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 83

13 diseases · 48 shared-gene connections
13 Diseases
9 Unique genes
0.422 Avg. similarity score
Achondroplasia Most-connected disease (12 links)
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Disease Searched: Severe achondroplasia-developmental delay-acanthosis nigricans syndrome 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 ⇵
Achondroplasia 12 12 1
Camptodactyly, tall stature, and hearing loss syndrome 12 12 1
Catshl syndrome 12 12 1
Crouzon syndrome with acanthosis nigricans 11 11 1
Muenke syndrome 10 10 1
Cheilitis 5 5 3
Flat urothelial hyperplasia 5 5 1
Hypochondroplasia 5 5 1
Keratinocytic nonepidermolytic nevus 5 5 2
Severe achondroplasia-developmental delay-acanthosis nigricans syndrome 5 5 1
Thanatophoric dysplasia 5 5 1
Ureter urothelial carcinoma 5 5 4
Myeloma 4 4 5

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

Gene ⇵ Member diseases ⇵ Linked diseases
FGFR3 13 / 13 Achondroplasia, Camptodactyly, tall stature, and hearing loss syndrome, Catshl syndrome, Cheilitis and 9 more
NRAS 2 / 13 Keratinocytic nonepidermolytic nevus, Myeloma
TP53 2 / 13 Cheilitis, Ureter urothelial carcinoma
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 ⇵
Bladder cancer
FGFR3, BRAF, NRAS, MYC, TP53
 KEGG 5 / 41 163× 4.49e-11 5.82e-9 ✓ sig.
Thyroid cancer
BRAF, NRAS, MYC, TP53
 KEGG 4 / 37 144× 9.50e-9 7.05e-7 ✓ sig.
Hepatocellular carcinoma
BRAF, NRAS, MYC, TP53, SMARCB1
 KEGG 5 / 170 39.2× 6.45e-8 3.80e-6 ✓ sig.
Endometrial cancer
BRAF, NRAS, MYC, TP53
 KEGG 4 / 59 90.5× 6.50e-8 3.83e-6 ✓ sig.
Central carbon metabolism in cancer
FGFR3, NRAS, MYC, TP53
 KEGG 4 / 71 75.2× 1.38e-7 7.42e-6 ✓ sig.
Chronic myeloid leukemia
BRAF, NRAS, MYC, TP53
 KEGG 4 / 77 69.3× 1.92e-7 9.89e-6 ✓ sig.
Colorectal cancer
BRAF, NRAS, MYC, TP53
 KEGG 4 / 87 61.4× 3.15e-7 1.53e-5 ✓ sig.
MAPK signaling pathway
FGFR3, BRAF, NRAS, MYC, TP53
 KEGG 5 / 299 22.3× 1.07e-6 4.44e-5 ✓ sig.
Breast cancer
BRAF, NRAS, MYC, TP53
 KEGG 4 / 148 36.1× 2.66e-6 9.66e-5 ✓ sig.
PI3K-Akt signaling pathway
FGFR3, NRAS, MYC, STK11, TP53
 KEGG 5 / 361 18.5× 2.72e-6 9.84e-5 ✓ sig.
Gastric cancer
BRAF, NRAS, MYC, TP53
 KEGG 4 / 150 35.6× 2.81e-6 1.01e-4 ✓ sig.
Hepatitis C
BRAF, NRAS, MYC, TP53
 KEGG 4 / 159 33.6× 3.54e-6 1.23e-4 ✓ sig.
Hepatitis B
BRAF, NRAS, MYC, TP53
 KEGG 4 / 163 32.7× 3.91e-6 1.34e-4 ✓ sig.
Proteoglycans in cancer
BRAF, NRAS, MYC, TP53
 KEGG 4 / 204 26.2× 9.53e-6 2.80e-4 ✓ sig.
Acute myeloid leukemia
BRAF, NRAS, MYC
 KEGG 3 / 68 58.9× 1.42e-5 3.91e-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 ⇵
MAPK cascade
FGFR3, BRAF, NRAS, MYC
 GO:0000165 4 / 147 56.5× 4.49e-7 4.44e-5 ✓ sig.
cellular response to xenobiotic stimulus
BRAF, MYC, TP53
 GO:0071466 3 / 65 95.8× 3.32e-6 2.28e-4 ✓ sig.
intrinsic apoptotic signaling pathway by p53 class mediator
STK11, TP53
 GO:0072332 2 / 29 143× 8.32e-5 2.70e-3 ✓ sig.
positive regulation of axonogenesis
BRAF, STK11
 GO:0050772 2 / 30 138× 8.91e-5 2.84e-3 ✓ sig.
negative regulation of fibroblast proliferation
MYC, TP53
 GO:0048147 2 / 35 119× 1.22e-4 3.56e-3 ✓ sig.
T cell differentiation in thymus
BRAF, TP53
 GO:0033077 2 / 41 101× 1.67e-4 4.47e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
TP53, SMARCB1
 GO:0045815 2 / 41 101× 1.67e-4 4.47e-3 ✓ sig.
cell population proliferation
FGFR3, MYC, TP53
 GO:0008283 3 / 263 23.7× 2.17e-4 5.38e-3 ✓ sig.
response to ionizing radiation
STK11, TP53
 GO:0010212 2 / 47 88.4× 2.20e-4 5.43e-3 ✓ sig.
chromosome organization
MYC, TP53
 GO:0051276 2 / 51 81.4× 2.60e-4 6.12e-3 ✓ sig.
ERK1 and ERK2 cascade
BRAF, MYC
 GO:0070371 2 / 55 75.5× 3.02e-4 6.82e-3 ✓ sig.
cellular response to UV
MYC, TP53
 GO:0034644 2 / 55 75.5× 3.02e-4 6.82e-3 ✓ sig.
positive regulation of miRNA transcription
MYC, TP53
 GO:1902895 2 / 56 74.2× 3.13e-4 7.00e-3 ✓ sig.
negative regulation of developmental growth
FGFR3
 GO:0048640 1 / 1 2,076× 4.82e-4 9.24e-3 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 2,076× 4.82e-4 9.24e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Keratinocytic nonepidermolytic nevus Myeloma 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Crouzon syndrome with acanthosis nigricans Hypochondroplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Achondroplasia Flat urothelial hyperplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Flat urothelial hyperplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Catshl syndrome Flat urothelial hyperplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Crouzon syndrome with acanthosis nigricans Flat urothelial hyperplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Flat urothelial hyperplasia Muenke syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Achondroplasia Hypochondroplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Hypochondroplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Catshl syndrome Hypochondroplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Achondroplasia Catshl syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypochondroplasia Muenke syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Muenke syndrome Thanatophoric dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Achondroplasia Severe achondroplasia-developmental delay-acanthosis nigricans syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Severe achondroplasia-developmental delay-acanthosis nigricans syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Catshl syndrome Severe achondroplasia-developmental delay-acanthosis nigricans syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Crouzon syndrome with acanthosis nigricans Severe achondroplasia-developmental delay-acanthosis nigricans syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Muenke syndrome Severe achondroplasia-developmental delay-acanthosis nigricans syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Crouzon syndrome with acanthosis nigricans Muenke syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Achondroplasia Camptodactyly, tall stature, and hearing loss syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Achondroplasia Crouzon syndrome with acanthosis nigricans 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Achondroplasia Muenke syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Achondroplasia Thanatophoric dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Catshl syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Catshl syndrome Thanatophoric dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Catshl syndrome Muenke syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Catshl syndrome Crouzon syndrome with acanthosis nigricans 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Thanatophoric dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Muenke syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Crouzon syndrome with acanthosis nigricans 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Crouzon syndrome with acanthosis nigricans Thanatophoric dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Crouzon syndrome with acanthosis nigricans Keratinocytic nonepidermolytic nevus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Catshl syndrome Keratinocytic nonepidermolytic nevus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Keratinocytic nonepidermolytic nevus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Achondroplasia Keratinocytic nonepidermolytic nevus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Achondroplasia Cheilitis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Cheilitis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Catshl syndrome Cheilitis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cheilitis Crouzon syndrome with acanthosis nigricans 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cheilitis Muenke syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Achondroplasia Ureter urothelial carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Ureter urothelial carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Catshl syndrome Ureter urothelial carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Crouzon syndrome with acanthosis nigricans Ureter urothelial carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Muenke syndrome Ureter urothelial carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Achondroplasia Myeloma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Camptodactyly, tall stature, and hearing loss syndrome Myeloma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Catshl syndrome Myeloma 0.200 1 2.58e-4 5.38e-4 ✓ sig.