Disease Clusters | GeDiPNet

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Cluster 267

7 diseases · 12 shared-gene connections

7 Diseases

45 Unique genes

0.148 Avg. similarity score

Intellectual developmental disorder expressive speech dysmorphic Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Cerebral atrophy 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.

Cerebral atrophy Intellectual developmental disorder expressive speech dysmorphic Schinzel-Giedion syndrome Bundle branch block Coronary aneurysm Intellectual developmental disorder speech dysmorphic

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Intellectual developmental disorder expressive speech dysmorphic	5	5	1
Schinzel-Giedion syndrome	5	5	1
Bundle branch block	4	4	4
Cerebral atrophy	3	3	7
Coronary aneurysm	3	3	32
Intellectual developmental disorder speech dysmorphic	3	3	5
Dock2 deficiency	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SETBP1	6 / 7	Bundle branch block, Cerebral atrophy, Coronary aneurysm, Intellectual developmental disorder expressive speech dysmorphic and 2 more
DOCK2	2 / 7	Coronary aneurysm, Dock2 deficiency

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 ⇵
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane GJA1, TUBA3C	Reactome	2 / 18	29.7×	2.02e-3	2.30e-2 ✓ sig.
Defective MAN1B1 causes MRT15 MAN1B1	Reactome	1 / 1	267×	3.75e-3	3.58e-2 ✓ sig.
Defective PMM2 causes PMM2-CDG (CDG-1a) PMM2	Reactome	1 / 1	267×	3.75e-3	3.58e-2 ✓ sig.
Regulation of gap junction activity GJA1	Reactome	1 / 3	89.0×	1.12e-2	7.44e-2
Synthesis of GDP-mannose PMM2	Reactome	1 / 3	89.0×	1.12e-2	7.44e-2
SUMOylation of DNA methylation proteins DNMT1	Reactome	1 / 4	66.7×	1.49e-2	8.82e-2
Assembly and cell surface presentation of NMDA receptors GRIN3A	Reactome	1 / 6	44.5×	2.23e-2	1.12e-1
Nef and signal transduction DOCK2	Reactome	1 / 8	33.4×	2.96e-2	1.31e-1
Ca2+ activated K+ channels KCNN2	Reactome	1 / 9	29.7×	3.32e-2	1.40e-1
RNA degradation EXOSC9, DDX6	KEGG	2 / 78	6.8×	3.44e-2	1.42e-1
Formation of annular gap junctions GJA1	Reactome	1 / 11	24.3×	4.05e-2	1.56e-1
Gap junction GJA1, TUBA3C	KEGG	2 / 89	6.0×	4.38e-2	1.63e-1
Gap junction degradation GJA1	Reactome	1 / 12	22.2×	4.41e-2	1.63e-1
Purine salvage DGUOK	Reactome	1 / 13	20.5×	4.77e-2	1.71e-1
mRNA decay by 5' to 3' exoribonuclease DDX6	Reactome	1 / 14	19.1×	5.12e-2	1.77e-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 ⇵
cerebral cortex radially oriented cell migration CCDC141, MDGA1	GO:0021799	2 / 13	63.9×	4.35e-4	8.75e-3 ✓ sig.
prepulse inhibition GRIN3A, MDGA1	GO:0060134	2 / 14	59.3×	5.07e-4	9.77e-3 ✓ sig.
nervous system development UGT8, CAMK1D, MDGA1, NAV2, NRXN3, SOX4, SMARCA2	GO:0007399	7 / 631	4.6×	7.19e-4	1.23e-2 ✓ sig.
cochlea morphogenesis MYO3B, TIFAB	GO:0090103	2 / 28	29.7×	2.06e-3	2.33e-2 ✓ sig.
regulation of granulocyte chemotaxis CAMK1D	GO:0071622	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
regulation of systemic arterial blood pressure by baroreceptor feedback NAV2	GO:0003025	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
glossopharyngeal nerve development NAV2	GO:0021563	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
vagus nerve development NAV2	GO:0021564	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
microtubule-based transport GJA1	GO:0099111	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
protein alpha-1,2-demannosylation MAN1B1	GO:0036508	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
negative regulation of growth rate TMPRSS4	GO:0045967	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
guanosine metabolic process DGUOK	GO:0008617	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
dGTP metabolic process DGUOK	GO:0046070	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
purine deoxyribonucleoside metabolic process DGUOK	GO:0046122	1 / 1	415×	2.41e-3	2.54e-2 ✓ sig.
brain development CCDC141, MACROD2, MDGA1, SOX4	GO:0007420	4 / 244	6.8×	2.78e-3	2.76e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Intellectual developmental disorder expressive speech dysmorphic	Schinzel-Giedion syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Bundle branch block	Intellectual developmental disorder expressive speech dysmorphic	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Bundle branch block	Schinzel-Giedion syndrome	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Intellectual developmental disorder expressive speech dysmorphic	Intellectual developmental disorder speech dysmorphic	0.167	1	3.25e-4	7.70e-4 ✓ sig.
Intellectual developmental disorder speech dysmorphic	Schinzel-Giedion syndrome	0.167	1	3.25e-4	7.70e-4 ✓ sig.
Cerebral atrophy	Intellectual developmental disorder expressive speech dysmorphic	0.125	1	4.55e-4	9.72e-4 ✓ sig.
Cerebral atrophy	Schinzel-Giedion syndrome	0.125	1	4.55e-4	9.72e-4 ✓ sig.
Bundle branch block	Intellectual developmental disorder speech dysmorphic	0.111	1	1.30e-3	2.06e-3 ✓ sig.
Bundle branch block	Cerebral atrophy	0.091	1	1.82e-3	2.68e-3 ✓ sig.
Coronary aneurysm	Intellectual developmental disorder expressive speech dysmorphic	0.030	1	2.08e-3	2.97e-3 ✓ sig.
Coronary aneurysm	Schinzel-Giedion syndrome	0.030	1	2.08e-3	2.97e-3 ✓ sig.
Coronary aneurysm	Dock2 deficiency	0.030	1	2.08e-3	2.97e-3 ✓ sig.

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