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 110

11 diseases · 27 shared-gene connections
11 Diseases
76 Unique genes
0.288 Avg. similarity score
Microform holoprosencephaly Most-connected disease (8 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 ⇵
Microform holoprosencephaly 8 8 16
Syntelencephaly 8 8 15
Holoprosencephaly 7 7 29
Septopreoptic holoprosencephaly 7 7 15
Semilobar holoprosencephaly 6 6 18
neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures 5 5 1
Congenital heart malformation 4 4 5
Gastrointestinal stromal tumor 4 4 47
22q11 deletion syndrome 3 3 1
ciliary dyskinesia, primary, 46 1 1 1
holoprosencephaly-hypokinesia-congenital contractures syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CDON 6 / 11 Gastrointestinal stromal tumor, Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly and 2 more
DISP1 6 / 11 Gastrointestinal stromal tumor, Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly and 2 more
DLL1 6 / 11 Holoprosencephaly, Microform holoprosencephaly, neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures, Semilobar holoprosencephaly and 2 more
FGF8 6 / 11 22q11 deletion syndrome, Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly and 2 more
FOXH1 6 / 11 Congenital heart malformation, Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly and 2 more
GLI2 6 / 11 Gastrointestinal stromal tumor, Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly and 2 more
PTCH1 6 / 11 Gastrointestinal stromal tumor, Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly and 2 more
CRIPTO 5 / 11 Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly, Septopreoptic holoprosencephaly and 1 more
GAS1 5 / 11 Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly, Septopreoptic holoprosencephaly and 1 more
NODAL 5 / 11 Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly, Septopreoptic holoprosencephaly and 1 more
SHH 5 / 11 Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly, Septopreoptic holoprosencephaly and 1 more
SIX3 5 / 11 Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly, Septopreoptic holoprosencephaly and 1 more
TGIF1 5 / 11 Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly, Septopreoptic holoprosencephaly and 1 more
ZIC2 5 / 11 Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly, Septopreoptic holoprosencephaly and 1 more
STIL 4 / 11 Holoprosencephaly, Semilobar holoprosencephaly, Septopreoptic holoprosencephaly, Syntelencephaly
FGFR1 3 / 11 Holoprosencephaly, Microform holoprosencephaly, Semilobar holoprosencephaly
BOC 2 / 11 Gastrointestinal stromal tumor, Holoprosencephaly
GPKOW 2 / 11 Holoprosencephaly, holoprosencephaly-hypokinesia-congenital contractures syndrome
STAG2 2 / 11 Holoprosencephaly, Semilobar holoprosencephaly
STK36 2 / 11 ciliary dyskinesia, primary, 46, Gastrointestinal stromal tumor
SUFU 2 / 11 Gastrointestinal stromal tumor, Microform holoprosencephaly
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 ⇵
Hedgehog signaling pathway
BOC, CDON, DISP1, GLI1, GLI2, GLI3, HHAT, HHIP, IHH, KIF3A, PTCH1, PTCH2
 KEGG 16 / 56 45.2× 4.21e-23 5.74e-20 ✓ sig.
Hedgehog 'off' state
GLI1, GLI2, GLI3, IFT172, IFT52, IFT88, KIF3A, PTCH1, SMO, SUFU, TULP3
 Reactome 11 / 56 31.0× 3.64e-14 1.00e-11 ✓ sig.
Activation of SMO
BOC, CDON, IHH, KIF3A, PTCH1, SMO, GAS1, SHH
 Reactome 8 / 18 70.2× 7.32e-14 1.92e-11 ✓ sig.
Ligand-receptor interactions
CDON, HHIP, IHH, PTCH1, GAS1, SHH
 Reactome 6 / 7 135× 3.66e-13 8.51e-11 ✓ sig.
Basal cell carcinoma
GLI1, GLI2, GLI3, HHIP, PTCH1, PTCH2, SMO, SUFU, SHH
 KEGG 9 / 63 22.6× 1.80e-10 2.46e-8 ✓ sig.
Pathways in cancer
FGF8, KIT, PDGFRA, CTNNA1, GLI1, GLI2, GLI3, HHIP, PTCH1, PTCH2, RB1, SMO
 KEGG 18 / 533 5.3× 3.82e-9 3.72e-7 ✓ sig.
GLI proteins bind promoters of Hh responsive genes to promote transcription
GLI1, GLI2, GLI3
 Reactome 3 / 3 158× 2.44e-7 1.42e-5 ✓ sig.
HHAT G278V abrogates palmitoylation of Hh-Np
HHAT, IHH, SHH
 Reactome 3 / 4 119× 9.70e-7 4.74e-5 ✓ sig.
Hedgehog 'on' state
GLI1, GLI2, GLI3, PTCH1, SMO, SUFU
 Reactome 6 / 70 13.5× 5.00e-6 1.90e-4 ✓ sig.
Citric acid cycle (TCA cycle)
SDHA, SDHB, SDHC
 Reactome 3 / 22 21.5× 3.44e-4 5.97e-3 ✓ sig.
Intraflagellar transport
IFT172, IFT52, IFT88, KIF3A
 Reactome 4 / 54 11.7× 3.68e-4 6.29e-3 ✓ sig.
Myogenesis
BOC, CDON, CTNNA1
 Reactome 3 / 27 17.6× 6.39e-4 9.65e-3 ✓ sig.
Release of Hh-Np from the secreting cell
IHH, SHH
 Reactome 2 / 7 45.2× 8.13e-4 1.16e-2 ✓ sig.
Citrate cycle (TCA cycle)
SDHA, SDHB, SDHC
 KEGG 3 / 30 15.8× 8.74e-4 1.22e-2 ✓ sig.
Melanoma
FGF8, PDGFRA, RB1, FGFR1
 KEGG 4 / 73 8.7× 1.16e-3 1.52e-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 ⇵
smoothened signaling pathway
B9D1, CC2D2A, CD3E, CDON, CTNNA1, DISP1, DYRK2, FOXF1, GLI1, GLI2, GLI3, HHAT
 GO:0007224 27 / 94 70.6× 3.40e-44 5.41e-40 ✓ sig.
determination of left/right symmetry
FGF8, FOXH1, CC2D2A, DISP1, FOXF1, IFT172, IFT52, NME7, SMO, SUFU, DLL1, NODAL
 GO:0007368 15 / 83 44.4× 3.12e-21 6.02e-18 ✓ sig.
heart looping
FGF8, FOXH1, C2CD3, IFT172, IFT52, IHH, SMO, SUFU, TGFBR2, DLL1, NODAL, SHH
 GO:0001947 13 / 64 49.9× 3.15e-19 4.54e-16 ✓ sig.
dorsal/ventral pattern formation
FGF8, DISP1, GLI1, GLI3, HHIP, IFT172, IFT52, PTCH1, SMO, SHH, TGIF1
 GO:0009953 11 / 47 57.5× 3.67e-17 3.84e-14 ✓ sig.
negative regulation of smoothened signaling pathway
CD3E, GLI3, GLIS2, HHIP, IFT172, PTCH1, PTCH2, RB1, SUFU, TULP3
 GO:0045879 10 / 35 70.3× 1.13e-16 1.05e-13 ✓ sig.
lung development
FGF8, PDGFRA, FOXF1, GLI1, GLI2, GLI3, TGFBR2, FGFR1, LAMA5, NODAL, SHH
 GO:0030324 11 / 108 25.0× 5.98e-13 2.87e-10 ✓ sig.
embryonic digit morphogenesis
B9D1, C2CD3, GLI3, IFT52, IHH, TMEM231, TULP3, SHH, LMBR1
 GO:0042733 9 / 57 38.8× 1.44e-12 6.38e-10 ✓ sig.
positive regulation of smoothened signaling pathway
CTNNA1, GLI1, IFT172, IHH, NDST1, SMO, STK36, SHH
 GO:0045880 8 / 39 50.4× 2.85e-12 1.19e-9 ✓ sig.
cilium assembly
B9D1, C2CD3, CC2D2A, IFT172, IFT52, IFT88, KIF3A, NME7, RAB23, STK36, TMEM17, TMEM231
 GO:0060271 13 / 237 13.5× 1.19e-11 4.32e-9 ✓ sig.
regulation of smoothened signaling pathway
C2CD3, GLI1, GLI3, IFT172, PTCH1, TULP3, GAS1
 GO:0008589 7 / 29 59.4× 2.01e-11 6.88e-9 ✓ sig.
in utero embryonic development
PDGFRA, B9D1, C2CD3, FOXF1, GLI3, IHH, PTCH1, SMO, TGFBR2, TMEM231, FGFR1, NODAL
 GO:0001701 13 / 252 12.7× 2.57e-11 8.49e-9 ✓ sig.
cell population proliferation
FGF8, KIT, GLI3, HIPK1, HIPK2, IHH, NDST1, RB1, SMO, FGFR1, NODAL, SHH
 GO:0008283 13 / 263 12.2× 4.39e-11 1.37e-8 ✓ sig.
spinal cord dorsal/ventral patterning
GLI2, GLI3, SMO, SUFU, SHH
 GO:0021513 5 / 8 154× 5.40e-11 1.65e-8 ✓ sig.
brain development
C2CD3, GLI3, IFT172, NME7, PTCH1, STK36, TGFBR2, TULP3, FGFR1, NODAL, SIX3, ZIC2
 GO:0007420 12 / 244 12.1× 2.78e-10 7.15e-8 ✓ sig.
camera-type eye development
B9D1, CC2D2A, GLI3, IHH, TMEM231, SHH, SIX3, TWSG1
 GO:0043010 8 / 74 26.6× 6.23e-10 1.48e-7 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Septopreoptic holoprosencephaly Syntelencephaly 0.938 15 2.03e-51 1.16e-49 ✓ sig.
Semilobar holoprosencephaly Septopreoptic holoprosencephaly 0.789 15 1.66e-48 8.82e-47 ✓ sig.
Semilobar holoprosencephaly Syntelencephaly 0.789 15 1.66e-48 8.82e-47 ✓ sig.
Holoprosencephaly Semilobar holoprosencephaly 0.548 17 2.18e-48 1.15e-46 ✓ sig.
Microform holoprosencephaly Semilobar holoprosencephaly 0.750 15 2.65e-47 1.38e-45 ✓ sig.
Microform holoprosencephaly Septopreoptic holoprosencephaly 0.778 14 3.75e-45 1.86e-43 ✓ sig.
Microform holoprosencephaly Syntelencephaly 0.778 14 3.75e-45 1.86e-43 ✓ sig.
Holoprosencephaly Septopreoptic holoprosencephaly 0.500 15 1.57e-43 7.56e-42 ✓ sig.
Holoprosencephaly Syntelencephaly 0.500 15 1.57e-43 7.56e-42 ✓ sig.
Holoprosencephaly Microform holoprosencephaly 0.484 15 2.52e-42 1.17e-40 ✓ sig.
Gastrointestinal stromal tumor Microform holoprosencephaly 0.085 5 9.06e-10 8.72e-9 ✓ sig.
Gastrointestinal stromal tumor Holoprosencephaly 0.069 5 2.39e-8 1.96e-7 ✓ sig.
Gastrointestinal stromal tumor Syntelencephaly 0.068 4 1.01e-7 7.50e-7 ✓ sig.
22q11 deletion syndrome Septopreoptic holoprosencephaly 0.063 1 9.74e-4 1.64e-3 ✓ sig.
neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures Septopreoptic holoprosencephaly 0.063 1 9.74e-4 1.64e-3 ✓ sig.
neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures Syntelencephaly 0.063 1 9.74e-4 1.64e-3 ✓ sig.
22q11 deletion syndrome Syntelencephaly 0.063 1 9.74e-4 1.64e-3 ✓ sig.
Microform holoprosencephaly neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures 0.059 1 1.04e-3 1.72e-3 ✓ sig.
22q11 deletion syndrome Microform holoprosencephaly 0.059 1 1.04e-3 1.72e-3 ✓ sig.
neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures Semilobar holoprosencephaly 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Holoprosencephaly holoprosencephaly-hypokinesia-congenital contractures syndrome 0.033 1 1.88e-3 2.75e-3 ✓ sig.
Holoprosencephaly neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures 0.033 1 1.88e-3 2.75e-3 ✓ sig.
ciliary dyskinesia, primary, 46 Gastrointestinal stromal tumor 0.021 1 3.05e-3 4.02e-3 ✓ sig.
Congenital heart malformation Septopreoptic holoprosencephaly 0.050 1 4.86e-3 5.99e-3 ✓ sig.
Congenital heart malformation Syntelencephaly 0.050 1 4.86e-3 5.99e-3 ✓ sig.
Congenital heart malformation Microform holoprosencephaly 0.048 1 5.19e-3 6.34e-3 ✓ sig.
Congenital heart malformation Semilobar holoprosencephaly 0.043 1 5.83e-3 7.05e-3 ✓ sig.