Disease Clusters | GeDiPNet

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Cluster 218

8 diseases · 25 shared-gene connections

8 Diseases

6 Unique genes

0.390 Avg. similarity score

Brachyrachia Most-connected disease (7 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.

Brachyrachia Congenital benign spinal muscular atrophy Digital arthropathy-brachydactyly, familial Parastremmatic dwarfism Scapuloperoneal spinal muscular atrophy Brachyolmia

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Brachyrachia	7	7	1
Congenital benign spinal muscular atrophy	7	7	1
Digital arthropathy-brachydactyly, familial	7	7	1
Parastremmatic dwarfism	7	7	1
Scapuloperoneal spinal muscular atrophy	7	7	1
Brachyolmia	5	5	3
TRPV4-related bone disorder	5	5	1
Urination disorders	5	5	4

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

Gene ⇵	Member diseases ⇵	Linked diseases
TRPV4	8 / 8	Brachyolmia, Brachyrachia, Congenital benign spinal muscular atrophy, Digital arthropathy-brachydactyly, familial and 4 more

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 ⇵
Vitamin E TTPA	Reactome	1 / 1	2,002×	5.00e-4	7.96e-3 ✓ sig.
Defective PAPSS2 causes SEMD-PA PAPSS2	Reactome	1 / 1	2,002×	5.00e-4	7.96e-3 ✓ sig.
Sulfur cycle PAPSS2	KEGG	1 / 2	1,001×	9.99e-4	1.35e-2 ✓ sig.
Nitric oxide stimulates guanylate cyclase NOS1	Reactome	1 / 3	667×	1.50e-3	1.85e-2 ✓ sig.
Transport and synthesis of PAPS PAPSS2	Reactome	1 / 6	334×	2.99e-3	3.07e-2 ✓ sig.
Hormone signaling NOS1, NPPA	KEGG	2 / 219	18.3×	4.73e-3	4.23e-2 ✓ sig.
Sulfur metabolism PAPSS2	KEGG	1 / 10	200×	4.99e-3	4.37e-2 ✓ sig.
Physiological factors NPPA	Reactome	1 / 12	167×	5.98e-3	4.92e-2 ✓ sig.
YAP1- and WWTR1 (TAZ)-stimulated gene expression NPPA	Reactome	1 / 14	143×	6.98e-3	5.45e-2
Selenocompound metabolism PAPSS2	KEGG	1 / 17	118×	8.46e-3	6.20e-2
Arginine biosynthesis NOS1	KEGG	1 / 23	87.0×	1.14e-2	7.44e-2
TRP channels TRPV4	Reactome	1 / 28	71.5×	1.39e-2	8.31e-2
ROS and RNS production in phagocytes NOS1	Reactome	1 / 34	58.9×	1.69e-2	9.37e-2
African trypanosomiasis NPPA	KEGG	1 / 37	54.1×	1.83e-2	9.81e-2
Molecules associated with elastic fibres LTBP3	Reactome	1 / 38	52.7×	1.88e-2	9.94e-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 ⇵
regulation of calcium ion transmembrane transport via high voltage-gated calcium channel NOS1, NPPA	GO:1902514	2 / 12	519×	5.66e-6	3.31e-4 ✓ sig.
response to hypoxia TRPV4, NOS1, NPPA	GO:0001666	3 / 176	53.1×	1.61e-5	7.59e-4 ✓ sig.
negative regulation of blood pressure NOS1, NPPA	GO:0045776	2 / 28	222×	3.24e-5	1.29e-3 ✓ sig.
vasodilation NOS1, NPPA	GO:0042311	2 / 50	125×	1.05e-4	3.12e-3 ✓ sig.
response to insulin TRPV4, NPPA	GO:0032868	2 / 83	75.0×	2.89e-4	6.54e-3 ✓ sig.
hyperosmotic salinity response TRPV4	GO:0042538	1 / 1	3,115×	3.21e-4	7.03e-3 ✓ sig.
blood vessel endothelial cell delamination TRPV4	GO:0097497	1 / 1	3,115×	3.21e-4	7.03e-3 ✓ sig.
synaptic signaling by nitric oxide NOS1	GO:0099163	1 / 1	3,115×	3.21e-4	7.03e-3 ✓ sig.
positive regulation of sodium ion transmembrane transport NOS1	GO:1902307	1 / 1	3,115×	3.21e-4	7.03e-3 ✓ sig.
negative regulation of collecting lymphatic vessel constriction NPPA	GO:1903815	1 / 1	3,115×	3.21e-4	7.03e-3 ✓ sig.
negative regulation of establishment of blood-brain barrier TTPA	GO:0090212	1 / 1	3,115×	3.21e-4	7.03e-3 ✓ sig.
positive regulation of striated muscle contraction TRPV4	GO:0045989	1 / 2	1,557×	6.42e-4	1.13e-2 ✓ sig.
regulation of response to osmotic stress TRPV4	GO:0047484	1 / 2	1,557×	6.42e-4	1.13e-2 ✓ sig.
response to 3-methylcholanthrene NPPA	GO:1904681	1 / 2	1,557×	6.42e-4	1.13e-2 ✓ sig.
sulfate assimilation PAPSS2	GO:0000103	1 / 2	1,557×	6.42e-4	1.13e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Scapuloperoneal spinal muscular atrophy	TRPV4-related bone disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Parastremmatic dwarfism	TRPV4-related bone disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Parastremmatic dwarfism	Scapuloperoneal spinal muscular atrophy	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Digital arthropathy-brachydactyly, familial	TRPV4-related bone disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Brachyrachia	Congenital benign spinal muscular atrophy	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Brachyrachia	Digital arthropathy-brachydactyly, familial	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Brachyrachia	Parastremmatic dwarfism	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Brachyrachia	Scapuloperoneal spinal muscular atrophy	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Brachyrachia	TRPV4-related bone disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Congenital benign spinal muscular atrophy	Digital arthropathy-brachydactyly, familial	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Congenital benign spinal muscular atrophy	Parastremmatic dwarfism	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Congenital benign spinal muscular atrophy	Scapuloperoneal spinal muscular atrophy	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Congenital benign spinal muscular atrophy	TRPV4-related bone disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Digital arthropathy-brachydactyly, familial	Parastremmatic dwarfism	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Digital arthropathy-brachydactyly, familial	Scapuloperoneal spinal muscular atrophy	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Brachyolmia	Brachyrachia	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Brachyolmia	Scapuloperoneal spinal muscular atrophy	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Brachyolmia	Parastremmatic dwarfism	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Brachyolmia	Digital arthropathy-brachydactyly, familial	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Brachyolmia	Congenital benign spinal muscular atrophy	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Congenital benign spinal muscular atrophy	Urination disorders	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Brachyrachia	Urination disorders	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Digital arthropathy-brachydactyly, familial	Urination disorders	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Parastremmatic dwarfism	Urination disorders	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Scapuloperoneal spinal muscular atrophy	Urination disorders	0.200	1	2.60e-4	6.40e-4 ✓ sig.

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