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Cluster 446

6 diseases · 7 shared-gene connections

6 Diseases

8 Unique genes

0.276 Avg. similarity score

Cerebellar ataxia, impaired intellectual development, and dysequilibrium Most-connected disease (3 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.

Cerebellar ataxia, impaired intellectual development, and dysequilibrium Dysequilibrium syndrome Hydrocephalus, congenital, 3, with brain anomalies Cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1 Microlissencephaly Lissencephaly 6, with microcephaly

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cerebellar ataxia, impaired intellectual development, and dysequilibrium	3	3	6
Dysequilibrium syndrome	3	3	6
Hydrocephalus, congenital, 3, with brain anomalies	3	3	1
Cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1	2	2	1
Microlissencephaly	2	2	3
Lissencephaly 6, with microcephaly	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
WDR81	4 / 6	Cerebellar ataxia, impaired intellectual development, and dysequilibrium, Dysequilibrium syndrome, Hydrocephalus, congenital, 3, with brain anomalies, Microlissencephaly
VLDLR	3 / 6	Cerebellar ataxia, impaired intellectual development, and dysequilibrium, Cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1, Dysequilibrium syndrome
ATP8A2	2 / 6	Cerebellar ataxia, impaired intellectual development, and dysequilibrium, Dysequilibrium syndrome
CA8	2 / 6	Cerebellar ataxia, impaired intellectual development, and dysequilibrium, Dysequilibrium syndrome
KATNB1	2 / 6	Lissencephaly 6, with microcephaly, Microlissencephaly
RIPPLY1	2 / 6	Cerebellar ataxia, impaired intellectual development, and dysequilibrium, Dysequilibrium syndrome
TUBB2B	2 / 6	Cerebellar ataxia, impaired intellectual development, and dysequilibrium, Dysequilibrium syndrome

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 ⇵
Recruitment of NuMA to mitotic centrosomes TUBB2B, NDE1	Reactome	2 / 94	31.9×	1.65e-3	1.65e-2 ✓ sig.
Mitotic Prometaphase TUBB2B, NDE1	Reactome	2 / 113	26.6×	2.37e-3	2.16e-2 ✓ sig.
EML4 and NUDC in mitotic spindle formation TUBB2B, NDE1	Reactome	2 / 117	25.7×	2.54e-3	2.26e-2 ✓ sig.
Resolution of Sister Chromatid Cohesion TUBB2B, NDE1	Reactome	2 / 126	23.8×	2.93e-3	2.51e-2 ✓ sig.
Reelin signalling pathway VLDLR	Reactome	1 / 5	300×	3.33e-3	2.74e-2 ✓ sig.
VLDL clearance VLDLR	Reactome	1 / 5	300×	3.33e-3	2.74e-2 ✓ sig.
RHO GTPases Activate Formins TUBB2B, NDE1	Reactome	2 / 140	21.4×	3.61e-3	2.90e-2 ✓ sig.
Separation of Sister Chromatids TUBB2B, NDE1	Reactome	2 / 190	15.8×	6.55e-3	4.35e-2 ✓ sig.
VLDLR internalisation and degradation VLDLR	Reactome	1 / 12	125×	7.97e-3	4.94e-2 ✓ sig.
Nitrogen metabolism CA8	KEGG	1 / 17	88.3×	1.13e-2	6.12e-2
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane TUBB2B	Reactome	1 / 18	83.4×	1.19e-2	6.32e-2
Cilium Assembly TUBB2B	Reactome	1 / 19	79.0×	1.26e-2	6.55e-2
Carboxyterminal post-translational modifications of tubulin TUBB2B	Reactome	1 / 27	55.6×	1.78e-2	8.03e-2
Sealing of the nuclear envelope (NE) by ESCRT-III TUBB2B	Reactome	1 / 31	48.4×	2.05e-2	8.70e-2
RHO GTPases activate IQGAPs TUBB2B	Reactome	1 / 32	46.9×	2.11e-2	8.84e-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 ⇵
involuntary skeletal muscle contraction ATP8A2	GO:0003011	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
cerebral cortex development TUBB2B, NDE1	GO:0021987	2 / 88	53.1×	6.03e-4	1.08e-2 ✓ sig.
positive regulation of axon guidance TUBB2B	GO:1902669	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
positive regulation of neuron projection development ATP8A2, KATNB1	GO:0010976	2 / 121	38.6×	1.13e-3	1.56e-2 ✓ sig.
chromosome localization NDE1	GO:0050000	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
glycoprotein transport VLDLR	GO:0034436	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
neuron migration TUBB2B, NDE1	GO:0001764	2 / 132	35.4×	1.35e-3	1.72e-2 ✓ sig.
mitotic chromosome movement towards spindle pole KATNB1	GO:0007079	1 / 4	584×	1.71e-3	1.96e-2 ✓ sig.
positive regulation of phospholipid translocation ATP8A2	GO:0061092	1 / 4	584×	1.71e-3	1.96e-2 ✓ sig.
nervous system development VLDLR, TUBB2B, NDE1	GO:0007399	3 / 631	11.1×	1.89e-3	2.07e-2 ✓ sig.
very-low-density lipoprotein particle clearance VLDLR	GO:0034447	1 / 5	467×	2.14e-3	2.19e-2 ✓ sig.
positive regulation of microtubule depolymerization KATNB1	GO:0031117	1 / 5	467×	2.14e-3	2.19e-2 ✓ sig.
somite specification RIPPLY1	GO:0001757	1 / 5	467×	2.14e-3	2.19e-2 ✓ sig.
mitotic centrosome separation NDE1	GO:0007100	1 / 6	389×	2.57e-3	2.40e-2 ✓ sig.
lipid transport VLDLR, ATP8A2	GO:0006869	2 / 189	24.7×	2.74e-3	2.49e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Cerebellar ataxia, impaired intellectual development, and dysequilibrium	Dysequilibrium syndrome	0.857	6	5.22e-23	8.37e-22 ✓ sig.
Hydrocephalus, congenital, 3, with brain anomalies	Microlissencephaly	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Lissencephaly 6, with microcephaly	Microlissencephaly	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Cerebellar ataxia, impaired intellectual development, and dysequilibrium	Hydrocephalus, congenital, 3, with brain anomalies	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Cerebellar ataxia, impaired intellectual development, and dysequilibrium	Cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1	Dysequilibrium syndrome	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Dysequilibrium syndrome	Hydrocephalus, congenital, 3, with brain anomalies	0.143	1	3.87e-4	7.33e-4 ✓ sig.

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