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Cluster 642

5 diseases · 10 shared-gene connections

5 Diseases

1 Unique genes

0.500 Avg. similarity score

Nabais sa-de vries syndrome 1 Most-connected disease (4 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.

Nabais sa-de vries syndrome 1 Nabais sa-de vries syndrome 2 Neurodevelopmental disorder with microcephaly and dysmorphic facies Neurodevelopmental disorder with relative macrocephaly and with or without cardiac or endocrine anomalies Neurodevelopmental disorder, gain of function

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Nabais sa-de vries syndrome 1	4	4	1
Nabais sa-de vries syndrome 2	4	4	1
Neurodevelopmental disorder with microcephaly and dysmorphic facies	4	4	1
Neurodevelopmental disorder with relative macrocephaly and with or without cardiac or endocrine anomalies	4	4	1
Neurodevelopmental disorder, gain of function	4	4	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SPOP	5 / 5	Nabais sa-de vries syndrome 1, Nabais sa-de vries syndrome 2, Neurodevelopmental disorder with microcephaly and dysmorphic facies, Neurodevelopmental disorder with relative macrocephaly and with or without cardiac or endocrine anomalies and 1 more

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 ⇵
Hedgehog signaling pathway SPOP	KEGG	1 / 56	214×	4.66e-3	3.48e-2 ✓ sig.
Hedgehog 'on' state SPOP	Reactome	1 / 70	172×	5.83e-3	4.04e-2 ✓ 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 ⇵
regulation of proteolysis SPOP	GO:0030162	1 / 15	1,246×	8.03e-4	1.28e-2 ✓ sig.
protein polyubiquitination SPOP	GO:0000209	1 / 153	122×	8.19e-3	4.22e-2 ✓ sig.
proteasome-mediated ubiquitin-dependent protein catabolic process SPOP	GO:0043161	1 / 343	54.5×	1.84e-2	6.22e-2
protein ubiquitination SPOP	GO:0016567	1 / 542	34.5×	2.90e-2	7.95e-2

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Nabais sa-de vries syndrome 1	Neurodevelopmental disorder with microcephaly and dysmorphic facies	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Nabais sa-de vries syndrome 1	Neurodevelopmental disorder with relative macrocephaly and with or without cardiac or endocrine anomalies	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Nabais sa-de vries syndrome 1	Neurodevelopmental disorder, gain of function	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Nabais sa-de vries syndrome 1	Nabais sa-de vries syndrome 2	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Nabais sa-de vries syndrome 2	Neurodevelopmental disorder with microcephaly and dysmorphic facies	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Nabais sa-de vries syndrome 2	Neurodevelopmental disorder with relative macrocephaly and with or without cardiac or endocrine anomalies	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Nabais sa-de vries syndrome 2	Neurodevelopmental disorder, gain of function	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Neurodevelopmental disorder with microcephaly and dysmorphic facies	Neurodevelopmental disorder with relative macrocephaly and with or without cardiac or endocrine anomalies	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Neurodevelopmental disorder with microcephaly and dysmorphic facies	Neurodevelopmental disorder, gain of function	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Neurodevelopmental disorder with relative macrocephaly and with or without cardiac or endocrine anomalies	Neurodevelopmental disorder, gain of function	0.500	1	6.46e-5	1.98e-4 ✓ sig.

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