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Cluster 315

7 diseases · 13 shared-gene connections

7 Diseases

11 Unique genes

0.246 Avg. similarity score

Deafness, autosomal dominant, 75 Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Abnormality of the urinary system 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.

Abnormality of the urinary system Deafness, autosomal dominant, 75 Developmental delay with or without dysmorphic facies and autism Developmental delay with or without intellectual or behavioral abnormalities Complex neurodevelopmental disorder with or without congenital anomalies Abnormal heart morphology

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Deafness, autosomal dominant, 75	5	5	1
Developmental delay with or without dysmorphic facies and autism	5	5	1
Developmental delay with or without intellectual or behavioral abnormalities	5	5	2
Complex neurodevelopmental disorder with or without congenital anomalies	4	4	5
Abnormal heart morphology	3	3	5
Abnormality of the urinary system	3	3	2
Taurodontism, microdontia, and dens invaginatus	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
TRRAP	6 / 7	Abnormal heart morphology, Abnormality of the urinary system, Complex neurodevelopmental disorder with or without congenital anomalies, Deafness, autosomal dominant, 75 and 2 more
KIF4A	2 / 7	Complex neurodevelopmental disorder with or without congenital anomalies, Taurodontism, microdontia, and dens invaginatus

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 ⇵
Interactions of Tat with host cellular proteins CDK9	Reactome	1 / 2	546×	1.83e-3	1.78e-2 ✓ sig.
Resolution of Sister Chromatid Cohesion TAOK1, STAG2	Reactome	2 / 126	17.3×	5.65e-3	3.96e-2 ✓ sig.
Estrogen-dependent gene expression CDK9, STAG2	Reactome	2 / 150	14.6×	7.92e-3	4.93e-2 ✓ sig.
Cohesin Loading onto Chromatin STAG2	Reactome	1 / 10	109×	9.12e-3	5.37e-2
SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion PLXNA2	Reactome	1 / 10	109×	9.12e-3	5.37e-2
Establishment of Sister Chromatid Cohesion STAG2	Reactome	1 / 11	99.3×	1.00e-2	5.69e-2
Separation of Sister Chromatids TAOK1, STAG2	Reactome	2 / 190	11.5×	1.25e-2	6.50e-2
Motor proteins MYH10, KIF4A	KEGG	2 / 194	11.3×	1.30e-2	6.64e-2
Sema3A PAK dependent Axon repulsion PLXNA2	Reactome	1 / 15	72.8×	1.37e-2	6.87e-2
CRMPs in Sema3A signaling PLXNA2	Reactome	1 / 16	68.2×	1.46e-2	7.13e-2
Virion - Lassa virus and SFTS virus MYH10	KEGG	1 / 17	64.2×	1.55e-2	7.39e-2
Formation of HIV-1 elongation complex containing HIV-1 Tat CDK9	Reactome	1 / 23	47.5×	2.09e-2	8.78e-2
RHO GTPases activate PAKs MYH10	Reactome	1 / 23	47.5×	2.09e-2	8.78e-2
SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription CDK9	Reactome	1 / 32	34.1×	2.89e-2	1.06e-1
Recycling pathway of L1 KIF4A	Reactome	1 / 40	27.3×	3.60e-2	1.20e-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 ⇵
negative regulation of transcription regulatory region DNA binding SOX11	GO:2000678	1 / 1	1,699×	5.89e-4	1.06e-2 ✓ sig.
regulation of DNA repair TRRAP, CDK9	GO:0006282	2 / 63	53.9×	6.03e-4	1.08e-2 ✓ sig.
mitotic cytokinesis MYH10, KIF4A	GO:0000281	2 / 68	50.0×	7.03e-4	1.19e-2 ✓ sig.
closure of optic fissure SOX11	GO:0061386	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.
cerebellar Purkinje cell layer maturation RERE	GO:0021691	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.
positive regulation of lens epithelial cell proliferation SOX11	GO:2001111	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.
fourth ventricle development MYH10	GO:0021592	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.
cerebellar granule cell precursor tangential migration PLXNA2	GO:0021935	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.
radial glia guided migration of Purkinje cell RERE	GO:0021942	1 / 3	566×	1.76e-3	1.99e-2 ✓ sig.
pyramidal neuron migration to cerebral cortex ZMIZ1	GO:0021852	1 / 3	566×	1.76e-3	1.99e-2 ✓ sig.
positive regulation of protein localization to chromatin CDK9	GO:0120187	1 / 3	566×	1.76e-3	1.99e-2 ✓ sig.
spindle elongation KIF4A	GO:0051231	1 / 3	566×	1.76e-3	1.99e-2 ✓ sig.
regulation of mRNA 3'-end processing CDK9	GO:0031440	1 / 4	425×	2.35e-3	2.30e-2 ✓ sig.
vitellogenesis ZMIZ1	GO:0007296	1 / 4	425×	2.35e-3	2.30e-2 ✓ sig.
soft palate development SOX11	GO:0060023	1 / 5	340×	2.94e-3	2.58e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Deafness, autosomal dominant, 75	Developmental delay with or without dysmorphic facies and autism	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Abnormality of the urinary system	Developmental delay with or without dysmorphic facies and autism	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Abnormality of the urinary system	Deafness, autosomal dominant, 75	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Deafness, autosomal dominant, 75	Developmental delay with or without intellectual or behavioral abnormalities	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Developmental delay with or without dysmorphic facies and autism	Developmental delay with or without intellectual or behavioral abnormalities	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Abnormality of the urinary system	Developmental delay with or without intellectual or behavioral abnormalities	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Abnormal heart morphology	Developmental delay with or without dysmorphic facies and autism	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Abnormal heart morphology	Deafness, autosomal dominant, 75	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Complex neurodevelopmental disorder with or without congenital anomalies	Developmental delay with or without dysmorphic facies and autism	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Complex neurodevelopmental disorder with or without congenital anomalies	Deafness, autosomal dominant, 75	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Complex neurodevelopmental disorder with or without congenital anomalies	Taurodontism, microdontia, and dens invaginatus	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Complex neurodevelopmental disorder with or without congenital anomalies	Developmental delay with or without intellectual or behavioral abnormalities	0.143	1	6.46e-4	1.09e-3 ✓ sig.
Abnormal heart morphology	Developmental delay with or without intellectual or behavioral abnormalities	0.143	1	6.46e-4	1.09e-3 ✓ sig.

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