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Cluster 159

9 diseases · 15 shared-gene connections

9 Diseases

16 Unique genes

0.220 Avg. similarity score

Anodontia Most-connected disease (7 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Severe neonatal spondylometaphyseal dysplasia 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.

Severe neonatal spondylometaphyseal dysplasia Anodontia Wolf-hirschhorn syndrome Tooth and nail syndrome Witkop syndrome tooth agenesis, selective, 1

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Anodontia	7	7	4
Wolf-hirschhorn syndrome	5	5	7
Tooth and nail syndrome	4	4	1
Witkop syndrome	4	4	1
tooth agenesis, selective, 1	4	4	1
Severe neonatal spondylometaphyseal dysplasia	2	2	1
Shwachman-diamond syndrome	2	2	7
Early-onset epilepsy-intellectual disability-brain anomalies syndrome	1	1	1
craniofacial dysplasia - osteopenia syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
MSX1	5 / 9	Anodontia, tooth agenesis, selective, 1, Tooth and nail syndrome, Witkop syndrome and 1 more
SBDS	3 / 9	Anodontia, Severe neonatal spondylometaphyseal dysplasia, Shwachman-diamond syndrome
IRX5	2 / 9	Anodontia, craniofacial dysplasia - osteopenia syndrome
PIGG	2 / 9	Early-onset epilepsy-intellectual disability-brain anomalies syndrome, Wolf-hirschhorn 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 ⇵
Protein export SRP54, SRPRA, SRP19	KEGG	3 / 31	72.6×	8.52e-6	3.12e-4 ✓ sig.
Ribosome biogenesis in eukaryotes SBDS, EFL1, EIF6	KEGG	3 / 125	18.0×	5.58e-4	9.01e-3 ✓ sig.
SRP-dependent cotranslational protein targeting to membrane SRP54, SRP19	Reactome	2 / 93	16.1×	6.63e-3	5.47e-2
FGFRL1 modulation of FGFR1 signaling FGFRL1	Reactome	1 / 13	57.7×	1.72e-2	9.84e-2
Synthesis of glycosylphosphatidylinositol (GPI) PIGG	Reactome	1 / 17	44.2×	2.24e-2	1.14e-1
Formation of HIV-1 elongation complex containing HIV-1 Tat NELFA	Reactome	1 / 23	32.6×	3.02e-2	1.35e-1
Glycosylphosphatidylinositol (GPI)-anchor biosynthesis PIGG	KEGG	1 / 30	25.0×	3.93e-2	1.55e-1
Formation of the Early Elongation Complex NELFA	Reactome	1 / 33	22.7×	4.31e-2	1.63e-1
Molecules associated with elastic fibres LTBP3	Reactome	1 / 38	19.8×	4.95e-2	1.76e-1
XBP1(S) activates chaperone genes SRPRA	Reactome	1 / 50	15.0×	6.46e-2	2.02e-1
RNA Polymerase II Transcription Elongation NELFA	Reactome	1 / 59	12.7×	7.58e-2	2.20e-1
Formation of RNA Pol II elongation complex NELFA	Reactome	1 / 61	12.3×	7.83e-2	2.24e-1
Lysine degradation NSD2	KEGG	1 / 63	11.9×	8.08e-2	2.28e-1
Viral life cycle - HIV-1 NELFA	KEGG	1 / 64	11.7×	8.20e-2	2.30e-1
TP53 Regulates Transcription of DNA Repair Genes NELFA	Reactome	1 / 65	11.5×	8.32e-2	2.31e-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 ⇵
cytosolic ribosome assembly SBDS, EFL1, EIF6	GO:0042256	3 / 5	701×	5.14e-9	9.48e-7 ✓ sig.
SRP-dependent cotranslational protein targeting to membrane SRP54, SRPRA, SRP19	GO:0006614	3 / 10	350×	6.16e-8	8.14e-6 ✓ sig.
SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition SRP54, SRPRA, SRP19	GO:0006617	3 / 14	250×	1.86e-7	2.10e-5 ✓ sig.
cotranslational protein targeting to membrane SRPRA, SRP19	GO:0006613	2 / 10	234×	3.08e-5	1.29e-3 ✓ sig.
protein targeting to ER SRP54, SRPRA	GO:0045047	2 / 15	156×	7.17e-5	2.44e-3 ✓ sig.
ribosome biogenesis SBDS, EFL1, EIF6	GO:0042254	3 / 122	28.7×	1.43e-4	4.07e-3 ✓ sig.
bone morphogenesis LTBP3, MSX1	GO:0060349	2 / 32	73.0×	3.36e-4	7.49e-3 ✓ sig.
negative regulation of odontoblast differentiation MSX1	GO:1901330	1 / 1	1,168×	8.56e-4	1.41e-2 ✓ sig.
assembly of large subunit precursor of preribosome EIF6	GO:1902626	1 / 1	1,168×	8.56e-4	1.41e-2 ✓ sig.
bone mineralization LTBP3, SBDS	GO:0030282	2 / 56	41.7×	1.03e-3	1.59e-2 ✓ sig.
mitotic spindle organization SBDS, NUF2	GO:0007052	2 / 58	40.3×	1.10e-3	1.66e-2 ✓ sig.
atrial septum secundum morphogenesis NSD2	GO:0003290	1 / 2	584×	1.71e-3	2.14e-2 ✓ sig.
cell surface receptor signaling pathway involved in heart development MSX1	GO:0061311	1 / 2	584×	1.71e-3	2.14e-2 ✓ sig.
positive regulation of mesenchymal cell apoptotic process MSX1	GO:2001055	1 / 3	389×	2.57e-3	2.69e-2 ✓ sig.
negative regulation of striated muscle cell differentiation MSX1	GO:0051154	1 / 3	389×	2.57e-3	2.69e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
tooth agenesis, selective, 1	Tooth and nail syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
tooth agenesis, selective, 1	Witkop syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Tooth and nail syndrome	Witkop syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Anodontia	Severe neonatal spondylometaphyseal dysplasia	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Anodontia	craniofacial dysplasia - osteopenia syndrome	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Anodontia	Tooth and nail syndrome	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Anodontia	Witkop syndrome	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Anodontia	tooth agenesis, selective, 1	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Early-onset epilepsy-intellectual disability-brain anomalies syndrome	Wolf-hirschhorn syndrome	0.125	1	4.55e-4	9.73e-4 ✓ sig.
Severe neonatal spondylometaphyseal dysplasia	Shwachman-diamond syndrome	0.125	1	4.55e-4	9.73e-4 ✓ sig.
tooth agenesis, selective, 1	Wolf-hirschhorn syndrome	0.125	1	4.55e-4	9.73e-4 ✓ sig.
Tooth and nail syndrome	Wolf-hirschhorn syndrome	0.125	1	4.55e-4	9.73e-4 ✓ sig.
Witkop syndrome	Wolf-hirschhorn syndrome	0.125	1	4.55e-4	9.73e-4 ✓ sig.
Anodontia	Shwachman-diamond syndrome	0.091	1	1.82e-3	2.68e-3 ✓ sig.
Anodontia	Wolf-hirschhorn syndrome	0.091	1	1.82e-3	2.68e-3 ✓ sig.

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