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Cluster 146

9 diseases · 16 shared-gene connections

9 Diseases

20 Unique genes

0.200 Avg. similarity score

1p36 deletion syndrome Most-connected disease (5 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.

1p36 deletion syndrome Dyssegmental dysplasia Schwartz-Jampel syndrome type 1 Silverman-Handmaker type dyssegmental dysplasia Stuve-wiedemann syndrome Schwartz-jampel syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
1p36 deletion syndrome	5	5	13
Dyssegmental dysplasia	5	5	2
Schwartz-Jampel syndrome type 1	5	5	1
Silverman-Handmaker type dyssegmental dysplasia	5	5	1
Stuve-wiedemann syndrome	5	5	6
Schwartz-jampel syndrome	4	4	3
intellectual disability, autosomal recessive 61	1	1	1
obsolete Stüve-Wiedemann syndrome	1	1	1
radio-tartaglia syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
HSPG2	6 / 9	1p36 deletion syndrome, Dyssegmental dysplasia, Schwartz-jampel syndrome, Schwartz-Jampel syndrome type 1 and 2 more
LDLRAD2	2 / 9	Dyssegmental dysplasia, Schwartz-jampel syndrome
LIFR	2 / 9	obsolete Stüve-Wiedemann syndrome, Stuve-wiedemann syndrome
RUSC2	2 / 9	intellectual disability, autosomal recessive 61, Stuve-wiedemann syndrome
SPEN	2 / 9	1p36 deletion syndrome, radio-tartaglia 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 ⇵
IL-6-type cytokine receptor ligand interactions LIFR, IL6ST	Reactome	2 / 17	70.6×	3.53e-4	6.09e-3 ✓ sig.
RUNX1 regulates transcription of genes involved in interleukin signaling LIFR	Reactome	1 / 5	120×	8.30e-3	6.10e-2
Estrogen-stimulated signaling through PRKCZ PRKCZ	Reactome	1 / 6	100×	9.95e-3	6.82e-2
Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion GNA11	Reactome	1 / 8	75.1×	1.32e-2	8.07e-2
Acetylcholine regulates insulin secretion GNA11	Reactome	1 / 9	66.7×	1.49e-2	8.66e-2
MAPK1 (ERK2) activation IL6ST	Reactome	1 / 9	66.7×	1.49e-2	8.66e-2
MAPK3 (ERK1) activation IL6ST	Reactome	1 / 10	60.1×	1.65e-2	9.23e-2
Interleukin-27 signaling IL6ST	Reactome	1 / 11	54.6×	1.82e-2	9.77e-2
Interleukin-6 signaling IL6ST	Reactome	1 / 11	54.6×	1.82e-2	9.77e-2
Interleukin-35 Signalling IL6ST	Reactome	1 / 12	50.0×	1.98e-2	1.02e-1
Defective EXT2 causes exostoses 2 HSPG2	Reactome	1 / 14	42.9×	2.31e-2	1.12e-1
Defective EXT1 causes exostoses 1, TRPS2 and CHDS HSPG2	Reactome	1 / 14	42.9×	2.31e-2	1.12e-1
VEGFR2 mediated cell proliferation PRKCZ	Reactome	1 / 14	42.9×	2.31e-2	1.12e-1
Signaling pathways regulating pluripotency of stem cells LIFR, IL6ST	KEGG	2 / 144	8.3×	2.36e-2	1.13e-1
TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) PRKCZ	Reactome	1 / 15	40.0×	2.47e-2	1.16e-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 ⇵
leukemia inhibitory factor signaling pathway LIFR, IL6ST	GO:0048861	2 / 4	467×	6.52e-6	3.70e-4 ✓ sig.
oncostatin-M-mediated signaling pathway LIFR, IL6ST	GO:0038165	2 / 4	467×	6.52e-6	3.70e-4 ✓ sig.
ciliary neurotrophic factor-mediated signaling pathway LIFR, IL6ST	GO:0070120	2 / 5	374×	1.09e-5	5.55e-4 ✓ sig.
positive regulation of platelet aggregation PDPN, IL6ST	GO:1901731	2 / 13	144×	8.43e-5	2.66e-3 ✓ sig.
neural fold bending LUZP1	GO:0021503	1 / 1	934×	1.07e-3	1.57e-2 ✓ sig.
contractile ring contraction LUZP1	GO:0036213	1 / 1	934×	1.07e-3	1.57e-2 ✓ sig.
regulation of myofibroblast contraction PDPN	GO:1904328	1 / 1	934×	1.07e-3	1.57e-2 ✓ sig.
granzyme-mediated apoptotic signaling pathway UBE4B	GO:0008626	1 / 1	934×	1.07e-3	1.57e-2 ✓ sig.
regulation of melanocyte differentiation GNA11	GO:0045634	1 / 1	934×	1.07e-3	1.57e-2 ✓ sig.
response to cytokine LIFR, IL6ST	GO:0034097	2 / 56	33.4×	1.62e-3	2.00e-2 ✓ sig.
cerebellar Purkinje cell layer maturation RERE	GO:0021691	1 / 2	467×	2.14e-3	2.34e-2 ✓ sig.
ciliary basal body-plasma membrane docking CEP290	GO:0097711	1 / 2	467×	2.14e-3	2.34e-2 ✓ sig.
camera-type eye development SKI, CEP290	GO:0043010	2 / 74	25.3×	2.81e-3	2.73e-2 ✓ sig.
radial glia guided migration of Purkinje cell RERE	GO:0021942	1 / 3	311×	3.21e-3	2.91e-2 ✓ sig.
nose morphogenesis SKI	GO:0043585	1 / 3	311×	3.21e-3	2.91e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Dyssegmental dysplasia	Schwartz-jampel syndrome	0.500	2	2.53e-8	2.03e-7 ✓ sig.
Schwartz-Jampel syndrome type 1	Silverman-Handmaker type dyssegmental dysplasia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Dyssegmental dysplasia	Schwartz-Jampel syndrome type 1	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Dyssegmental dysplasia	Silverman-Handmaker type dyssegmental dysplasia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Schwartz-jampel syndrome	Schwartz-Jampel syndrome type 1	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Schwartz-jampel syndrome	Silverman-Handmaker type dyssegmental dysplasia	0.250	1	1.95e-4	5.28e-4 ✓ sig.
intellectual disability, autosomal recessive 61	Stuve-wiedemann syndrome	0.143	1	3.90e-4	8.52e-4 ✓ sig.
obsolete Stüve-Wiedemann syndrome	Stuve-wiedemann syndrome	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Schwartz-Jampel syndrome type 1	Stuve-wiedemann syndrome	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Silverman-Handmaker type dyssegmental dysplasia	Stuve-wiedemann syndrome	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Dyssegmental dysplasia	Stuve-wiedemann syndrome	0.125	1	7.79e-4	1.39e-3 ✓ sig.
1p36 deletion syndrome	Schwartz-Jampel syndrome type 1	0.071	1	8.44e-4	1.48e-3 ✓ sig.
1p36 deletion syndrome	Silverman-Handmaker type dyssegmental dysplasia	0.071	1	8.44e-4	1.48e-3 ✓ sig.
1p36 deletion syndrome	radio-tartaglia syndrome	0.071	1	8.44e-4	1.48e-3 ✓ sig.
1p36 deletion syndrome	Dyssegmental dysplasia	0.067	1	1.69e-3	2.51e-3 ✓ sig.
1p36 deletion syndrome	Schwartz-jampel syndrome	0.063	1	2.53e-3	3.44e-3 ✓ sig.

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