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Cluster 230

9 diseases · 15 shared-gene connections

9 Diseases

35 Unique genes

0.198 Avg. similarity score

Bilateral perisylvian polymicrogyria Most-connected disease (7 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Spastic paraplegia 84, autosomal recessive 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.

Spastic paraplegia 84, autosomal recessive Bilateral perisylvian polymicrogyria Perisylvian syndrome Polymicrogyria Heparin cofactor 2 deficiency Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Bilateral perisylvian polymicrogyria	7	7	3
Perisylvian syndrome	4	4	10
Polymicrogyria	4	4	29
Heparin cofactor 2 deficiency	3	3	3
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis	3	3	1
Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked	3	3	1
Spastic paraplegia 84, autosomal recessive	3	3	1
Bilateral frontoparietal polymicrogyria	2	2	1
Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
PI4KA	6 / 9	Bilateral perisylvian polymicrogyria, Heparin cofactor 2 deficiency, Perisylvian syndrome, Polymicrogyria and 2 more
ADGRG1	4 / 9	Bilateral frontoparietal polymicrogyria, Bilateral perisylvian polymicrogyria, Perisylvian syndrome, Polymicrogyria
SRPX2	4 / 9	Bilateral perisylvian polymicrogyria, Perisylvian syndrome, Polymicrogyria, Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked
CCND2	2 / 9	Perisylvian syndrome, Polymicrogyria
SCN3A	2 / 9	Perisylvian syndrome, Polymicrogyria
SHMT2	2 / 9	Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities, Polymicrogyria
TUBB2B	2 / 9	Perisylvian syndrome, Polymicrogyria

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 ⇵
Aggrephagy TUBA1A, TUBB2B, DYNC1H1, TUBA8	Reactome	4 / 40	34.3×	5.13e-6	1.68e-4 ✓ sig.
Recruitment of NuMA to mitotic centrosomes TUBA1A, TUBB2B, DYNC1H1, OFD1, TUBA8	Reactome	5 / 94	18.3×	7.11e-6	2.20e-4 ✓ sig.
COPI-independent Golgi-to-ER retrograde traffic TUBA1A, TUBB2B, DYNC1H1, TUBA8	Reactome	4 / 51	26.9×	1.37e-5	3.78e-4 ✓ sig.
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane TUBA1A, TUBB2B, TUBA8	Reactome	3 / 18	57.2×	1.80e-5	4.76e-4 ✓ sig.
HSP90 chaperone cycle for steroid hormone receptors (SHR) TUBA1A, TUBB2B, DYNC1H1, TUBA8	Reactome	4 / 55	25.0×	1.85e-5	4.90e-4 ✓ sig.
Cilium Assembly TUBA1A, TUBB2B, TUBA8	Reactome	3 / 19	54.2×	2.13e-5	5.48e-4 ✓ sig.
Carboxyterminal post-translational modifications of tubulin TUBA1A, TUBB2B, TUBA8	Reactome	3 / 27	38.1×	6.32e-5	1.32e-3 ✓ sig.
The role of GTSE1 in G2/M progression after G2 checkpoint TUBA1A, TUBB2B, PSMC3, TUBA8	Reactome	4 / 77	17.8×	7.03e-5	1.43e-3 ✓ sig.
MET activates PTK2 signaling LAMA2, LAMA5, COL3A1	Reactome	3 / 30	34.3×	8.72e-5	1.70e-3 ✓ sig.
Sealing of the nuclear envelope (NE) by ESCRT-III TUBA1A, TUBB2B, TUBA8	Reactome	3 / 31	33.2×	9.64e-5	1.84e-3 ✓ sig.
RHO GTPases activate IQGAPs TUBA1A, TUBB2B, TUBA8	Reactome	3 / 32	32.2×	1.06e-4	1.99e-3 ✓ sig.
COPI-mediated anterograde transport TUBA1A, TUBB2B, DYNC1H1, TUBA8	Reactome	4 / 101	13.6×	2.02e-4	3.31e-3 ✓ sig.
Separation of Sister Chromatids TUBA1A, TUBB2B, DYNC1H1, PSMC3, TUBA8	Reactome	5 / 190	9.0×	2.08e-4	3.38e-3 ✓ sig.
Recycling pathway of L1 TUBA1A, TUBB2B, TUBA8	Reactome	3 / 40	25.7×	2.08e-4	3.39e-3 ✓ sig.
Mitotic Prometaphase TUBA1A, TUBB2B, DYNC1H1, TUBA8	Reactome	4 / 113	12.1×	3.11e-4	4.62e-3 ✓ sig.

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

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
cerebral cortex development TUBA1A, TUBB2B, WDR62, COL3A1	GO:0021987	4 / 88	24.3×	2.15e-5	9.78e-4 ✓ sig.
positive regulation of cell migration involved in sprouting angiogenesis SRPX2, NUS1, AKT3	GO:0090050	3 / 37	43.3×	4.48e-5	1.70e-3 ✓ sig.
response to glycoside ATP1A2, ATP1A3	GO:1903416	2 / 6	178×	5.09e-5	1.87e-3 ✓ sig.
microtubule-based process TUBA1A, TUBB2B, TUBA8	GO:0007017	3 / 46	34.8×	8.65e-5	2.78e-3 ✓ sig.
regulation of embryonic development EHMT1, LAMA2, LAMA5	GO:0045995	3 / 47	34.1×	9.22e-5	2.91e-3 ✓ sig.
neuron migration TUBA1A, TUBB2B, COL3A1, MAP1B	GO:0001764	4 / 132	16.2×	1.05e-4	3.21e-3 ✓ sig.
mitotic cell cycle TUBA1A, TUBB2B, OFD1, TUBA8	GO:0000278	4 / 142	15.0×	1.39e-4	3.92e-3 ✓ sig.
adult locomotory behavior CCND2, TUBA1A, ATP1A2	GO:0008344	3 / 56	28.6×	1.56e-4	4.26e-3 ✓ sig.
microtubule cytoskeleton organization TUBA1A, TUBB2B, TUBA8, MAP1B	GO:0000226	4 / 149	14.3×	1.68e-4	4.47e-3 ✓ sig.
establishment or maintenance of transmembrane electrochemical gradient ATP1A2, ATP1A3	GO:0010248	2 / 11	97.1×	1.85e-4	4.82e-3 ✓ sig.
cell communication by electrical coupling involved in cardiac conduction ATP1A2, ATP1A3	GO:0086064	2 / 12	89.0×	2.22e-4	5.47e-3 ✓ sig.
negative regulation of neuron migration ADGRG1, COL3A1	GO:2001223	2 / 12	89.0×	2.22e-4	5.47e-3 ✓ sig.
organelle transport along microtubule TUBA1A, BORCS5	GO:0072384	2 / 14	76.3×	3.06e-4	6.87e-3 ✓ sig.
sodium ion export across plasma membrane ATP1A2, ATP1A3	GO:0036376	2 / 15	71.2×	3.52e-4	7.52e-3 ✓ sig.
locomotory exploration behavior TUBA1A, ATP1A2	GO:0035641	2 / 16	66.7×	4.02e-4	8.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Perisylvian syndrome	Polymicrogyria	0.176	6	5.18e-15	6.27e-14 ✓ sig.
Bilateral perisylvian polymicrogyria	Perisylvian syndrome	0.273	3	1.94e-10	1.78e-9 ✓ sig.
Bilateral perisylvian polymicrogyria	Polymicrogyria	0.100	3	5.90e-9	4.82e-8 ✓ sig.
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis	Spastic paraplegia 84, autosomal recessive	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Bilateral frontoparietal polymicrogyria	Bilateral perisylvian polymicrogyria	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Bilateral perisylvian polymicrogyria	Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Bilateral perisylvian polymicrogyria	Spastic paraplegia 84, autosomal recessive	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Bilateral perisylvian polymicrogyria	Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Heparin cofactor 2 deficiency	Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Heparin cofactor 2 deficiency	Spastic paraplegia 84, autosomal recessive	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Bilateral perisylvian polymicrogyria	Heparin cofactor 2 deficiency	0.167	1	5.81e-4	1.00e-3 ✓ sig.
Bilateral frontoparietal polymicrogyria	Perisylvian syndrome	0.091	1	6.46e-4	1.09e-3 ✓ sig.
Perisylvian syndrome	Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked	0.091	1	6.46e-4	1.09e-3 ✓ sig.
Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities	Polymicrogyria	0.033	1	1.87e-3	2.57e-3 ✓ sig.
Polymicrogyria	Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked	0.033	1	1.87e-3	2.57e-3 ✓ sig.

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