Disease Clusters | GeDiPNet

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Cluster 429

6 diseases · 10 shared-gene connections

6 Diseases

8 Unique genes

0.282 Avg. similarity score

Fetal growth restriction Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Mental retardation, autosomal dominant 56 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.

Mental retardation, autosomal dominant 56 Fetal growth restriction Intellectual developmental disorder, autosomal dominant 56 Ovarian steroid cell tumor Epilepsy and intellectual disability Ulnar-mammary syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Fetal growth restriction	4	4	1
Intellectual developmental disorder, autosomal dominant 56	4	4	1
Mental retardation, autosomal dominant 56	4	4	1
Ovarian steroid cell tumor	4	4	6
Epilepsy and intellectual disability	3	3	3
Ulnar-mammary syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
CLTC	5 / 6	Epilepsy and intellectual disability, Fetal growth restriction, Intellectual developmental disorder, autosomal dominant 56, Mental retardation, autosomal dominant 56 and 1 more
TBX3	2 / 6	Ovarian steroid cell tumor, Ulnar-mammary 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 ⇵
Defective DHDDS causes retinitis pigmentosa 59 NUS1, DHDDS	Reactome	2 / 2	1,501×	3.88e-7	1.83e-5 ✓ sig.
Synthesis of Dolichyl-phosphate NUS1, DHDDS	Reactome	2 / 6	500×	5.82e-6	1.86e-4 ✓ sig.
Terpenoid backbone biosynthesis NUS1, DHDDS	KEGG	2 / 23	131×	9.75e-5	1.86e-3 ✓ sig.
Endocrine and other factor-regulated calcium reabsorption CLTC, GNAS	KEGG	2 / 53	56.7×	5.26e-4	6.94e-3 ✓ sig.
Entry of Influenza Virion into Host Cell via Endocytosis CLTC	Reactome	1 / 2	751×	1.33e-3	1.41e-2 ✓ sig.
Telomere C-strand (Lagging Strand) Synthesis POLD1	Reactome	1 / 5	300×	3.33e-3	2.74e-2 ✓ sig.
Processive synthesis on the C-strand of the telomere POLD1	Reactome	1 / 8	188×	5.32e-3	3.80e-2 ✓ sig.
Downregulation of ERBB4 signaling ERBB4	Reactome	1 / 9	167×	5.98e-3	4.10e-2 ✓ sig.
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) POLD1	Reactome	1 / 10	150×	6.64e-3	4.39e-2 ✓ sig.
Processive synthesis on the lagging strand POLD1	Reactome	1 / 10	150×	6.64e-3	4.39e-2 ✓ sig.
PI3K events in ERBB4 signaling ERBB4	Reactome	1 / 10	150×	6.64e-3	4.39e-2 ✓ sig.
Retrograde neurotrophin signalling CLTC	Reactome	1 / 11	136×	7.31e-3	4.67e-2 ✓ sig.
Removal of the Flap Intermediate from the C-strand POLD1	Reactome	1 / 11	136×	7.31e-3	4.67e-2 ✓ sig.
Signaling by ERBB4 ERBB4	Reactome	1 / 11	136×	7.31e-3	4.67e-2 ✓ sig.
Formation of annular gap junctions CLTC	Reactome	1 / 11	136×	7.31e-3	4.67e-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 ⇵
dolichyl diphosphate biosynthetic process NUS1, DHDDS	GO:0006489	2 / 5	934×	1.60e-6	1.27e-4 ✓ sig.
dolichyl monophosphate biosynthetic process NUS1, DHDDS	GO:0043048	2 / 5	934×	1.60e-6	1.27e-4 ✓ sig.
mammary gland development TBX3, ERBB4	GO:0030879	2 / 37	126×	1.06e-4	3.23e-3 ✓ sig.
polyprenol biosynthetic process DHDDS	GO:0016094	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
mesoderm morphogenesis TBX3	GO:0048332	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
negative regulation of cell proliferation involved in heart morphogenesis TBX3	GO:2000137	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
limbic system development TBX3	GO:0021761	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
central nervous system morphogenesis ERBB4	GO:0021551	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
establishment of planar polarity involved in nephron morphogenesis ERBB4	GO:0072046	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
hepatoblast differentiation TBX3	GO:0061017	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
follicle-stimulating hormone secretion TBX3	GO:0046884	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
ureteric peristalsis TBX3	GO:0072105	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
atrioventricular bundle cell differentiation TBX3	GO:0003167	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
specification of animal organ position TBX3	GO:0010159	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
mammary placode formation TBX3	GO:0060596	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Fetal growth restriction	Mental retardation, autosomal dominant 56	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Fetal growth restriction	Intellectual developmental disorder, autosomal dominant 56	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual developmental disorder, autosomal dominant 56	Mental retardation, autosomal dominant 56	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Epilepsy and intellectual disability	Fetal growth restriction	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Epilepsy and intellectual disability	Mental retardation, autosomal dominant 56	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Epilepsy and intellectual disability	Intellectual developmental disorder, autosomal dominant 56	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Fetal growth restriction	Ovarian steroid cell tumor	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Intellectual developmental disorder, autosomal dominant 56	Ovarian steroid cell tumor	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Mental retardation, autosomal dominant 56	Ovarian steroid cell tumor	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Ovarian steroid cell tumor	Ulnar-mammary syndrome	0.143	1	3.87e-4	7.33e-4 ✓ sig.

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