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Cluster 486

6 diseases · 5 shared-gene connections

6 Diseases

21 Unique genes

0.049 Avg. similarity score

Syndromic complex neurodevelopmental disorder Most-connected disease (5 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.

Syndromic complex neurodevelopmental disorder Chopra-amiel-gordon syndrome Intellectual developmental disorder dysmorphic ptosis Neurodevelopmental disorder with or without cataracts and movement disorder Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities Ververi-brady syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Syndromic complex neurodevelopmental disorder	5	5	19
Chopra-amiel-gordon syndrome	1	1	1
Intellectual developmental disorder dysmorphic ptosis	1	1	2
Neurodevelopmental disorder with or without cataracts and movement disorder	1	1	1
Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities	1	1	1
Ververi-brady syndrome	1	1	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
ANKRD17	2 / 6	Chopra-amiel-gordon syndrome, Syndromic complex neurodevelopmental disorder
BRPF1	2 / 6	Intellectual developmental disorder dysmorphic ptosis, Syndromic complex neurodevelopmental disorder
QRICH1	2 / 6	Syndromic complex neurodevelopmental disorder, Ververi-brady syndrome
ZBTB11	2 / 6	Neurodevelopmental disorder with or without cataracts and movement disorder, Syndromic complex neurodevelopmental disorder
ZMYM2	2 / 6	Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities, Syndromic complex neurodevelopmental 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)

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 ⇵
Selenocompound metabolism SEPHS1	KEGG	1 / 17	33.6×	2.93e-2	1.07e-1
Signaling by cytosolic FGFR1 fusion mutants ZMYM2	Reactome	1 / 18	31.8×	3.10e-2	1.10e-1
Regulation of TP53 Activity through Acetylation BRPF1	Reactome	1 / 23	24.9×	3.95e-2	1.26e-1
Deadenylation of mRNA PAN2	Reactome	1 / 24	23.8×	4.12e-2	1.29e-1
TRP channels TRPM3	Reactome	1 / 28	20.4×	4.79e-2	1.41e-1
Signaling by FGFR1 in disease ZMYM2	Reactome	1 / 33	17.3×	5.62e-2	1.55e-1
Lysine degradation ASH1L	KEGG	1 / 63	9.1×	1.05e-1	2.22e-1
PKMTs methylate histone lysines ASH1L	Reactome	1 / 71	8.1×	1.17e-1	2.38e-1
RNA degradation PAN2	KEGG	1 / 78	7.3×	1.28e-1	2.50e-1
Viral mRNA Translation RPL10L	Reactome	1 / 89	6.4×	1.45e-1	2.70e-1
HATs acetylate histones BRPF1	Reactome	1 / 93	6.1×	1.51e-1	2.77e-1
SRP-dependent cotranslational protein targeting to membrane RPL10L	Reactome	1 / 93	6.1×	1.51e-1	2.77e-1
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) RPL10L	Reactome	1 / 95	6.0×	1.54e-1	2.80e-1
Formation of a pool of free 40S subunits RPL10L	Reactome	1 / 101	5.7×	1.63e-1	2.90e-1
L13a-mediated translational silencing of Ceruloplasmin expression RPL10L	Reactome	1 / 111	5.2×	1.77e-1	3.07e-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 ⇵
regulation of DNA-templated transcription BRPF1, ASH1L, NFIB, SETD5, MYT1L, ZFHX4, ZMYND8, ZBTB11	GO:0006355	8 / 1,454	4.9×	1.07e-4	3.25e-3 ✓ sig.
chromatin organization BRPF1, ASH1L, SETD5, ZMYND11, ZMYND8	GO:0006325	5 / 449	9.9×	1.16e-4	3.44e-3 ✓ sig.
neuron fate specification NFIB, MYT1L	GO:0048665	2 / 24	74.2×	3.27e-4	7.13e-3 ✓ sig.
regeneration NFIB	GO:0031099	1 / 1	890×	1.12e-3	1.55e-2 ✓ sig.
lung ciliated cell differentiation NFIB	GO:0061141	1 / 1	890×	1.12e-3	1.55e-2 ✓ sig.
negative regulation of epithelial cell proliferation involved in lung morphogenesis NFIB	GO:2000795	1 / 1	890×	1.12e-3	1.55e-2 ✓ sig.
tarsal gland development ASH1L	GO:1903699	1 / 1	890×	1.12e-3	1.55e-2 ✓ sig.
uterine gland development ASH1L	GO:1903709	1 / 1	890×	1.12e-3	1.55e-2 ✓ sig.
cell differentiation involved in salivary gland development NFIB	GO:0060689	1 / 2	445×	2.25e-3	2.24e-2 ✓ sig.
negative regulation of mesenchymal cell proliferation involved in lung development NFIB	GO:2000791	1 / 2	445×	2.25e-3	2.24e-2 ✓ sig.
selenocysteine biosynthetic process SEPHS1	GO:0016260	1 / 2	445×	2.25e-3	2.24e-2 ✓ sig.
glial cell fate specification NFIB	GO:0021780	1 / 3	297×	3.37e-3	2.76e-2 ✓ sig.
principal sensory nucleus of trigeminal nerve development NFIB	GO:0021740	1 / 3	297×	3.37e-3	2.76e-2 ✓ sig.
positive regulation of MDA-5 signaling pathway ANKRD17	GO:1900245	1 / 4	222×	4.49e-3	3.17e-2 ✓ sig.
negative regulation of transcription by RNA polymerase III SETD5	GO:0016480	1 / 4	222×	4.49e-3	3.17e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Chopra-amiel-gordon syndrome	Syndromic complex neurodevelopmental disorder	0.050	1	1.23e-3	1.81e-3 ✓ sig.
Neurodevelopmental disorder with or without cataracts and movement disorder	Syndromic complex neurodevelopmental disorder	0.050	1	1.23e-3	1.81e-3 ✓ sig.
Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities	Syndromic complex neurodevelopmental disorder	0.050	1	1.23e-3	1.81e-3 ✓ sig.
Intellectual developmental disorder dysmorphic ptosis	Syndromic complex neurodevelopmental disorder	0.048	1	2.45e-3	3.19e-3 ✓ sig.
Syndromic complex neurodevelopmental disorder	Ververi-brady syndrome	0.048	1	2.45e-3	3.19e-3 ✓ sig.

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