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Cluster 413

5 diseases · 6 shared-gene connections

5 Diseases

68 Unique genes

0.110 Avg. similarity score

Childhood-onset benign chorea with striatal involvement 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.

Childhood-onset benign chorea with striatal involvement Conduct disorder Dyskinesia, limb and orofacial, infantile-onset Tooth disease severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Childhood-onset benign chorea with striatal involvement	3	3	1
Conduct disorder	3	3	52
Dyskinesia, limb and orofacial, infantile-onset	3	3	1
Tooth disease	2	2	18
severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
PDE10A	4 / 5	Childhood-onset benign chorea with striatal involvement, Conduct disorder, Dyskinesia, limb and orofacial, infantile-onset, Tooth disease
GATAD2B	2 / 5	Conduct disorder, severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
PPM1K	2 / 5	Conduct disorder, Tooth disease

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 ⇵
Tyrosine metabolism ADH1B, ADH1C, TYR	KEGG	3 / 36	14.7×	1.08e-3	1.44e-2 ✓ sig.
Ethanol oxidation ADH1B, ADH1C	Reactome	2 / 12	29.4×	2.01e-3	2.29e-2 ✓ sig.
RHO GTPases activate PKNs YWHAZ, RHOA	Reactome	2 / 20	17.7×	5.62e-3	4.73e-2 ✓ sig.
Receptor-type tyrosine-protein phosphatases PTPRD, PTPRF	Reactome	2 / 20	17.7×	5.62e-3	4.73e-2 ✓ sig.
Synaptic adhesion-like molecules PTPRD, PTPRF	Reactome	2 / 21	16.8×	6.19e-3	5.04e-2
PAOs oxidise polyamines to amines SMOX	Reactome	1 / 2	88.3×	1.13e-2	7.37e-2
NOTCH4 Activation and Transmission of Signal to the Nucleus YWHAZ	Reactome	1 / 2	88.3×	1.13e-2	7.37e-2
Adherens junction ACP1, PTPRF, RHOA	KEGG	3 / 93	5.7×	1.57e-2	8.94e-2
Interconversion of polyamines SMOX	Reactome	1 / 3	58.9×	1.69e-2	9.37e-2
RUNX2 regulates osteoblast differentiation AR	Reactome	1 / 3	58.9×	1.69e-2	9.37e-2
Axonal growth stimulation RHOA	Reactome	1 / 4	44.2×	2.25e-2	1.10e-1
SLIT2:ROBO1 increases RHOA activity RHOA	Reactome	1 / 4	44.2×	2.25e-2	1.10e-1
Reuptake of GABA SLC6A1	Reactome	1 / 4	44.2×	2.25e-2	1.10e-1
Deactivation of the beta-catenin transactivating complex YWHAZ, TLE1	Reactome	2 / 42	8.4×	2.35e-2	1.13e-1
Fatty acid degradation ADH1B, ADH1C	KEGG	2 / 43	8.2×	2.46e-2	1.15e-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 ⇵
chemical synaptic transmission ACP1, DRD4, HTR1B, RIT2, SLC6A1, GRM5	GO:0007268	6 / 236	7.0×	2.17e-4	5.34e-3 ✓ sig.
cell surface receptor protein tyrosine phosphatase signaling pathway PTPRD, PTPRF	GO:0007185	2 / 7	78.5×	2.71e-4	6.25e-3 ✓ sig.
magnesium ion homeostasis KCNA1, CNNM1	GO:0010960	2 / 8	68.7×	3.60e-4	7.59e-3 ✓ sig.
single strand break repair LIG4, SIRT1	GO:0000012	2 / 12	45.8×	8.41e-4	1.35e-2 ✓ sig.
ossification involved in bone maturation ZBTB16, RHOA	GO:0043931	2 / 12	45.8×	8.41e-4	1.35e-2 ✓ sig.
G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger CNR1, DRD4, HTR1B	GO:0007187	3 / 54	15.3×	1.00e-3	1.51e-2 ✓ sig.
detection of mechanical stimulus PKD1L2, PKD1L3	GO:0050982	2 / 15	36.6×	1.33e-3	1.79e-2 ✓ sig.
attachment of mitotic spindle microtubules to kinetochore MAD1L1, SIRT1	GO:0051315	2 / 19	28.9×	2.14e-3	2.35e-2 ✓ sig.
epithelial cell morphogenesis AR, PKHD1	GO:0003382	2 / 19	28.9×	2.14e-3	2.35e-2 ✓ sig.
positive regulation of cellular senescence PAWR, SIRT1	GO:2000774	2 / 20	27.5×	2.38e-3	2.50e-2 ✓ sig.
central nervous system development EMX2, LIG4, ZBTB16, PDGFC	GO:0007417	4 / 158	7.0×	2.63e-3	2.63e-2 ✓ sig.
negative regulation of protein secretion DRD4, SYT4	GO:0050709	2 / 22	25.0×	2.88e-3	2.76e-2 ✓ sig.
regulation of centrosome duplication PKHD1, SIRT1	GO:0010824	2 / 22	25.0×	2.88e-3	2.76e-2 ✓ sig.
Ras protein signal transduction RGL1, RIT1, RIT2	GO:0007265	3 / 79	10.4×	2.99e-3	2.82e-2 ✓ sig.
androgen receptor signaling pathway AR, RHOA	GO:0030521	2 / 23	23.9×	3.14e-3	2.91e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Childhood-onset benign chorea with striatal involvement	Dyskinesia, limb and orofacial, infantile-onset	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Childhood-onset benign chorea with striatal involvement	Tooth disease	0.053	1	1.17e-3	1.88e-3 ✓ sig.
Dyskinesia, limb and orofacial, infantile-onset	Tooth disease	0.053	1	1.17e-3	1.88e-3 ✓ sig.
Childhood-onset benign chorea with striatal involvement	Conduct disorder	0.019	1	3.38e-3	4.37e-3 ✓ sig.
Conduct disorder	Dyskinesia, limb and orofacial, infantile-onset	0.019	1	3.38e-3	4.37e-3 ✓ sig.
Conduct disorder	severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome	0.019	1	3.38e-3	4.37e-3 ✓ sig.

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