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 36

17 diseases · 41 shared-gene connections
17 Diseases
37 Unique genes
0.231 Avg. similarity score
Branchial arch abnormalities syndrome Most-connected disease (11 links)
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Disease Searched: Liver cavernous hemangioma 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 ⇵
Branchial arch abnormalities syndrome 11 11 1
Branchial cleft anomalies 11 11 1
Multiple malformations syndrome (bcahh) 11 11 1
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome 9 9 1
Liver cavernous hemangioma 5 5 3
Minor salivary gland adenocarcinoma 5 5 5
Vissers-bodmer syndrome 5 5 3
Congenital small ears 4 4 5
Hydatidiform mole 4 4 12
Intraocular medulloepithelioma 4 4 4
Spinal cord ependymoma 4 4 7
Vein of galen aneurysm 4 4 6
Agammaglobulinemia 6, autosomal recessive 1 1 1
Deafness, autosomal recessive 29 1 1 1
Hereditary neutrophilia 1 1 1
Holoprosencephaly 12 with or without pancreatic agenesis 1 1 1
Partial hydatidiform mole 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
KMT2D 12 / 17 Branchial arch abnormalities syndrome, Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome, Branchial cleft anomalies, Congenital small ears and 8 more
CD79B 2 / 17 Agammaglobulinemia 6, autosomal recessive, Minor salivary gland adenocarcinoma
CLDN14 2 / 17 Deafness, autosomal recessive 29, Vein of galen aneurysm
CNOT1 2 / 17 Holoprosencephaly 12 with or without pancreatic agenesis, Vissers-bodmer syndrome
CSF3R 2 / 17 Hereditary neutrophilia, Liver cavernous hemangioma
KHDC3L 2 / 17 Hydatidiform mole, Partial hydatidiform mole
NLRP7 2 / 17 Hydatidiform mole, Partial hydatidiform mole
TP53 2 / 17 Hydatidiform mole, Minor salivary gland adenocarcinoma
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 ⇵
Breast cancer
TP53, BRCA2, NOTCH2, APC, HRAS
 KEGG 5 / 148 11.0× 8.42e-5 1.66e-3 ✓ sig.
MicroRNAs in cancer
TP53, IKBKB, NOTCH2, APC, HRAS, DICER1
 KEGG 6 / 311 6.3× 3.39e-4 4.95e-3 ✓ sig.
Neurotrophin signaling pathway
TP53, MAP3K1, IKBKB, HRAS
 KEGG 4 / 120 10.8× 4.85e-4 6.53e-3 ✓ sig.
Endometrial cancer
TP53, APC, HRAS
 KEGG 3 / 59 16.5× 7.77e-4 9.33e-3 ✓ sig.
Apoptosis
LMNA, TP53, IKBKB, HRAS
 KEGG 4 / 137 9.5× 7.99e-4 9.55e-3 ✓ sig.
Pathways in cancer
TP53, CSF3R, BRCA2, IKBKB, NOTCH2, APC, HRAS
 KEGG 7 / 533 4.3× 1.05e-3 1.18e-2 ✓ sig.
Signaling by BRAF and RAF fusions
LMNA, AKAP9, HRAS
 Reactome 3 / 67 14.5× 1.13e-3 1.24e-2 ✓ sig.
Hepatitis C
CLDN14, TP53, IKBKB, HRAS
 KEGG 4 / 159 8.2× 1.39e-3 1.45e-2 ✓ sig.
Hepatitis B
TP53, MAP3K1, IKBKB, HRAS
 KEGG 4 / 163 8.0× 1.52e-3 1.56e-2 ✓ sig.
Pancreatic cancer
TP53, BRCA2, IKBKB
 KEGG 3 / 77 12.6× 1.68e-3 1.68e-2 ✓ sig.
Chronic myeloid leukemia
TP53, IKBKB, HRAS
 KEGG 3 / 77 12.6× 1.68e-3 1.68e-2 ✓ sig.
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
CNOT1, TP53
 Reactome 2 / 20 32.5× 1.69e-3 1.69e-2 ✓ sig.
Hepatocellular carcinoma
SMARCA2, TP53, APC, HRAS
 KEGG 4 / 170 7.6× 1.78e-3 1.75e-2 ✓ sig.
Regulation of TP53 Activity through Acetylation
KAT6A, TP53
 Reactome 2 / 23 28.2× 2.24e-3 2.07e-2 ✓ sig.
Colorectal cancer
TP53, APC, HRAS
 KEGG 3 / 87 11.2× 2.39e-3 2.17e-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 ⇵
cellular senescence
LMNA, KAT6A, TP53, BRCA2, HRAS
 GO:0090398 5 / 57 44.3× 8.93e-8 1.15e-5 ✓ sig.
regulation of hemopoiesis
KAT6A, KAT6B, NOTCH2
 GO:1903706 3 / 16 94.7× 3.93e-6 2.61e-4 ✓ sig.
cardiac septum morphogenesis
BMP5, TP53, NOTCH2
 GO:0060411 3 / 16 94.7× 3.93e-6 2.61e-4 ✓ sig.
negative regulation of cell population proliferation
BMP5, LMNA, SMARCA2, TP53, NF2, APC, HRAS
 GO:0008285 7 / 444 8.0× 2.27e-5 1.02e-3 ✓ sig.
regulation of developmental process
KAT6A, KAT6B, NOTCH2
 GO:0050793 3 / 32 47.3× 3.41e-5 1.38e-3 ✓ sig.
nucleotide-excision repair
TP53, ERCC5, BRCA2
 GO:0006289 3 / 42 36.1× 7.78e-5 2.57e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
KMT2D, BMP5, HOXA2, SMARCA2, TP53, PRKD1, KAT6B, IKBKB, NOTCH2, HRAS
 GO:0045944 10 / 1,208 4.2× 8.56e-5 2.75e-3 ✓ sig.
negative regulation of Schwann cell proliferation
NF2, DICER1
 GO:0010626 2 / 8 126× 1.06e-4 3.23e-3 ✓ sig.
chromosome organization
KAT6A, TP53, BRCA2
 GO:0051276 3 / 51 29.7× 1.39e-4 3.92e-3 ✓ sig.
response to UV-C
ERCC5, BRCA2
 GO:0010225 2 / 10 101× 1.70e-4 4.51e-3 ✓ sig.
regulation of protein localization to nucleus
LMNA, NF2
 GO:1900180 2 / 10 101× 1.70e-4 4.51e-3 ✓ sig.
pattern specification process
BMP5, HOXA2, APC
 GO:0007389 3 / 60 25.3× 2.26e-4 5.54e-3 ✓ sig.
heterochromatin formation
KMT2D, LMNA, SMARCA2
 GO:0031507 3 / 70 21.6× 3.57e-4 7.59e-3 ✓ sig.
positive regulation of dendrite development
KHDC3L, BMP5
 GO:1900006 2 / 16 63.1× 4.50e-4 8.85e-3 ✓ sig.
positive regulation of cell population proliferation
KMT2D, BMP5, SMARCA2, CSF3R, NOTCH2, HRAS
 GO:0008284 6 / 532 5.7× 5.68e-4 1.03e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hydatidiform mole Partial hydatidiform mole 0.167 2 4.59e-7 2.93e-6 ✓ sig.
Branchial arch abnormalities syndrome Branchial cleft anomalies 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Branchial cleft anomalies Multiple malformations syndrome (bcahh) 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Multiple malformations syndrome (bcahh) 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Branchial cleft anomalies 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Branchial arch abnormalities syndrome Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Branchial arch abnormalities syndrome Multiple malformations syndrome (bcahh) 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Branchial arch abnormalities syndrome Vissers-bodmer syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Liver cavernous hemangioma Multiple malformations syndrome (bcahh) 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Multiple malformations syndrome (bcahh) Vissers-bodmer syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Holoprosencephaly 12 with or without pancreatic agenesis Vissers-bodmer syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Hereditary neutrophilia Liver cavernous hemangioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Branchial arch abnormalities syndrome Liver cavernous hemangioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Branchial cleft anomalies Liver cavernous hemangioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Branchial cleft anomalies Vissers-bodmer syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Liver cavernous hemangioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Vissers-bodmer syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Minor salivary gland adenocarcinoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Minor salivary gland adenocarcinoma Multiple malformations syndrome (bcahh) 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Branchial cleft anomalies Minor salivary gland adenocarcinoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Branchial arch abnormalities syndrome Minor salivary gland adenocarcinoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Intraocular medulloepithelioma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Intraocular medulloepithelioma Multiple malformations syndrome (bcahh) 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Branchial cleft anomalies Intraocular medulloepithelioma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Branchial arch abnormalities syndrome Intraocular medulloepithelioma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Agammaglobulinemia 6, autosomal recessive Minor salivary gland adenocarcinoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Congenital small ears 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital small ears Multiple malformations syndrome (bcahh) 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Branchial cleft anomalies Congenital small ears 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Branchial arch abnormalities syndrome Congenital small ears 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Branchial arch abnormalities syndrome Vein of galen aneurysm 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Branchial cleft anomalies Vein of galen aneurysm 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Multiple malformations syndrome (bcahh) Vein of galen aneurysm 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Deafness, autosomal recessive 29 Vein of galen aneurysm 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Branchial arch abnormalities syndrome Spinal cord ependymoma 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Branchial cleft anomalies Spinal cord ependymoma 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Multiple malformations syndrome (bcahh) Spinal cord ependymoma 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Spinal cord ependymoma 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Hydatidiform mole Multiple malformations syndrome (bcahh) 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Branchial cleft anomalies Hydatidiform mole 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Branchial arch abnormalities syndrome Hydatidiform mole 0.083 1 7.10e-4 1.17e-3 ✓ sig.