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Cluster 420

6 diseases · 6 shared-gene connections

6 Diseases

77 Unique genes

0.040 Avg. similarity score

Congenital anomalies of the kidney and urinary tract Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Renal hypodysplasia/aplasia 2 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.

Renal hypodysplasia/aplasia 2 Congenital anomalies of the kidney and urinary tract Renal agenesis Renal dysplasia, cystic, susceptibility to Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome Neurodevelopmental disorder with or without urinary tract abnormalities

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Congenital anomalies of the kidney and urinary tract	4	4	67
Renal agenesis	3	3	16
Renal dysplasia, cystic, susceptibility to	2	2	1
Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome	1	1	1
Neurodevelopmental disorder with or without urinary tract abnormalities	1	1	1
Renal hypodysplasia/aplasia 2	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
BICC1	3 / 6	Congenital anomalies of the kidney and urinary tract, Renal agenesis, Renal dysplasia, cystic, susceptibility to
CELSR3	2 / 6	Congenital anomalies of the kidney and urinary tract, Neurodevelopmental disorder with or without urinary tract abnormalities
CTU2	2 / 6	Congenital anomalies of the kidney and urinary tract, Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome
FGF20	2 / 6	Renal agenesis, Renal hypodysplasia/aplasia 2
FRAS1	2 / 6	Congenital anomalies of the kidney and urinary tract, Renal agenesis
GREB1L	2 / 6	Congenital anomalies of the kidney and urinary tract, Renal agenesis
RET	2 / 6	Congenital anomalies of the kidney and urinary tract, Renal agenesis
ROBO1	2 / 6	Congenital anomalies of the kidney and urinary tract, Renal agenesis
TBX18	2 / 6	Congenital anomalies of the kidney and urinary tract, Renal agenesis

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 ⇵
ECM-receptor interaction ITGA8, COL4A1, FRAS1, FREM1, FREM2, NPNT	KEGG	6 / 89	10.5×	2.17e-5	4.95e-4 ✓ sig.
Signaling by ROBO receptors ROBO1, ROBO2, SLIT2	Reactome	3 / 12	39.0×	5.35e-5	1.04e-3 ✓ sig.
Regulation of commissural axon pathfinding by SLIT and ROBO ROBO1, ROBO2	Reactome	2 / 3	104×	1.21e-4	2.00e-3 ✓ sig.
Metabolism of Angiotensinogen to Angiotensins ACE, REN, AGT	Reactome	3 / 17	27.5×	1.62e-4	2.52e-3 ✓ sig.
Role of ABL in ROBO-SLIT signaling ROBO1, SLIT2	Reactome	2 / 4	78.0×	2.41e-4	3.49e-3 ✓ sig.
SLIT2:ROBO1 increases RHOA activity ROBO1, SLIT2	Reactome	2 / 4	78.0×	2.41e-4	3.49e-3 ✓ sig.
Renin-angiotensin system ACE, REN, AGT	KEGG	3 / 23	20.3×	4.09e-4	5.29e-3 ✓ sig.
Hippo signaling pathway ACTG1, BMP4, BMP7, DLG5, GDF6, WNT9B	KEGG	6 / 157	6.0×	5.00e-4	6.19e-3 ✓ sig.
Regulation of expression of SLITs and ROBOs ROBO1, SLIT2	Reactome	2 / 8	39.0×	1.11e-3	1.14e-2 ✓ sig.
Axon guidance BMP7, ROBO1, ROBO2, SLIT2, SRGAP1, LRIG2	KEGG	6 / 183	5.1×	1.12e-3	1.15e-2 ✓ sig.
Molecules associated with elastic fibres ITGA8, BMP4, BMP7	Reactome	3 / 38	12.3×	1.82e-3	1.66e-2 ✓ sig.
FGFR1c ligand binding and activation FGF20, ANOS1	Reactome	2 / 12	26.0×	2.57e-3	2.15e-2 ✓ sig.
Hypertrophic cardiomyopathy ITGA8, ACE, ACTG1, AGT	KEGG	4 / 99	6.3×	3.71e-3	2.79e-2 ✓ sig.
Renin secretion ACE, REN, AGT	KEGG	3 / 69	6.8×	9.80e-3	5.38e-2
Negative regulation of FGFR1 signaling FGF20, ANOS1	Reactome	2 / 26	12.0×	1.19e-2	6.06e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
kidney development GREB1L, ITGA8, ACE, BICC1, BMP4, BMP7, FOXC1, FREM2, GATA3, HNF1B, SALL1, SIX2	GO:0001822	18 / 146	29.9×	4.43e-22	8.60e-19 ✓ sig.
ureteric bud development RET, BMP4, BMP7, FOXC1, ROBO2, SALL1, SLIT2, EYA1, NPNT	GO:0001657	9 / 41	53.3×	6.66e-14	3.68e-11 ✓ sig.
metanephros development GREB1L, ITGA8, BMP4, BMP7, GDF6, ROBO2, SIX2, EYA1	GO:0001656	8 / 38	51.1×	2.53e-12	1.02e-9 ✓ sig.
branching involved in ureteric bud morphogenesis GREB1L, BMP4, PAX2, SALL1, EYA1, NPNT, WNT9B, PBX1	GO:0001658	8 / 45	43.1×	1.09e-11	3.86e-9 ✓ sig.
pulmonary valve morphogenesis BMP4, JAG1, NOTCH2, ROBO1, ROBO2, SLIT2	GO:0003184	6 / 18	80.9×	7.16e-11	2.10e-8 ✓ sig.
nephric duct formation BMP4, GATA3, HNF1B, PAX2	GO:0072179	4 / 4	243×	2.66e-10	6.74e-8 ✓ sig.
mesonephros development BMP4, BMP7, GATA3, PAX2, REN	GO:0001823	5 / 13	93.3×	1.31e-9	2.73e-7 ✓ sig.
aortic valve morphogenesis BMP4, GATA3, JAG1, ROBO1, ROBO2, SLIT2	GO:0003180	6 / 37	39.4×	8.43e-9	1.41e-6 ✓ sig.
mesodermal cell fate specification PAX2, SIX2, TBX6, EYA1	GO:0007501	4 / 7	139×	9.24e-9	1.53e-6 ✓ sig.
anatomical structure morphogenesis FAT4, FOXC1, FRAS1, FREM1, FREM2, GATA3, SIX2, TBX6, EYA1	GO:0009653	9 / 160	13.7×	1.94e-8	2.94e-6 ✓ sig.
positive regulation of transcription by RNA polymerase II ITGA8, BMP4, BMP7, CDC5L, ETV4, FOXC1, GATA3, HNF1B, JAG1, KAT6B, KMT2D, NOTCH2	GO:0045944	20 / 1,208	4.0×	5.91e-8	7.60e-6 ✓ sig.
ureter maturation RET, GATA3, PAX2	GO:0035799	3 / 4	182×	2.68e-7	2.70e-5 ✓ sig.
maintenance of blood vessel diameter homeostasis by renin-angiotensin ACE, REN, AGT	GO:0002034	3 / 5	146×	6.69e-7	5.77e-5 ✓ sig.
cell fate determination GATA3, JAG1, NOTCH2, PAX2	GO:0001709	4 / 18	53.9×	7.80e-7	6.55e-5 ✓ sig.
smooth muscle cell differentiation ITGA8, BMP4, TBX18, NPNT	GO:0051145	4 / 18	53.9×	7.80e-7	6.55e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Congenital anomalies of the kidney and urinary tract	Renal agenesis	0.077	6	4.03e-11	3.90e-10 ✓ sig.
Renal agenesis	Renal dysplasia, cystic, susceptibility to	0.059	1	1.03e-3	1.57e-3 ✓ sig.
Renal agenesis	Renal hypodysplasia/aplasia 2	0.059	1	1.03e-3	1.57e-3 ✓ sig.
Congenital anomalies of the kidney and urinary tract	Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome	0.015	1	4.33e-3	5.28e-3 ✓ sig.
Congenital anomalies of the kidney and urinary tract	Neurodevelopmental disorder with or without urinary tract abnormalities	0.015	1	4.33e-3	5.28e-3 ✓ sig.
Congenital anomalies of the kidney and urinary tract	Renal dysplasia, cystic, susceptibility to	0.015	1	4.33e-3	5.28e-3 ✓ sig.

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