Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 161

9 diseases · 19 shared-gene connections
9 Diseases
34 Unique genes
0.273 Avg. similarity score
Congenital digestive system anomaly Most-connected disease (6 links)
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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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Congenital digestive system anomaly 6 6 1
Medullary thyroid cancer 6 6 1
multiple endocrine neoplasia type 2B 6 6 1
Congenital hypoplasia of kidney 5 5 8
multiple endocrine neoplasia type 2A 5 5 1
Medullary carcinoma 4 4 2
Papillary thyroid cancer 3 3 14
Renal agenesis 2 2 15
renal dysplasia, cystic, susceptibility to 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
RET 8 / 9 Congenital digestive system anomaly, Congenital hypoplasia of kidney, Medullary carcinoma, Medullary thyroid cancer and 4 more
BICC1 2 / 9 Renal agenesis, renal dysplasia, cystic, susceptibility to
EYA1 2 / 9 Congenital hypoplasia of kidney, Renal agenesis
WNT9B 2 / 9 Congenital hypoplasia of kidney, 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 ⇵
Thyroid cancer
RET, BRAF, CCDC6
 KEGG 3 / 37 28.6× 1.51e-4 3.12e-3 ✓ sig.
ECM-receptor interaction
ITGA8, FRAS1, NPNT
 KEGG 3 / 89 11.9× 1.99e-3 2.28e-2 ✓ sig.
RAF activation
BRAF, PPP2R5C
 Reactome 2 / 32 22.1× 3.66e-3 3.54e-2 ✓ sig.
RAF/MAP kinase cascade
FGF20, RET, GFRA1
 Reactome 3 / 124 8.5× 5.09e-3 4.43e-2 ✓ sig.
Negative regulation of MAPK pathway
BRAF, PPP2R5C
 Reactome 2 / 38 18.6× 5.13e-3 4.45e-2 ✓ sig.
RET signaling
RET, GFRA1
 Reactome 2 / 40 17.7× 5.67e-3 4.76e-2 ✓ sig.
Breast cancer
FGF20, WNT9B, BRAF
 KEGG 3 / 148 7.2× 8.30e-3 6.10e-2
Regulation of thyroid hormone activity
DIO3
 Reactome 1 / 3 118× 8.47e-3 6.20e-2
Regulation of commissural axon pathfinding by SLIT and ROBO
ROBO1
 Reactome 1 / 3 118× 8.47e-3 6.20e-2
Gastric cancer
FGF20, WNT9B, BRAF
 KEGG 3 / 150 7.1× 8.61e-3 6.27e-2
Regulation of PTEN gene transcription
SNAI1, SNAI2
 Reactome 2 / 53 13.3× 9.79e-3 6.78e-2
Biosynthesis of D-series resolvins
HPGD
 Reactome 1 / 4 88.3× 1.13e-2 7.36e-2
Role of ABL in ROBO-SLIT signaling
ROBO1
 Reactome 1 / 4 88.3× 1.13e-2 7.36e-2
SLIT2:ROBO1 increases RHOA activity
ROBO1
 Reactome 1 / 4 88.3× 1.13e-2 7.36e-2
Synthesis of Lipoxins (LX)
HPGD
 Reactome 1 / 5 70.6× 1.41e-2 8.38e-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 ⇵
branching involved in ureteric bud morphogenesis
GREB1L, EYA1, NPNT, WNT9B, PAX2
 GO:0001658 5 / 45 61.1× 1.70e-8 2.72e-6 ✓ sig.
cochlea morphogenesis
TBX18, EYA1, PAX2, ZEB1
 GO:0090103 4 / 28 78.5× 1.81e-7 1.99e-5 ✓ sig.
kidney development
GREB1L, ITGA8, HPGD, BICC1, GFRA1, WNT9B
 GO:0001822 6 / 146 22.6× 2.30e-7 2.44e-5 ✓ sig.
smooth muscle cell differentiation
ITGA8, TBX18, NPNT
 GO:0051145 3 / 18 91.6× 4.41e-6 2.71e-4 ✓ sig.
roof of mouth development
FRAS1, WNT9B, SNAI1, SNAI2
 GO:0060021 4 / 70 31.4× 7.69e-6 4.25e-4 ✓ sig.
positive regulation of metanephric glomerulus development
RET, PAX2
 GO:0072300 2 / 3 366× 9.63e-6 5.06e-4 ✓ sig.
cell differentiation
FGF20, ITGA8, EYA1, NPNT, ROBO1, PAX2, PRMT7, BRAF, NKX2-1, ZEB1
 GO:0030154 10 / 1,051 5.2× 1.15e-5 5.81e-4 ✓ sig.
ureter maturation
RET, PAX2
 GO:0035799 2 / 4 275× 1.92e-5 8.71e-4 ✓ sig.
negative regulation of vitamin D biosynthetic process
SNAI1, SNAI2
 GO:0010957 2 / 4 275× 1.92e-5 8.71e-4 ✓ sig.
positive regulation of axonogenesis
ROBO1, BRAF, ZEB2
 GO:0050772 3 / 30 55.0× 2.16e-5 9.55e-4 ✓ sig.
positive regulation of transforming growth factor beta receptor signaling pathway
ITGA8, NPNT, ZEB2
 GO:0030511 3 / 34 48.5× 3.17e-5 1.27e-3 ✓ sig.
animal organ development
FRAS1, PAX2, NKX2-1, ZEB1
 GO:0048513 4 / 102 21.6× 3.42e-5 1.35e-3 ✓ sig.
aortic valve morphogenesis
ROBO1, SNAI1, SNAI2
 GO:0003180 3 / 37 44.6× 4.10e-5 1.55e-3 ✓ sig.
metanephros development
GREB1L, ITGA8, EYA1
 GO:0001656 3 / 38 43.4× 4.44e-5 1.65e-3 ✓ sig.
cartilage morphogenesis
SNAI1, SNAI2
 GO:0060536 2 / 6 183× 4.80e-5 1.74e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital hypoplasia of kidney Renal agenesis 0.143 3 4.18e-8 3.30e-7 ✓ sig.
Congenital digestive system anomaly multiple endocrine neoplasia type 2B 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital digestive system anomaly multiple endocrine neoplasia type 2A 0.500 1 6.49e-5 2.34e-4 ✓ sig.
multiple endocrine neoplasia type 2A multiple endocrine neoplasia type 2B 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Medullary thyroid cancer multiple endocrine neoplasia type 2A 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Medullary thyroid cancer multiple endocrine neoplasia type 2B 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital digestive system anomaly Medullary thyroid cancer 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Medullary carcinoma multiple endocrine neoplasia type 2A 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Medullary carcinoma multiple endocrine neoplasia type 2B 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Medullary carcinoma Medullary thyroid cancer 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital digestive system anomaly Medullary carcinoma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital hypoplasia of kidney Medullary thyroid cancer 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Congenital digestive system anomaly Congenital hypoplasia of kidney 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Congenital hypoplasia of kidney multiple endocrine neoplasia type 2A 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Congenital hypoplasia of kidney multiple endocrine neoplasia type 2B 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Congenital digestive system anomaly Papillary thyroid cancer 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Medullary thyroid cancer Papillary thyroid cancer 0.067 1 9.09e-4 1.56e-3 ✓ sig.
multiple endocrine neoplasia type 2B Papillary thyroid cancer 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Renal agenesis renal dysplasia, cystic, susceptibility to 0.063 1 9.74e-4 1.64e-3 ✓ sig.