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Cluster 397

5 diseases · 10 shared-gene connections

5 Diseases

4 Unique genes

0.345 Avg. similarity score

Brachydactyly-syndactyly syndrome Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Brachydactyly-syndactyly 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.

Brachydactyly-syndactyly syndrome Brachymesophalangy Hemimelia of limb Synpolydactyly Zygodactyly

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Brachydactyly-syndactyly syndrome	4	4	1
Brachymesophalangy	4	4	1
Hemimelia of limb	4	4	2
Synpolydactyly	4	4	3
Zygodactyly	4	4	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
HOXD13	5 / 5	Brachydactyly-syndactyly syndrome, Brachymesophalangy, Hemimelia of limb, Synpolydactyly and 1 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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
Chondroitin sulfate biosynthesis CHST11	Reactome	1 / 20	150×	6.65e-3	5.47e-2
Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate CHST11	KEGG	1 / 21	143×	6.98e-3	5.64e-2
Signaling by BMP NOG	Reactome	1 / 28	107×	9.29e-3	6.78e-2
Molecules associated with elastic fibres FBLN1	Reactome	1 / 38	79.0×	1.26e-2	8.17e-2
TGF-beta signaling pathway NOG	KEGG	1 / 108	27.8×	3.55e-2	1.47e-1
Cytoskeleton in muscle cells FBLN1	KEGG	1 / 232	12.9×	7.51e-2	2.19e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
embryonic digit morphogenesis HOXD13, NOG, CHST11	GO:0042733	3 / 57	246×	1.07e-7	1.30e-5 ✓ sig.
embryonic limb morphogenesis HOXD13, CHST11	GO:0030326	2 / 59	158×	5.86e-5	2.09e-3 ✓ sig.
pattern specification process HOXD13, NOG	GO:0007389	2 / 60	156×	6.06e-5	2.15e-3 ✓ sig.
cartilage development NOG, CHST11	GO:0051216	2 / 89	105×	1.34e-4	3.87e-3 ✓ sig.
branch elongation of an epithelium HOXD13	GO:0060602	1 / 1	4,672×	2.14e-4	5.46e-3 ✓ sig.
polysaccharide localization CHST11	GO:0033037	1 / 1	4,672×	2.14e-4	5.46e-3 ✓ sig.
skeletal system development HOXD13, NOG	GO:0001501	2 / 151	61.9×	3.85e-4	8.25e-3 ✓ sig.
positive regulation of glomerulus development NOG	GO:0090193	1 / 2	2,336×	4.28e-4	8.87e-3 ✓ sig.
neural plate morphogenesis NOG	GO:0001839	1 / 3	1,557×	6.42e-4	1.16e-2 ✓ sig.
cell differentiation in hindbrain NOG	GO:0021533	1 / 3	1,557×	6.42e-4	1.16e-2 ✓ sig.
short-term synaptic potentiation NOG	GO:1990926	1 / 3	1,557×	6.42e-4	1.16e-2 ✓ sig.
neural plate anterior/posterior regionalization NOG	GO:0021999	1 / 3	1,557×	6.42e-4	1.16e-2 ✓ sig.
embryonic hindgut morphogenesis HOXD13	GO:0048619	1 / 3	1,557×	6.42e-4	1.16e-2 ✓ sig.
negative regulation of cardiac epithelial to mesenchymal transition NOG	GO:0062044	1 / 3	1,557×	6.42e-4	1.16e-2 ✓ sig.
positive regulation of substrate-dependent cell migration, cell attachment to substrate FBLN1	GO:1904237	1 / 3	1,557×	6.42e-4	1.16e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Brachydactyly-syndactyly syndrome	Brachymesophalangy	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Brachydactyly-syndactyly syndrome	Zygodactyly	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Brachymesophalangy	Zygodactyly	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Brachydactyly-syndactyly syndrome	Hemimelia of limb	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Brachymesophalangy	Hemimelia of limb	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Hemimelia of limb	Zygodactyly	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Brachydactyly-syndactyly syndrome	Synpolydactyly	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Brachymesophalangy	Synpolydactyly	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Synpolydactyly	Zygodactyly	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Hemimelia of limb	Synpolydactyly	0.200	1	3.90e-4	8.67e-4 ✓ sig.

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