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 130

10 diseases · 18 shared-gene connections
10 Diseases
86 Unique genes
0.185 Avg. similarity score
Cerebellar diseases Most-connected disease (5 links)
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Disease Searched: dyskeratosis congenita, autosomal dominant 3 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 ⇵
Cerebellar diseases 5 5 7
Revesz debuse syndrome 5 5 1
Revesz syndrome 5 5 1
Thyroid carcinoma 5 5 9
Bone marrow diseases 4 4 4
dyskeratosis congenita, autosomal dominant 3 4 4 1
Differentiated thyroid carcinoma 3 3 49
Hurthle cell thyroid cancer 2 2 1
Thyroid cancer 2 2 34
Mowat-wilson syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TINF2 6 / 10 Bone marrow diseases, Cerebellar diseases, dyskeratosis congenita, autosomal dominant 3, Revesz debuse syndrome and 2 more
NDUFA13 3 / 10 Differentiated thyroid carcinoma, Hurthle cell thyroid cancer, Thyroid carcinoma
NRG1 3 / 10 Differentiated thyroid carcinoma, Thyroid cancer, Thyroid carcinoma
PCNX2 3 / 10 Differentiated thyroid carcinoma, Thyroid cancer, Thyroid carcinoma
TRMO 3 / 10 Differentiated thyroid carcinoma, Thyroid cancer, Thyroid carcinoma
FOXE1 2 / 10 Differentiated thyroid carcinoma, Thyroid cancer
MBIP 2 / 10 Differentiated thyroid carcinoma, Thyroid cancer
SEPTIN11 2 / 10 Differentiated thyroid carcinoma, Thyroid carcinoma
SLK 2 / 10 Differentiated thyroid carcinoma, Thyroid cancer
SOWAHB 2 / 10 Differentiated thyroid carcinoma, Thyroid carcinoma
STN1 2 / 10 Differentiated thyroid carcinoma, Thyroid cancer
TERT 2 / 10 Differentiated thyroid carcinoma, Thyroid cancer
VAV3 2 / 10 Differentiated thyroid carcinoma, Thyroid carcinoma
ZEB2 2 / 10 Cerebellar diseases, Mowat-wilson syndrome
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
BRAF, CCDC6, HRAS, KRAS, NCOA4, NRAS, NTRK1, PAX8, PPARG, RET, TFG, TPR
 KEGG 12 / 37 45.3× 1.31e-17 6.70e-15 ✓ sig.
Pathways in cancer
GSTP1, ALK, BRAF, CCDC6, HRAS, KRAS, LPAR4, NCOA4, NRAS, NTRK1, PAX8, PPARG
 KEGG 18 / 533 4.7× 3.07e-8 2.47e-6 ✓ sig.
RAS GTPase cycle mutants
HRAS, KRAS, NRAS
 Reactome 3 / 3 140× 3.55e-7 2.11e-5 ✓ sig.
FoxO signaling pathway
BRAF, GRM1, HRAS, KRAS, NRAS, PRKAG2, SMAD3, TGFB2, SOD2
 KEGG 9 / 133 9.5× 4.27e-7 2.49e-5 ✓ sig.
SHC1 events in ERBB4 signaling
HRAS, KRAS, NRAS, NRG1
 Reactome 4 / 14 39.9× 2.32e-6 1.08e-4 ✓ sig.
GRB2 events in ERBB2 signaling
HRAS, KRAS, NRAS, NRG1
 Reactome 4 / 14 39.9× 2.32e-6 1.08e-4 ✓ sig.
Activation of RAS in B cells
HRAS, KRAS, NRAS
 Reactome 3 / 5 83.8× 3.51e-6 1.52e-4 ✓ sig.
Long-term depression
NOS1, BRAF, GRM1, HRAS, KRAS, NRAS
 KEGG 6 / 60 14.0× 4.15e-6 1.75e-4 ✓ sig.
Estrogen-stimulated signaling through PRKCZ
HRAS, KRAS, NRAS
 Reactome 3 / 6 69.8× 6.98e-6 2.65e-4 ✓ sig.
Central carbon metabolism in cancer
HRAS, KRAS, NRAS, NTRK1, NTRK3, RET
 KEGG 6 / 71 11.8× 1.12e-5 3.88e-4 ✓ sig.
RAS signaling downstream of NF1 loss-of-function variants
HRAS, KRAS, NRAS
 Reactome 3 / 7 59.9× 1.22e-5 4.17e-4 ✓ sig.
FLT3 Signaling
HRAS, KRAS, NRAS
 Reactome 3 / 7 59.9× 1.22e-5 4.17e-4 ✓ sig.
Non-small cell lung cancer
ALK, BRAF, HRAS, KRAS, NRAS, RET
 KEGG 6 / 73 11.5× 1.31e-5 4.43e-4 ✓ sig.
Signaling by ERBB2 TMD/JMD mutants
HRAS, KRAS, NRAS, NRG1
 Reactome 4 / 22 25.4× 1.62e-5 5.31e-4 ✓ sig.
Chronic myeloid leukemia
BRAF, HRAS, KRAS, NRAS, SMAD3, TGFB2
 KEGG 6 / 77 10.9× 1.78e-5 5.72e-4 ✓ 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 ⇵
thyroid gland development
BRAF, FOXE1, NKX2-1, PAX8, SMAD3, TG
 GO:0030878 6 / 30 43.5× 4.33e-9 8.15e-7 ✓ sig.
cell surface receptor protein tyrosine kinase signaling pathway
AHI1, ALK, NRG1, NTRK1, NTRK3, RET
 GO:0007169 6 / 120 10.9× 1.91e-5 8.97e-4 ✓ sig.
positive regulation of gene expression
BRAF, HRAS, KRAS, MBIP, NKX2-1, NTRK3, PPARG, RET, TRIM24, SMAD3, TGFB2
 GO:0010628 11 / 504 4.7× 1.94e-5 9.08e-4 ✓ sig.
telomere capping
TINF2, STN1, POT1
 GO:0016233 3 / 12 54.3× 2.01e-5 9.32e-4 ✓ sig.
cell differentiation
AHI1, PTF1A, BRAF, ETV6, FOXE1, NKX2-1, NRG1, NTRK1, NTRK3, PAX8, PPARG, HEMGN
 GO:0030154 16 / 1,051 3.3× 2.09e-5 9.60e-4 ✓ sig.
substantia propria of cornea development
KCNQ3, TGFB2
 GO:1903701 2 / 2 217× 2.09e-5 9.61e-4 ✓ sig.
positive regulation of DNA-templated transcription
NOS1, PTF1A, FOXE1, NCOA4, NFIA, NKX2-1, PAX8, PPARG, RET, SKAP1, TRIM24, TRIM27
 GO:0045893 13 / 778 3.6× 5.36e-5 1.96e-3 ✓ sig.
MAPK cascade
BRAF, HRAS, KRAS, NRAS, RET, SMAD3
 GO:0000165 6 / 147 8.9× 5.99e-5 2.13e-3 ✓ sig.
telomere assembly
TINF2, POT1
 GO:0032202 2 / 3 145× 6.26e-5 2.20e-3 ✓ sig.
negative regulation of neuron apoptotic process
BRAF, HRAS, KRAS, NTRK1, TERT, SOD2
 GO:0043524 6 / 160 8.1× 9.58e-5 3.04e-3 ✓ sig.
generation of neurons
PTF1A, NFIA, TGFB2
 GO:0048699 3 / 20 32.6× 1.01e-4 3.17e-3 ✓ sig.
response to L-ascorbic acid
GSTP1, SOD2
 GO:0033591 2 / 4 109× 1.25e-4 3.68e-3 ✓ sig.
regulation of transforming growth factor beta2 production
SMAD3, TGFB2
 GO:0032909 2 / 4 109× 1.25e-4 3.68e-3 ✓ sig.
response to isolation stress
KRAS, SOD2
 GO:0035900 2 / 4 109× 1.25e-4 3.68e-3 ✓ sig.
positive regulation of miRNA transcription
PPARG, TERT, SMAD3, TGFB2
 GO:1902895 4 / 56 15.5× 1.28e-4 3.75e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Differentiated thyroid carcinoma Thyroid carcinoma 0.135 7 7.57e-17 1.22e-15 ✓ sig.
Differentiated thyroid carcinoma Thyroid cancer 0.105 8 9.84e-14 1.27e-12 ✓ sig.
Thyroid cancer Thyroid carcinoma 0.073 3 8.19e-7 4.87e-6 ✓ sig.
Revesz debuse syndrome Revesz syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
dyskeratosis congenita, autosomal dominant 3 Revesz syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
dyskeratosis congenita, autosomal dominant 3 Revesz debuse syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Bone marrow diseases Revesz syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Bone marrow diseases dyskeratosis congenita, autosomal dominant 3 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Bone marrow diseases Revesz debuse syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cerebellar diseases Revesz syndrome 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Cerebellar diseases Revesz debuse syndrome 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Cerebellar diseases Mowat-wilson syndrome 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Cerebellar diseases dyskeratosis congenita, autosomal dominant 3 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Hurthle cell thyroid cancer Thyroid carcinoma 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Revesz debuse syndrome Thyroid carcinoma 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Revesz syndrome Thyroid carcinoma 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Bone marrow diseases Cerebellar diseases 0.091 1 1.82e-3 2.68e-3 ✓ sig.
Differentiated thyroid carcinoma Hurthle cell thyroid cancer 0.020 1 3.18e-3 4.17e-3 ✓ sig.