shared-gene connections

5 Diseases

21 Unique genes

0.107 Avg. similarity score

Distal muscular dystrophy 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.

Distal muscular dystrophy Distal myopathy Distal axonal motor neuropathy-myofibrillar myopathy syndrome Distal myopathy with vocal cord weakness Inclusion body myopathy with early-onset paget disease with or without frontotemporal dementia 3

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Distal muscular dystrophy	4	4	7
Distal myopathy	4	4	19
Distal axonal motor neuropathy-myofibrillar myopathy syndrome	2	2	1
Distal myopathy with vocal cord weakness	2	2	1
Inclusion body myopathy with early-onset paget disease with or without frontotemporal dementia 3	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
HNRNPA1	3 / 5	Distal muscular dystrophy, Distal myopathy, Inclusion body myopathy with early-onset paget disease with or without frontotemporal dementia 3
HSPB8	3 / 5	Distal axonal motor neuropathy-myofibrillar myopathy syndrome, Distal muscular dystrophy, Distal myopathy
MATR3	3 / 5	Distal muscular dystrophy, Distal myopathy, Distal myopathy with vocal cord weakness
MYH7	2 / 5	Distal muscular dystrophy, Distal myopathy
TTN	2 / 5	Distal muscular dystrophy, Distal 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 ⇵
Cytoskeleton in muscle cells LDB3, MYH7, TTN, FLNC, SPTAN1, NEB	KEGG	6 / 232	14.8×	2.07e-6	7.79e-5 ✓ sig.
Hypertrophic cardiomyopathy MYH7, TTN, CAV3	KEGG	3 / 99	17.3×	6.49e-4	8.17e-3 ✓ sig.
Dilated cardiomyopathy MYH7, TTN, CAV3	KEGG	3 / 105	16.3×	7.70e-4	9.29e-3 ✓ sig.
FGFR2 alternative splicing HNRNPA1, TIA1	Reactome	2 / 26	44.0×	9.23e-4	1.07e-2 ✓ sig.
Smooth Muscle Contraction DYSF, CAV3	Reactome	2 / 34	33.6×	1.58e-3	1.60e-2 ✓ sig.
Defective GNE causes sialuria, Nonaka myopathy and inclusion body myopathy 2 GNE	Reactome	1 / 1	572×	1.75e-3	1.73e-2 ✓ sig.
Striated Muscle Contraction TTN, NEB	Reactome	2 / 36	31.8×	1.77e-3	1.74e-2 ✓ sig.
Amyotrophic lateral sclerosis VCP, HNRNPA1, MATR3, SQSTM1	KEGG	4 / 368	6.2×	3.43e-3	2.80e-2 ✓ sig.
Viral myocarditis MYH7, CAV3	KEGG	2 / 70	16.3×	6.55e-3	4.35e-2 ✓ sig.
Mitophagy - animal VCP, SQSTM1	KEGG	2 / 105	10.9×	1.43e-2	7.05e-2
Pexophagy SQSTM1	Reactome	1 / 10	57.2×	1.74e-2	7.88e-2
HSF1 activation VCP	Reactome	1 / 12	47.7×	2.08e-2	8.77e-2
Purine ribonucleoside monophosphate biosynthesis ADSS1	Reactome	1 / 12	47.7×	2.08e-2	8.77e-2
Cell-extracellular matrix interactions FLNC	Reactome	1 / 12	47.7×	2.08e-2	8.77e-2
Caspase-mediated cleavage of cytoskeletal proteins SPTAN1	Reactome	1 / 12	47.7×	2.08e-2	8.77e-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 ⇵
sarcomere organization LDB3, TTN, FLNC	GO:0045214	3 / 43	62.1×	1.47e-5	7.31e-4 ✓ sig.
detection of muscle stretch TTN, CAV3	GO:0035995	2 / 7	254×	2.52e-5	1.10e-3 ✓ sig.
visual perception BEST1, IMPG1, IMPG2, PRPH2	GO:0007601	4 / 215	16.6×	8.75e-5	2.80e-3 ✓ sig.
cardiac muscle hypertrophy TTN, CAV3	GO:0003300	2 / 13	137×	9.31e-5	2.93e-3 ✓ sig.
muscle filament sliding MYH7, TTN	GO:0030049	2 / 15	119×	1.25e-4	3.63e-3 ✓ sig.
detection of light stimulus involved in visual perception BEST1, PRPH2	GO:0050908	2 / 24	74.2×	3.27e-4	7.13e-3 ✓ sig.
striated muscle contraction MYH7, TTN	GO:0006941	2 / 24	74.2×	3.27e-4	7.13e-3 ✓ sig.
cardiac muscle cell development TTN, CAV3	GO:0055013	2 / 25	71.2×	3.55e-4	7.57e-3 ✓ sig.
regulation of calcium ion transport BEST1, CAV3	GO:0051924	2 / 25	71.2×	3.55e-4	7.57e-3 ✓ sig.
positive regulation of ubiquitin-dependent protein catabolic process VCP, CAV3	GO:2000060	2 / 30	59.3×	5.13e-4	9.67e-3 ✓ sig.
skeletal muscle contraction MYH7, TTN	GO:0003009	2 / 32	55.6×	5.85e-4	1.06e-2 ✓ sig.
ATP metabolic process VCP, MYH7	GO:0046034	2 / 36	49.4×	7.41e-4	1.23e-2 ✓ sig.
regulation of heart rate MYH7, CAV3	GO:0002027	2 / 39	45.6×	8.69e-4	1.34e-2 ✓ sig.
cardiac muscle contraction MYH7, TTN	GO:0060048	2 / 43	41.4×	1.06e-3	1.51e-2 ✓ sig.
response to low light intensity stimulus PRPH2	GO:0009645	1 / 1	890×	1.12e-3	1.55e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Distal muscular dystrophy	Distal myopathy	0.227	5	3.29e-14	3.83e-13 ✓ sig.
Distal axonal motor neuropathy-myofibrillar myopathy syndrome	Distal muscular dystrophy	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Distal muscular dystrophy	Distal myopathy with vocal cord weakness	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Distal muscular dystrophy	Inclusion body myopathy with early-onset paget disease with or without frontotemporal dementia 3	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Distal axonal motor neuropathy-myofibrillar myopathy syndrome	Distal myopathy	0.050	1	1.23e-3	1.81e-3 ✓ sig.
Distal myopathy	Distal myopathy with vocal cord weakness	0.050	1	1.23e-3	1.81e-3 ✓ sig.
Distal myopathy	Inclusion body myopathy with early-onset paget disease with or without frontotemporal dementia 3	0.050	1	1.23e-3	1.81e-3 ✓ sig.

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