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Cluster 473

6 diseases · 11 shared-gene connections

6 Diseases

8 Unique genes

0.283 Avg. similarity score

Dextrocardia Most-connected disease (5 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.

Dextrocardia Congenital heart defects, multiple types, 1, x-linked Congenital heart disease with heterotaxy syndrome Heterotaxy, visceral, 1, x-linked VACTERL association, X-linked Gut malrotation

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Dextrocardia	5	5	7
Congenital heart defects, multiple types, 1, x-linked	4	4	1
Congenital heart disease with heterotaxy syndrome	4	4	2
Heterotaxy, visceral, 1, x-linked	4	4	1
VACTERL association, X-linked	4	4	1
Gut malrotation	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
ZIC3	5 / 6	Congenital heart defects, multiple types, 1, x-linked, Congenital heart disease with heterotaxy syndrome, Dextrocardia, Heterotaxy, visceral, 1, x-linked and 1 more
CFAP53	2 / 6	Dextrocardia, Gut malrotation

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 ⇵
TGF-beta signaling pathway ZFYVE16, NODAL	KEGG	2 / 108	27.8×	2.17e-3	2.02e-2 ✓ sig.
RHO GTPases Activate ROCKs ROCK2	Reactome	1 / 5	300×	3.33e-3	2.74e-2 ✓ sig.
Signaling pathways regulating pluripotency of stem cells ZIC3, NODAL	KEGG	2 / 144	20.9×	3.81e-3	3.02e-2 ✓ sig.
Sema4D induced cell migration and growth-cone collapse ROCK2	Reactome	1 / 11	136×	7.31e-3	4.67e-2 ✓ sig.
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation ZIC3	Reactome	1 / 13	115×	8.63e-3	5.19e-2
Transcriptional regulation of pluripotent stem cells ZIC3	Reactome	1 / 17	88.3×	1.13e-2	6.12e-2
Signaling by BMP ZFYVE16	Reactome	1 / 28	53.6×	1.85e-2	8.20e-2
EPHB-mediated forward signaling ROCK2	Reactome	1 / 39	38.5×	2.57e-2	9.90e-2
RNA Polymerase II Transcription Elongation SUPT16H	Reactome	1 / 59	25.4×	3.86e-2	1.25e-1
Formation of RNA Pol II elongation complex SUPT16H	Reactome	1 / 61	24.6×	3.99e-2	1.27e-1
VEGFA-VEGFR2 Pathway ROCK2	Reactome	1 / 62	24.2×	4.06e-2	1.28e-1
TP53 Regulates Transcription of DNA Repair Genes SUPT16H	Reactome	1 / 65	23.1×	4.25e-2	1.32e-1
G alpha (12/13) signalling events ROCK2	Reactome	1 / 80	18.8×	5.21e-2	1.48e-1
RNA Polymerase II Pre-transcription Events SUPT16H	Reactome	1 / 84	17.9×	5.46e-2	1.52e-1
Regulation of TP53 Activity through Phosphorylation SUPT16H	Reactome	1 / 92	16.3×	5.97e-2	1.60e-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 ⇵
determination of left/right symmetry CFAP53, ZIC3, NODAL	GO:0007368	3 / 83	84.4×	4.66e-6	3.00e-4 ✓ sig.
primitive streak formation ZIC3, NODAL	GO:0090009	2 / 11	425×	8.80e-6	4.92e-4 ✓ sig.
embryonic pattern specification ZIC3, NODAL	GO:0009880	2 / 32	146×	7.90e-5	2.60e-3 ✓ sig.
gastrulation ZIC3, NODAL	GO:0007369	2 / 38	123×	1.12e-4	3.35e-3 ✓ sig.
stem cell population maintenance ZIC3, NODAL	GO:0019827	2 / 47	99.4×	1.72e-4	4.55e-3 ✓ sig.
heart looping ZIC3, NODAL	GO:0001947	2 / 64	73.0×	3.19e-4	7.04e-3 ✓ sig.
central nervous system segmentation ZIC3	GO:0035283	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
positive regulation of connective tissue growth factor production ROCK2	GO:0032723	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
polarity specification of proximal/distal axis NODAL	GO:0010085	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
floor plate morphogenesis NODAL	GO:0033505	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
axial mesodermal cell fate specification NODAL	GO:0048327	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
epiblast cell-extraembryonic ectoderm cell signaling NODAL	GO:0060802	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
cell differentiation CFAP53, MYRF, ZIC3, NODAL	GO:0030154	4 / 1,051	8.9×	5.80e-4	1.05e-2 ✓ sig.
trophectodermal cellular morphogenesis NODAL	GO:0001831	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
negative regulation of protein localization to lysosome ROCK2	GO:0150033	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Congenital heart defects, multiple types, 1, x-linked	VACTERL association, X-linked	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Congenital heart defects, multiple types, 1, x-linked	Heterotaxy, visceral, 1, x-linked	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Heterotaxy, visceral, 1, x-linked	VACTERL association, X-linked	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Congenital heart defects, multiple types, 1, x-linked	Congenital heart disease with heterotaxy syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Congenital heart disease with heterotaxy syndrome	VACTERL association, X-linked	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Congenital heart disease with heterotaxy syndrome	Heterotaxy, visceral, 1, x-linked	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Congenital heart defects, multiple types, 1, x-linked	Dextrocardia	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Dextrocardia	VACTERL association, X-linked	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Dextrocardia	Heterotaxy, visceral, 1, x-linked	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Dextrocardia	Gut malrotation	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Congenital heart disease with heterotaxy syndrome	Dextrocardia	0.111	1	9.04e-4	1.41e-3 ✓ sig.

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