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Cluster 381

7 diseases · 16 shared-gene connections

7 Diseases

2 Unique genes

0.437 Avg. similarity score

Early-onset epilepsy Most-connected disease (6 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant 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.

Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant Early-onset epilepsy Mental retardation, autosomal dominant 13 Neuronal migration abnormalities Severe intellectual disability with neuronal migration disorder Spinal muscular atrophy, lower extremity predominant, autosomal dominant

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Early-onset epilepsy	6	6	2
Mental retardation, autosomal dominant 13	5	5	1
Neuronal migration abnormalities	5	5	1
Severe intellectual disability with neuronal migration disorder	5	5	1
Spinal muscular atrophy, lower extremity predominant, autosomal dominant	5	5	1
Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant	5	5	1
Epileptic encephalopathy, early infantile, 56	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
DYNC1H1	6 / 7	Early-onset epilepsy, Mental retardation, autosomal dominant 13, Neuronal migration abnormalities, Severe intellectual disability with neuronal migration disorder and 2 more
YWHAG	2 / 7	Early-onset epilepsy, Epileptic encephalopathy, early infantile, 56

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 ⇵
Loss of Nlp from mitotic centrosomes DYNC1H1, YWHAG	Reactome	2 / 70	172×	3.35e-5	7.94e-4 ✓ sig.
Loss of proteins required for interphase microtubule organization from the centrosome DYNC1H1, YWHAG	Reactome	2 / 70	172×	3.35e-5	7.94e-4 ✓ sig.
AURKA Activation by TPX2 DYNC1H1, YWHAG	Reactome	2 / 73	165×	3.64e-5	8.49e-4 ✓ sig.
Recruitment of mitotic centrosome proteins and complexes DYNC1H1, YWHAG	Reactome	2 / 82	146×	4.61e-5	1.02e-3 ✓ sig.
Regulation of PLK1 Activity at G2/M Transition DYNC1H1, YWHAG	Reactome	2 / 88	136×	5.31e-5	1.14e-3 ✓ sig.
Recruitment of NuMA to mitotic centrosomes DYNC1H1, YWHAG	Reactome	2 / 94	128×	6.06e-5	1.27e-3 ✓ sig.
Anchoring of the basal body to the plasma membrane DYNC1H1, YWHAG	Reactome	2 / 98	123×	6.59e-5	1.36e-3 ✓ sig.
Regulation of localization of FOXO transcription factors YWHAG	Reactome	1 / 11	546×	1.83e-3	1.78e-2 ✓ sig.
Activation of BAD and translocation to mitochondria YWHAG	Reactome	1 / 12	500×	2.00e-3	1.90e-2 ✓ sig.
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex YWHAG	Reactome	1 / 12	500×	2.00e-3	1.90e-2 ✓ sig.
RHO GTPases activate PKNs YWHAG	Reactome	1 / 20	300×	3.33e-3	2.74e-2 ✓ sig.
Aggrephagy DYNC1H1	Reactome	1 / 40	150×	6.65e-3	4.39e-2 ✓ sig.
Vasopressin-regulated water reabsorption DYNC1H1	KEGG	1 / 44	136×	7.31e-3	4.67e-2 ✓ sig.
COPI-independent Golgi-to-ER retrograde traffic DYNC1H1	Reactome	1 / 51	118×	8.48e-3	5.13e-2
HSP90 chaperone cycle for steroid hormone receptors (SHR) DYNC1H1	Reactome	1 / 55	109×	9.14e-3	5.37e-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 ⇵
regulation of metaphase plate congression DYNC1H1	GO:0090235	1 / 5	1,869×	5.35e-4	9.88e-3 ✓ sig.
establishment of spindle localization DYNC1H1	GO:0051293	1 / 6	1,557×	6.42e-4	1.11e-2 ✓ sig.
positive regulation of T cell mediated immune response to tumor cell YWHAG	GO:0002842	1 / 8	1,168×	8.56e-4	1.33e-2 ✓ sig.
positive regulation of spindle assembly DYNC1H1	GO:1905832	1 / 8	1,168×	8.56e-4	1.33e-2 ✓ sig.
positive regulation of intracellular transport DYNC1H1	GO:0032388	1 / 10	934×	1.07e-3	1.51e-2 ✓ sig.
retrograde axonal transport DYNC1H1	GO:0008090	1 / 11	849×	1.18e-3	1.59e-2 ✓ sig.
negative regulation of T cell mediated immune response to tumor cell YWHAG	GO:0002841	1 / 11	849×	1.18e-3	1.59e-2 ✓ sig.
P-body assembly DYNC1H1	GO:0033962	1 / 16	584×	1.71e-3	1.96e-2 ✓ sig.
regulation of mitotic spindle organization DYNC1H1	GO:0060236	1 / 20	467×	2.14e-3	2.19e-2 ✓ sig.
negative regulation of protein kinase activity YWHAG	GO:0006469	1 / 21	445×	2.25e-3	2.24e-2 ✓ sig.
positive regulation of cell-cell adhesion YWHAG	GO:0022409	1 / 21	445×	2.25e-3	2.24e-2 ✓ sig.
nuclear migration DYNC1H1	GO:0007097	1 / 22	425×	2.35e-3	2.30e-2 ✓ sig.
protein K6-linked ubiquitination YWHAG	GO:0085020	1 / 26	359×	2.78e-3	2.51e-2 ✓ sig.
stress granule assembly DYNC1H1	GO:0034063	1 / 32	292×	3.42e-3	2.78e-2 ✓ sig.
regulation of neuron differentiation YWHAG	GO:0045664	1 / 32	292×	3.42e-3	2.78e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Mental retardation, autosomal dominant 13	Severe intellectual disability with neuronal migration disorder	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mental retardation, autosomal dominant 13	Neuronal migration abnormalities	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mental retardation, autosomal dominant 13	Spinal muscular atrophy, lower extremity predominant, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mental retardation, autosomal dominant 13	Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Neuronal migration abnormalities	Severe intellectual disability with neuronal migration disorder	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Neuronal migration abnormalities	Spinal muscular atrophy, lower extremity predominant, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Neuronal migration abnormalities	Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Severe intellectual disability with neuronal migration disorder	Spinal muscular atrophy, lower extremity predominant, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Severe intellectual disability with neuronal migration disorder	Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Spinal muscular atrophy, lower extremity predominant, autosomal dominant	Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Early-onset epilepsy	Severe intellectual disability with neuronal migration disorder	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Early-onset epilepsy	Neuronal migration abnormalities	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Early-onset epilepsy	Spinal muscular atrophy, lower extremity predominant, autosomal dominant	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Early-onset epilepsy	Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Early-onset epilepsy	Mental retardation, autosomal dominant 13	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Early-onset epilepsy	Epileptic encephalopathy, early infantile, 56	0.333	1	1.29e-4	3.27e-4 ✓ sig.

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