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 28

19 diseases · 44 shared-gene connections
19 Diseases
50 Unique genes
0.198 Avg. similarity score
Epidermal nevus Most-connected disease (12 links)
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Disease Searched: Hypophosphatemic rickets 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 ⇵
Epidermal nevus 12 12 7
Schimmelpenning-feuerstein-mims syndrome 10 10 3
Penile neoplasms 7 7 4
Autoimmune lymphoproliferative disorder 6 6 11
Bladder cancer 6 6 4
Splenic neoplasms 6 6 1
Nonmedullary thyroid cancer 5 5 7
Woolly hair nevus 5 5 1
Congenital arteriovenous malformation 4 4 9
Follicular thyroid cancer 4 4 7
Hypophosphatemic rickets 4 4 12
Melanocytic nevus 4 4 11
Neurofibrosarcoma 4 4 1
Seminoma 4 4 3
ciliary dyskinesia, primary, 39 3 3 1
autoimmune lymphoproliferative syndrome type 2A 1 1 1
bamforth-lazarus syndrome 1 1 1
immunodeficiency 64 1 1 1
lymphoproliferative syndrome 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
HRAS 12 / 19 Bladder cancer, Congenital arteriovenous malformation, Epidermal nevus, Follicular thyroid cancer and 8 more
NRAS 7 / 19 Autoimmune lymphoproliferative disorder, Epidermal nevus, Follicular thyroid cancer, Melanocytic nevus and 3 more
KRAS 5 / 19 Autoimmune lymphoproliferative disorder, Bladder cancer, Epidermal nevus, Penile neoplasms and 1 more
LRRC56 4 / 19 ciliary dyskinesia, primary, 39, Congenital arteriovenous malformation, Epidermal nevus, Hypophosphatemic rickets
FGFR3 3 / 19 Bladder cancer, Epidermal nevus, Seminoma
PIK3CA 3 / 19 Congenital arteriovenous malformation, Epidermal nevus, Penile neoplasms
CASP10 2 / 19 Autoimmune lymphoproliferative disorder, autoimmune lymphoproliferative syndrome type 2A
CASP8 2 / 19 Autoimmune lymphoproliferative disorder, Melanocytic nevus
FOXE1 2 / 19 bamforth-lazarus syndrome, Nonmedullary thyroid cancer
ITK 2 / 19 Autoimmune lymphoproliferative disorder, lymphoproliferative syndrome 1
MINPP1 2 / 19 Follicular thyroid cancer, Nonmedullary thyroid cancer
RASGRP1 2 / 19 Autoimmune lymphoproliferative disorder, immunodeficiency 64
SRGAP1 2 / 19 Follicular thyroid cancer, Nonmedullary thyroid cancer
TP53 2 / 19 Melanocytic nevus, Penile neoplasms
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 ⇵
Apoptosis
CASP10, CASP8, FAS, FASLG, NRAS, KRAS, HRAS, MAP2K1, PIK3CA, ATM, TP53
 KEGG 11 / 137 19.3× 7.25e-12 1.28e-9 ✓ sig.
Hepatitis B
CASP10, CASP8, FAS, FASLG, NRAS, KRAS, HRAS, RB1, MAP2K1, PIK3CA, TP53
 KEGG 11 / 163 16.2× 4.85e-11 7.05e-9 ✓ sig.
Thyroid cancer
NRAS, KRAS, HRAS, MAP2K1, TP53, PAX8, PPARG
 KEGG 7 / 37 45.4× 1.31e-10 1.75e-8 ✓ sig.
Pathways in cancer
CASP8, FAS, FASLG, NRAS, RASGRP1, KRAS, FGF23, FGFR3, HRAS, RB1, GLI2, MAP2K1
 KEGG 16 / 533 7.2× 2.20e-10 2.76e-8 ✓ sig.
Signaling by FGFR3 fusions in cancer
NRAS, KRAS, FGFR3, HRAS, PIK3CA
 Reactome 5 / 10 120× 2.53e-10 3.13e-8 ✓ sig.
Signaling by FGFR3 point mutants in cancer
NRAS, KRAS, FGF23, FGFR3, HRAS, PIK3CA
 Reactome 6 / 22 65.5× 2.71e-10 3.33e-8 ✓ sig.
Bladder cancer
NRAS, KRAS, FGFR3, HRAS, RB1, MAP2K1, TP53
 KEGG 7 / 41 41.0× 2.83e-10 3.46e-8 ✓ sig.
Melanoma
NRAS, KRAS, FGF23, HRAS, RB1, MAP2K1, PIK3CA, TP53
 KEGG 8 / 73 26.3× 5.50e-10 6.27e-8 ✓ sig.
Hepatitis C
CASP8, FAS, FASLG, NRAS, KRAS, HRAS, RB1, MAP2K1, PIK3CA, TP53
 KEGG 10 / 159 15.1× 8.11e-10 8.88e-8 ✓ sig.
Activation of RAS in B cells
NRAS, RASGRP1, KRAS, HRAS
 Reactome 4 / 5 192× 1.32e-9 1.36e-7 ✓ sig.
FasL/ CD95L signaling
CASP10, CASP8, FAS, FASLG
 Reactome 4 / 5 192× 1.32e-9 1.36e-7 ✓ sig.
MAPK signaling pathway
FAS, FASLG, NRAS, RASGRP1, KRAS, FGF23, FGFR3, HRAS, CACNA1H, MAP2K1, TEK, TP53
 KEGG 12 / 299 9.6× 2.37e-9 2.33e-7 ✓ sig.
Ras signaling pathway
FASLG, NRAS, RASGRP1, KRAS, FGF23, FGFR3, HRAS, MAP2K1, PIK3CA, TEK, PLA2G6
 KEGG 11 / 237 11.1× 2.66e-9 2.60e-7 ✓ sig.
GnRH secretion
NRAS, KRAS, HRAS, CACNA1H, MAP2K1, PIK3CA, CGA
 KEGG 7 / 65 25.9× 8.12e-9 7.05e-7 ✓ sig.
SHC-mediated cascade:FGFR3
NRAS, KRAS, FGF23, FGFR3, HRAS
 Reactome 5 / 18 66.7× 8.38e-9 7.22e-7 ✓ 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 ⇵
intracellular phosphate ion homeostasis
FGF23, SLC34A3, ENPP1, SLC34A1
 GO:0030643 4 / 10 149× 9.41e-9 1.58e-6 ✓ sig.
thyroid gland development
MAP2K1, CGA, PAX8, NKX2-1, FOXE1
 GO:0030878 5 / 30 62.3× 1.51e-8 2.42e-6 ✓ sig.
Ras protein signal transduction
NRAS, RASGRP1, KRAS, HRAS, RB1, TP53
 GO:0007265 6 / 79 28.4× 6.45e-8 8.40e-6 ✓ sig.
cellular senescence
PRKCD, HRAS, MAP2K1, ATM, TP53
 GO:0090398 5 / 57 32.8× 4.21e-7 4.09e-5 ✓ sig.
positive regulation of neuron apoptotic process
CASP10, CASP8, FASLG, ATM, TP53
 GO:0043525 5 / 65 28.7× 8.17e-7 7.10e-5 ✓ sig.
biomineral tissue development
PHEX, DMP1, ENPP1, WDR72
 GO:0031214 4 / 35 42.7× 2.23e-6 1.60e-4 ✓ sig.
MAPK cascade
NRAS, KRAS, FGF23, FGFR3, HRAS, MAP2K1
 GO:0000165 6 / 147 15.3× 2.56e-6 1.79e-4 ✓ sig.
cellular response to parathyroid hormone stimulus
FGF23, PHEX, SLC34A1
 GO:0071374 3 / 11 102× 2.93e-6 2.00e-4 ✓ sig.
response to magnesium ion
FGF23, SLC34A1, ENTPD6
 GO:0032026 3 / 12 93.4× 3.90e-6 2.51e-4 ✓ sig.
neuron apoptotic process
KRAS, HRAS, RB1, ATM, TP53
 GO:0051402 5 / 98 19.1× 6.29e-6 3.68e-4 ✓ sig.
positive regulation of gene expression
ACTA2, KRAS, HRAS, MAP2K1, VDR, ATM, TP53, PPARG, NKX2-1
 GO:0010628 9 / 504 6.7× 6.58e-6 3.81e-4 ✓ sig.
animal organ development
CASP8, ENPP1, ADGRV1, NKX2-1, FOXE1
 GO:0048513 5 / 102 18.3× 7.65e-6 4.31e-4 ✓ sig.
phosphate ion homeostasis
FGF23, ENPP1, SLC34A1
 GO:0055062 3 / 15 74.7× 8.02e-6 4.48e-4 ✓ sig.
thymus development
MAP2K1, ATM, TYR, FOXE1
 GO:0048538 4 / 50 29.9× 9.54e-6 5.13e-4 ✓ sig.
glial cell proliferation
KRAS, RB1, TP53
 GO:0014009 3 / 18 62.3× 1.43e-5 7.02e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Follicular thyroid cancer Nonmedullary thyroid cancer 0.364 4 5.23e-13 6.51e-12 ✓ sig.
Epidermal nevus Schimmelpenning-feuerstein-mims syndrome 0.375 3 5.75e-11 5.89e-10 ✓ sig.
Bladder cancer Epidermal nevus 0.333 3 2.30e-10 2.22e-9 ✓ sig.
Epidermal nevus Penile neoplasms 0.333 3 2.30e-10 2.22e-9 ✓ sig.
Congenital arteriovenous malformation Epidermal nevus 0.214 3 4.83e-9 4.09e-8 ✓ sig.
Penile neoplasms Schimmelpenning-feuerstein-mims syndrome 0.333 2 1.52e-7 1.03e-6 ✓ sig.
Bladder cancer Seminoma 0.333 2 1.52e-7 1.03e-6 ✓ sig.
Bladder cancer Schimmelpenning-feuerstein-mims syndrome 0.333 2 1.52e-7 1.03e-6 ✓ sig.
Bladder cancer Penile neoplasms 0.286 2 3.04e-7 1.96e-6 ✓ sig.
Follicular thyroid cancer Schimmelpenning-feuerstein-mims syndrome 0.222 2 5.31e-7 3.28e-6 ✓ sig.
Nonmedullary thyroid cancer Schimmelpenning-feuerstein-mims syndrome 0.222 2 5.31e-7 3.28e-6 ✓ sig.
Epidermal nevus Seminoma 0.222 2 5.31e-7 3.28e-6 ✓ sig.
Autoimmune lymphoproliferative disorder Schimmelpenning-feuerstein-mims syndrome 0.154 2 1.39e-6 7.99e-6 ✓ sig.
Melanocytic nevus Schimmelpenning-feuerstein-mims syndrome 0.154 2 1.39e-6 7.99e-6 ✓ sig.
Congenital arteriovenous malformation Penile neoplasms 0.167 2 1.82e-6 1.02e-5 ✓ sig.
Melanocytic nevus Penile neoplasms 0.143 2 2.78e-6 1.51e-5 ✓ sig.
Epidermal nevus Follicular thyroid cancer 0.154 2 3.72e-6 1.98e-5 ✓ sig.
Epidermal nevus Nonmedullary thyroid cancer 0.154 2 3.72e-6 1.98e-5 ✓ sig.
Autoimmune lymphoproliferative disorder Epidermal nevus 0.118 2 9.72e-6 4.84e-5 ✓ sig.
Epidermal nevus Melanocytic nevus 0.118 2 9.72e-6 4.84e-5 ✓ sig.
Epidermal nevus Hypophosphatemic rickets 0.111 2 1.17e-5 5.73e-5 ✓ sig.
Congenital arteriovenous malformation Hypophosphatemic rickets 0.100 2 2.00e-5 9.51e-5 ✓ sig.
Autoimmune lymphoproliferative disorder Melanocytic nevus 0.095 2 2.54e-5 1.19e-4 ✓ sig.
Splenic neoplasms Woolly hair nevus 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Seminoma Woolly hair nevus 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Schimmelpenning-feuerstein-mims syndrome Woolly hair nevus 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Seminoma Splenic neoplasms 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Neurofibrosarcoma Schimmelpenning-feuerstein-mims syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Schimmelpenning-feuerstein-mims syndrome Splenic neoplasms 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Penile neoplasms Woolly hair nevus 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Penile neoplasms Splenic neoplasms 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Bladder cancer Splenic neoplasms 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Bladder cancer Woolly hair nevus 0.200 1 2.60e-4 6.48e-4 ✓ sig.
bamforth-lazarus syndrome Nonmedullary thyroid cancer 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Follicular thyroid cancer Neurofibrosarcoma 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Neurofibrosarcoma Nonmedullary thyroid cancer 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Epidermal nevus Neurofibrosarcoma 0.125 1 4.55e-4 9.70e-4 ✓ sig.
ciliary dyskinesia, primary, 39 Epidermal nevus 0.125 1 4.55e-4 9.70e-4 ✓ sig.
ciliary dyskinesia, primary, 39 Congenital arteriovenous malformation 0.100 1 5.84e-4 1.15e-3 ✓ sig.
Autoimmune lymphoproliferative disorder autoimmune lymphoproliferative syndrome type 2A 0.083 1 7.14e-4 1.33e-3 ✓ sig.
Autoimmune lymphoproliferative disorder lymphoproliferative syndrome 1 0.083 1 7.14e-4 1.33e-3 ✓ sig.
Autoimmune lymphoproliferative disorder immunodeficiency 64 0.083 1 7.14e-4 1.33e-3 ✓ sig.
ciliary dyskinesia, primary, 39 Hypophosphatemic rickets 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Hypophosphatemic rickets Splenic neoplasms 0.077 1 7.79e-4 1.40e-3 ✓ sig.