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 232

9 diseases · 17 shared-gene connections
9 Diseases
23 Unique genes
0.295 Avg. similarity score
Holoprosencephaly 3 Most-connected disease (5 links)
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Disease Searched: Microphthalmia with coloboma 5 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 ⇵
Holoprosencephaly 3 5 5 1
Microphthalmia with coloboma 5 5 5 1
Partial agenesis of corpus callosum 5 5 3
Preaxial polydactyly with upper back hypertrichosis 5 5 1
Schizencephaly 5 5 5
Solitary median maxillary central incisor 5 5 1
Eye abnormalities 2 2 17
Frank-ter haar syndrome 1 1 1
Neurodevelopmental disorder with severe motor impairment and absent language 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
SHH 7 / 9 Eye abnormalities, Holoprosencephaly 3, Microphthalmia with coloboma 5, Partial agenesis of corpus callosum and 3 more
COL4A1 2 / 9 Eye abnormalities, Schizencephaly
SH3PXD2B 2 / 9 Eye abnormalities, Frank-ter haar syndrome
TAF8 2 / 9 Neurodevelopmental disorder with severe motor impairment and absent language, Partial agenesis of corpus callosum
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 ⇵
Pathways in cancer
SHH, APAF1, APC, COL4A1, JAG1, TGFB2, TGFBR2, EGLN3, DCC
 KEGG 9 / 533 8.8× 2.92e-7 1.35e-5 ✓ sig.
Hippo signaling pathway
APC, BMPR1A, BMPR1B, TGFB2, TGFBR2
 KEGG 5 / 157 16.6× 9.96e-6 2.70e-4 ✓ sig.
Colorectal cancer
APC, TGFB2, TGFBR2, DCC
 KEGG 4 / 87 24.0× 2.05e-5 4.88e-4 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
COL4A1, TGFB2, TGFBR2, AGER
 KEGG 4 / 101 20.7× 3.69e-5 7.89e-4 ✓ sig.
TGF-beta signaling pathway
BMPR1A, BMPR1B, TGFB2, TGFBR2
 KEGG 4 / 108 19.3× 4.80e-5 9.81e-4 ✓ sig.
Gastric cancer
SHH, APC, TGFB2, TGFBR2
 KEGG 4 / 150 13.9× 1.72e-4 2.72e-3 ✓ sig.
Signaling by BMP
BMPR1A, BMPR1B
 Reactome 2 / 28 37.3× 1.29e-3 1.31e-2 ✓ sig.
APC truncation mutants are not K63 polyubiquitinated
APC
 Reactome 1 / 1 522× 1.92e-3 1.76e-2 ✓ sig.
Cytokine-cytokine receptor interaction
BMPR1A, BMPR1B, TGFB2, TGFBR2
 KEGG 4 / 298 7.0× 2.27e-3 1.99e-2 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
APC, BMPR1A, BMPR1B
 KEGG 3 / 144 10.9× 2.51e-3 2.15e-2 ✓ sig.
Hepatitis B
APAF1, TGFB2, TGFBR2
 KEGG 3 / 163 9.6× 3.56e-3 2.76e-2 ✓ sig.
TGFBR2 MSI Frameshift Mutants in Cancer
TGFBR2
 Reactome 1 / 2 261× 3.83e-3 2.90e-2 ✓ sig.
Hepatocellular carcinoma
APC, TGFB2, TGFBR2
 KEGG 3 / 170 9.2× 4.01e-3 3.00e-2 ✓ sig.
Axon guidance
SHH, BMPR1B, DCC
 KEGG 3 / 183 8.6× 4.92e-3 3.47e-2 ✓ sig.
Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors
TFAP2A
 Reactome 1 / 3 174× 5.73e-3 3.84e-2 ✓ sig.

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
regulation of cell population proliferation
SHH, JAG1, TFAP2A, TGFB2, TGFBR2, SIX3
 GO:0042127 6 / 201 24.3× 1.25e-7 1.51e-5 ✓ sig.
eye development
BMPR1B, SH3PXD2B, TGFB2, SIX3
 GO:0001654 4 / 49 66.3× 3.56e-7 3.61e-5 ✓ sig.
cardiac right ventricle morphogenesis
BMPR1A, JAG1, TGFB2
 GO:0003215 3 / 13 187× 4.62e-7 4.50e-5 ✓ sig.
heart development
SHH, BMPR1A, NDST1, SH3PXD2B, TGFB2, TGFBR2
 GO:0007507 6 / 273 17.9× 7.54e-7 6.73e-5 ✓ sig.
optic vesicle morphogenesis
TFAP2A, SIX3
 GO:0003404 2 / 2 812× 1.45e-6 1.15e-4 ✓ sig.
roof of mouth development
SHH, BMPR1A, TFAP2A, TGFBR2
 GO:0060021 4 / 70 46.4× 1.51e-6 1.19e-4 ✓ sig.
endocardial cushion morphogenesis
APC, BMPR1A, TGFB2
 GO:0003203 3 / 19 128× 1.56e-6 1.22e-4 ✓ sig.
camera-type eye development
SHH, BMPR1B, JAG1, SIX3
 GO:0043010 4 / 74 43.9× 1.89e-6 1.42e-4 ✓ sig.
forebrain development
SHH, APAF1, NDST1, EMX2
 GO:0030900 4 / 76 42.8× 2.11e-6 1.55e-4 ✓ sig.
cellular response to growth factor stimulus
BMPR1A, BMPR1B, TGFB2, TGFBR2
 GO:0071363 4 / 76 42.8× 2.11e-6 1.55e-4 ✓ sig.
positive regulation of mesenchymal cell proliferation
SHH, BMPR1A, TGFBR2
 GO:0002053 3 / 26 93.7× 4.16e-6 2.66e-4 ✓ sig.
outflow tract septum morphogenesis
BMPR1A, TGFB2, TGFBR2
 GO:0003148 3 / 28 87.1× 5.23e-6 3.20e-4 ✓ sig.
embryonic forelimb morphogenesis
SHH, IFT122, TFAP2A
 GO:0035115 3 / 33 73.9× 8.67e-6 4.77e-4 ✓ sig.
cell surface receptor protein serine/threonine kinase signaling pathway
BMPR1A, BMPR1B, TGFBR2
 GO:0007178 3 / 33 73.9× 8.67e-6 4.77e-4 ✓ sig.
branching involved in blood vessel morphogenesis
SHH, COL4A1, TGFBR2
 GO:0001569 3 / 33 73.9× 8.67e-6 4.77e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Eye abnormalities Schizencephaly 0.095 2 1.13e-5 6.10e-5 ✓ sig.
Holoprosencephaly 3 Preaxial polydactyly with upper back hypertrichosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Holoprosencephaly 3 Solitary median maxillary central incisor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Holoprosencephaly 3 Microphthalmia with coloboma 5 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Microphthalmia with coloboma 5 Preaxial polydactyly with upper back hypertrichosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Microphthalmia with coloboma 5 Solitary median maxillary central incisor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Preaxial polydactyly with upper back hypertrichosis Solitary median maxillary central incisor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Partial agenesis of corpus callosum Preaxial polydactyly with upper back hypertrichosis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Holoprosencephaly 3 Partial agenesis of corpus callosum 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Partial agenesis of corpus callosum Solitary median maxillary central incisor 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Microphthalmia with coloboma 5 Partial agenesis of corpus callosum 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Microphthalmia with coloboma 5 Schizencephaly 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Schizencephaly Solitary median maxillary central incisor 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Holoprosencephaly 3 Schizencephaly 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Preaxial polydactyly with upper back hypertrichosis Schizencephaly 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Neurodevelopmental disorder with severe motor impairment and absent language Partial agenesis of corpus callosum 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Eye abnormalities Frank-ter haar syndrome 0.056 1 1.10e-3 1.65e-3 ✓ sig.