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Cluster 313

6 diseases · 10 shared-gene connections

6 Diseases

13 Unique genes

0.208 Avg. similarity score

Arhinia-choanal atresia-microphthalmia syndrome Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Facioscapulohumeral muscular dystrophy 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.

Facioscapulohumeral muscular dystrophy Arhinia-choanal atresia-microphthalmia syndrome Bosma arhinia microphthalmia syndrome Chediak-higashi syndrome Facial nerve disorder Congenital hereditary facial paralysis with variable hearing loss syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Arhinia-choanal atresia-microphthalmia syndrome	4	4	1
Bosma arhinia microphthalmia syndrome	4	4	1
Chediak-higashi syndrome	4	4	2
Facial nerve disorder	4	4	8
Facioscapulohumeral muscular dystrophy	3	3	5
Congenital hereditary facial paralysis with variable hearing loss syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SMCHD1	5 / 6	Arhinia-choanal atresia-microphthalmia syndrome, Bosma arhinia microphthalmia syndrome, Chediak-higashi syndrome, Facial nerve disorder and 1 more
HOXB1	2 / 6	Congenital hereditary facial paralysis with variable hearing loss syndrome, Facial nerve disorder

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 ⇵
COPI-independent Golgi-to-ER retrograde traffic DCTN4, TUBB6	Reactome	2 / 51	36.2×	1.34e-3	1.76e-2 ✓ sig.
HSP90 chaperone cycle for steroid hormone receptors (SHR) DCTN4, TUBB6	Reactome	2 / 55	33.6×	1.56e-3	1.97e-2 ✓ sig.
Defective ACTH causes Obesity and Pro-opiomelanocortinin deficiency (POMCD) POMC	Reactome	1 / 2	462×	2.16e-3	2.51e-2 ✓ sig.
Peptide hormone biosynthesis POMC	Reactome	1 / 2	462×	2.16e-3	2.51e-2 ✓ sig.
Opioid Signalling POMC	Reactome	1 / 3	308×	3.24e-3	3.33e-2 ✓ sig.
SUMOylation of DNA methylation proteins DNMT3B	Reactome	1 / 4	231×	4.32e-3	4.10e-2 ✓ sig.
COPI-mediated anterograde transport DCTN4, TUBB6	Reactome	2 / 101	18.3×	5.14e-3	4.62e-2 ✓ sig.
MHC class II antigen presentation DCTN4, TUBB6	Reactome	2 / 123	15.0×	7.54e-3	5.91e-2
Glucocorticoid biosynthesis POMC	Reactome	1 / 10	92.4×	1.08e-2	7.43e-2
Androgen biosynthesis POMC	Reactome	1 / 11	84.0×	1.18e-2	7.88e-2
Motor proteins DCTN4, TUBB6	KEGG	2 / 194	9.5×	1.80e-2	1.01e-1
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane TUBB6	Reactome	1 / 18	51.3×	1.93e-2	1.05e-1
Cilium Assembly TUBB6	Reactome	1 / 19	48.6×	2.04e-2	1.08e-1
Endogenous sterols POMC	Reactome	1 / 25	37.0×	2.67e-2	1.26e-1
Salmonella infection DCTN4, TUBB6	KEGG	2 / 248	7.5×	2.85e-2	1.30e-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 ⇵
dosage compensation by inactivation of X chromosome SMCHD1, LRIF1	GO:0009048	2 / 10	287×	2.00e-5	9.30e-4 ✓ sig.
cellular pigmentation POMC	GO:0033059	1 / 1	1,437×	6.96e-4	1.23e-2 ✓ sig.
positive regulation of oxytocin production POMC	GO:0140668	1 / 1	1,437×	6.96e-4	1.23e-2 ✓ sig.
lymphocyte mediated immunity LYST	GO:0002449	1 / 1	1,437×	6.96e-4	1.23e-2 ✓ sig.
positive regulation of neutrophil mediated killing of fungus POMC	GO:0070965	1 / 2	719×	1.39e-3	1.90e-2 ✓ sig.
regulation of corticosterone secretion POMC	GO:2000852	1 / 2	719×	1.39e-3	1.90e-2 ✓ sig.
mast cell secretory granule organization LYST	GO:0033364	1 / 2	719×	1.39e-3	1.90e-2 ✓ sig.
rhombomere 5 development HOXB1	GO:0021571	1 / 2	719×	1.39e-3	1.90e-2 ✓ sig.
facial nucleus development HOXB1	GO:0021754	1 / 2	719×	1.39e-3	1.90e-2 ✓ sig.
rhombomere development HOXB1	GO:0021546	1 / 2	719×	1.39e-3	1.90e-2 ✓ sig.
rhombomere 4 development HOXB1	GO:0021570	1 / 2	719×	1.39e-3	1.90e-2 ✓ sig.
response to melanocyte-stimulating hormone POMC	GO:1990680	1 / 3	479×	2.09e-3	2.39e-2 ✓ sig.
modulation of process of another organism POMC	GO:0035821	1 / 3	479×	2.09e-3	2.39e-2 ✓ sig.
regulation of glycogen metabolic process POMC	GO:0070873	1 / 5	287×	3.47e-3	3.15e-2 ✓ sig.
endosome to lysosome transport via multivesicular body sorting pathway LYST	GO:0032510	1 / 6	240×	4.17e-3	3.45e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Arhinia-choanal atresia-microphthalmia syndrome	Bosma arhinia microphthalmia syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Arhinia-choanal atresia-microphthalmia syndrome	Chediak-higashi syndrome	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Bosma arhinia microphthalmia syndrome	Chediak-higashi syndrome	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Arhinia-choanal atresia-microphthalmia syndrome	Facioscapulohumeral muscular dystrophy	0.167	1	3.25e-4	7.71e-4 ✓ sig.
Bosma arhinia microphthalmia syndrome	Facioscapulohumeral muscular dystrophy	0.167	1	3.25e-4	7.71e-4 ✓ sig.
Arhinia-choanal atresia-microphthalmia syndrome	Facial nerve disorder	0.111	1	5.20e-4	1.06e-3 ✓ sig.
Bosma arhinia microphthalmia syndrome	Facial nerve disorder	0.111	1	5.20e-4	1.06e-3 ✓ sig.
Congenital hereditary facial paralysis with variable hearing loss syndrome	Facial nerve disorder	0.111	1	5.20e-4	1.06e-3 ✓ sig.
Chediak-higashi syndrome	Facioscapulohumeral muscular dystrophy	0.143	1	6.49e-4	1.24e-3 ✓ sig.
Chediak-higashi syndrome	Facial nerve disorder	0.100	1	1.04e-3	1.74e-3 ✓ sig.

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