Disease Clusters | GeDiPNet

← Back to all clusters

Cluster 253

7 diseases · 19 shared-gene connections

7 Diseases

5 Unique genes

0.393 Avg. similarity score

Arts syndrome Most-connected disease (6 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.

Arts syndrome Prpp synthetase superactivity X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome phosphoribosylpyrophosphate synthetase superactivity Ataxia with deafness and vision loss PRPS1 deficiency disorder

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Arts syndrome	6	6	1
Prpp synthetase superactivity	6	6	1
X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome	6	6	1
phosphoribosylpyrophosphate synthetase superactivity	6	6	1
Ataxia with deafness and vision loss	5	5	2
PRPS1 deficiency disorder	5	5	1
X-linked nonsyndromic hearing loss	4	4	4

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

Gene ⇵	Member diseases ⇵	Linked diseases
PRPS1	7 / 7	Arts syndrome, Ataxia with deafness and vision loss, phosphoribosylpyrophosphate synthetase superactivity, Prpp synthetase superactivity and 3 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 ⇵
5-Phosphoribose 1-diphosphate biosynthesis PRPS1	Reactome	1 / 3	801×	1.25e-3	1.60e-2 ✓ sig.
TFAP2 (AP-2) family regulates transcription of other transcription factors PITX2	Reactome	1 / 4	601×	1.66e-3	2.00e-2 ✓ sig.
Extracellular matrix organization COL4A6	Reactome	1 / 15	160×	6.23e-3	5.06e-2
Anchoring fibril formation COL4A6	Reactome	1 / 15	160×	6.23e-3	5.06e-2
Crosslinking of collagen fibrils COL4A6	Reactome	1 / 18	133×	7.47e-3	5.69e-2
Non-integrin membrane-ECM interactions COL4A6	Reactome	1 / 24	100×	9.95e-3	6.82e-2
Laminin interactions COL4A6	Reactome	1 / 28	85.8×	1.16e-2	7.50e-2
Pentose phosphate pathway PRPS1	KEGG	1 / 31	77.5×	1.28e-2	7.92e-2
Collagen chain trimerization COL4A6	Reactome	1 / 44	54.6×	1.82e-2	9.77e-2
Assembly of collagen fibrils and other multimeric structures COL4A6	Reactome	1 / 51	47.1×	2.11e-2	1.06e-1
Collagen degradation COL4A6	Reactome	1 / 52	46.2×	2.15e-2	1.07e-1
Collagen biosynthesis and modifying enzymes COL4A6	Reactome	1 / 67	35.9×	2.76e-2	1.23e-1
Biosynthesis of amino acids PRPS1	KEGG	1 / 75	32.0×	3.08e-2	1.31e-1
Integrin cell surface interactions COL4A6	Reactome	1 / 81	29.7×	3.33e-2	1.37e-1
ECM-receptor interaction COL4A6	KEGG	1 / 89	27.0×	3.65e-2	1.44e-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 ⇵
subthalamic nucleus development PITX2	GO:0021763	1 / 1	3,737×	2.68e-4	6.20e-3 ✓ sig.
superior vena cava morphogenesis PITX2	GO:0060578	1 / 1	3,737×	2.68e-4	6.20e-3 ✓ sig.
urate biosynthetic process PRPS1	GO:0034418	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
hypothalamus cell migration PITX2	GO:0021855	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
prolactin secreting cell differentiation PITX2	GO:0060127	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
left lung morphogenesis PITX2	GO:0060460	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
pulmonary vein morphogenesis PITX2	GO:0060577	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
cell proliferation involved in outflow tract morphogenesis PITX2	GO:0061325	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
hypoxanthine biosynthetic process PRPS1	GO:0046101	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
pulmonary myocardium development PITX2	GO:0003350	1 / 3	1,246×	8.03e-4	1.30e-2 ✓ sig.
deltoid tuberosity development PITX2	GO:0035993	1 / 3	1,246×	8.03e-4	1.30e-2 ✓ sig.
endodermal digestive tract morphogenesis PITX2	GO:0061031	1 / 3	1,246×	8.03e-4	1.30e-2 ✓ sig.
ribonucleoside monophosphate biosynthetic process PRPS1	GO:0009156	1 / 4	934×	1.07e-3	1.57e-2 ✓ sig.
somatotropin secreting cell differentiation PITX2	GO:0060126	1 / 4	934×	1.07e-3	1.57e-2 ✓ sig.
atrioventricular valve development PITX2	GO:0003171	1 / 5	747×	1.34e-3	1.79e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Arts syndrome	X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
PRPS1 deficiency disorder	X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Prpp synthetase superactivity	PRPS1 deficiency disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Prpp synthetase superactivity	X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
phosphoribosylpyrophosphate synthetase superactivity	PRPS1 deficiency disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
phosphoribosylpyrophosphate synthetase superactivity	X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
phosphoribosylpyrophosphate synthetase superactivity	Prpp synthetase superactivity	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Arts syndrome	PRPS1 deficiency disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Arts syndrome	phosphoribosylpyrophosphate synthetase superactivity	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Arts syndrome	Prpp synthetase superactivity	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Ataxia with deafness and vision loss	X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Ataxia with deafness and vision loss	Prpp synthetase superactivity	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Arts syndrome	Ataxia with deafness and vision loss	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Ataxia with deafness and vision loss	phosphoribosylpyrophosphate synthetase superactivity	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Ataxia with deafness and vision loss	PRPS1 deficiency disorder	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Arts syndrome	X-linked nonsyndromic hearing loss	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Prpp synthetase superactivity	X-linked nonsyndromic hearing loss	0.200	1	2.60e-4	6.40e-4 ✓ sig.
X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome	X-linked nonsyndromic hearing loss	0.200	1	2.60e-4	6.40e-4 ✓ sig.
phosphoribosylpyrophosphate synthetase superactivity	X-linked nonsyndromic hearing loss	0.200	1	2.60e-4	6.40e-4 ✓ sig.

Disease Clusters?