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 77

14 diseases · 41 shared-gene connections
14 Diseases
22 Unique genes
0.394 Avg. similarity score
Benign renal pelvis neoplasm Most-connected disease (12 links)
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Disease Searched: Dopamine beta-hydroxylase deficiency 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 ⇵
Benign renal pelvis neoplasm 12 12 2
Mixed epithelial stromal tumor of the kidney 12 12 2
Inclusion body fibromatosis 9 9 2
Benign kidney neoplasm 8 8 2
Congenital mesoblastic nephroma 7 7 3
Ossifying renal tumor of infancy 6 6 4
Cystic nephroma 5 5 3
Thrombocytopenia 5 5 5 1
Hematologic neoplasms 4 4 5
Rhabdomyosarcoma with mixed embryonal and alveolar features 4 4 3
Fibrous hamartoma of infancy 3 3 5
Lipoblastoma 3 3 8
Myofibromatosis 3 3 4
Dopamine beta-hydroxylase deficiency 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
ETV6 12 / 14 Benign kidney neoplasm, Benign renal pelvis neoplasm, Congenital mesoblastic nephroma, Cystic nephroma and 8 more
NTRK3 11 / 14 Benign kidney neoplasm, Benign renal pelvis neoplasm, Congenital mesoblastic nephroma, Cystic nephroma and 7 more
CTNNB1 2 / 14 Lipoblastoma, Ossifying renal tumor of infancy
EGFR 2 / 14 Congenital mesoblastic nephroma, Fibrous hamartoma of infancy
HSPA5 2 / 14 Dopamine beta-hydroxylase deficiency, Hematologic 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 ⇵
MicroRNAs in cancer
ABCB1, NOTCH3, PDGFRB, EGFR, DICER1, PDGFB
 KEGG 6 / 311 10.5× 1.51e-5 3.81e-4 ✓ sig.
Prostate cancer
PDGFRB, EGFR, CTNNB1, PDGFB
 KEGG 4 / 98 22.3× 2.72e-5 6.17e-4 ✓ sig.
Focal adhesion
PDGFRB, EGFR, CTNNB1, COL1A1, PDGFB
 KEGG 5 / 203 13.4× 2.74e-5 6.19e-4 ✓ sig.
JAK-STAT signaling pathway
PDGFRB, EGFR, LIFR, PDGFB
 KEGG 4 / 168 13.0× 2.22e-4 3.33e-3 ✓ sig.
Central carbon metabolism in cancer
NTRK3, PDGFRB, EGFR
 KEGG 3 / 71 23.1× 2.81e-4 4.01e-3 ✓ sig.
Human papillomavirus infection
NOTCH3, PDGFRB, EGFR, CTNNB1, COL1A1
 KEGG 5 / 333 8.2× 2.84e-4 4.04e-3 ✓ sig.
Melanoma
PDGFRB, EGFR, PDGFB
 KEGG 3 / 73 22.4× 3.05e-4 4.28e-3 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
PDGFRB, EGFR, PDGFB
 Reactome 3 / 75 21.8× 3.31e-4 4.56e-3 ✓ sig.
Glioma
PDGFRB, EGFR, PDGFB
 KEGG 3 / 76 21.5× 3.44e-4 4.70e-3 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
PDGFRB, EGFR, PDGFB
 KEGG 3 / 80 20.5× 4.00e-4 5.30e-3 ✓ sig.
Transcriptional misregulation in cancer
ETV6, H3C2, FUS, DDIT3
 KEGG 4 / 198 11.0× 4.15e-4 5.47e-3 ✓ sig.
Rap1 signaling pathway
PDGFRB, EGFR, CTNNB1, PDGFB
 KEGG 4 / 211 10.3× 5.28e-4 6.58e-3 ✓ sig.
NOTCH3 Activation and Transmission of Signal to the Nucleus
NOTCH3, EGFR
 Reactome 2 / 19 57.5× 5.38e-4 6.67e-3 ✓ sig.
Gap junction
PDGFRB, EGFR, PDGFB
 KEGG 3 / 89 18.4× 5.47e-4 6.77e-3 ✓ sig.
PIP3 activates AKT signaling
PDGFRB, EGFR, PDGFB
 Reactome 3 / 93 17.6× 6.22e-4 7.48e-3 ✓ 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 ⇵
positive regulation of cell migration
NTRK3, HSPA5, PDGFRB, EGFR, COL1A1, PDGFB
 GO:0030335 6 / 292 17.5× 8.36e-7 7.32e-5 ✓ sig.
positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway
PDGFRB, PDGFB
 GO:0035793 2 / 3 566× 3.97e-6 2.56e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
ETV6, HSPA5, NOTCH3, EGFR, FBXW7, PLAG1, TCEA1, CTNNB1, DDIT3
 GO:0045944 9 / 1,208 6.3× 4.41e-6 2.80e-4 ✓ sig.
smooth muscle adaptation
PDGFRB, PDGFB
 GO:0014805 2 / 4 425× 7.93e-6 4.45e-4 ✓ sig.
cell surface receptor protein tyrosine kinase signaling pathway
NTRK3, PDGFRB, EGFR, PDGFB
 GO:0007169 4 / 120 28.3× 1.08e-5 5.62e-4 ✓ sig.
gene expression
H3C2, FUS, CTNNB1, PDGFB, DDIT3
 GO:0010467 5 / 269 15.8× 1.28e-5 6.43e-4 ✓ sig.
establishment of blood-retinal barrier
ABCB1, CTNNB1
 GO:1990963 2 / 6 283× 1.98e-5 8.96e-4 ✓ sig.
positive regulation of cell population proliferation
NTRK3, PDGFRB, EGFR, LIFR, CTNNB1, PDGFB
 GO:0008284 6 / 532 9.6× 2.62e-5 1.11e-3 ✓ sig.
positive regulation of smooth muscle cell proliferation
NOTCH3, PDGFRB, PDGFB
 GO:0048661 3 / 52 49.0× 3.01e-5 1.23e-3 ✓ sig.
positive regulation of miRNA transcription
NOTCH3, EGFR, PDGFB
 GO:1902895 3 / 56 45.5× 3.77e-5 1.46e-3 ✓ sig.
negative regulation of gene expression
FBXW7, PLAG1, DICER1, CTNNB1, PDGFB
 GO:0010629 5 / 339 12.5× 3.90e-5 1.50e-3 ✓ sig.
PERK-mediated unfolded protein response
HSPA5, DDIT3
 GO:0036499 2 / 11 154× 7.23e-5 2.38e-3 ✓ sig.
ER overload response
HSPA5, DDIT3
 GO:0006983 2 / 11 154× 7.23e-5 2.38e-3 ✓ sig.
establishment of blood-brain barrier
ABCB1, CTNNB1
 GO:0060856 2 / 11 154× 7.23e-5 2.38e-3 ✓ sig.
positive regulation of ERK1 and ERK2 cascade
PDGFRB, EGFR, FBXW7, PDGFB
 GO:0070374 4 / 201 16.9× 8.16e-5 2.60e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital mesoblastic nephroma Fibrous hamartoma of infancy 0.500 3 1.62e-11 1.61e-10 ✓ sig.
Lipoblastoma Ossifying renal tumor of infancy 0.300 3 3.62e-10 3.23e-9 ✓ sig.
Benign kidney neoplasm Mixed epithelial stromal tumor of the kidney 0.667 2 8.34e-9 6.59e-8 ✓ sig.
Benign kidney neoplasm Inclusion body fibromatosis 0.667 2 8.34e-9 6.59e-8 ✓ sig.
Inclusion body fibromatosis Mixed epithelial stromal tumor of the kidney 0.667 2 8.34e-9 6.59e-8 ✓ sig.
Benign renal pelvis neoplasm Mixed epithelial stromal tumor of the kidney 0.667 2 8.34e-9 6.59e-8 ✓ sig.
Benign renal pelvis neoplasm Inclusion body fibromatosis 0.667 2 8.34e-9 6.59e-8 ✓ sig.
Benign kidney neoplasm Benign renal pelvis neoplasm 0.667 2 8.34e-9 6.59e-8 ✓ sig.
Cystic nephroma Mixed epithelial stromal tumor of the kidney 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Cystic nephroma Inclusion body fibromatosis 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Congenital mesoblastic nephroma Inclusion body fibromatosis 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Congenital mesoblastic nephroma Mixed epithelial stromal tumor of the kidney 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Benign renal pelvis neoplasm Cystic nephroma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Benign renal pelvis neoplasm Congenital mesoblastic nephroma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Benign kidney neoplasm Cystic nephroma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Benign kidney neoplasm Congenital mesoblastic nephroma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Benign kidney neoplasm Ossifying renal tumor of infancy 0.400 2 5.00e-8 3.62e-7 ✓ sig.
Inclusion body fibromatosis Ossifying renal tumor of infancy 0.400 2 5.00e-8 3.62e-7 ✓ sig.
Mixed epithelial stromal tumor of the kidney Ossifying renal tumor of infancy 0.400 2 5.00e-8 3.62e-7 ✓ sig.
Benign renal pelvis neoplasm Ossifying renal tumor of infancy 0.400 2 5.00e-8 3.62e-7 ✓ sig.
Inclusion body fibromatosis Myofibromatosis 0.400 2 5.00e-8 3.62e-7 ✓ sig.
Mixed epithelial stromal tumor of the kidney Myofibromatosis 0.400 2 5.00e-8 3.62e-7 ✓ sig.
Benign renal pelvis neoplasm Myofibromatosis 0.400 2 5.00e-8 3.62e-7 ✓ sig.
Congenital mesoblastic nephroma Cystic nephroma 0.400 2 7.50e-8 5.34e-7 ✓ sig.
Benign renal pelvis neoplasm Fibrous hamartoma of infancy 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Fibrous hamartoma of infancy Mixed epithelial stromal tumor of the kidney 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Congenital mesoblastic nephroma Ossifying renal tumor of infancy 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Lipoblastoma Mixed epithelial stromal tumor of the kidney 0.222 2 2.33e-7 1.55e-6 ✓ sig.
Benign renal pelvis neoplasm Lipoblastoma 0.222 2 2.33e-7 1.55e-6 ✓ sig.
Benign renal pelvis neoplasm Thrombocytopenia 5 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mixed epithelial stromal tumor of the kidney Thrombocytopenia 5 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Inclusion body fibromatosis Thrombocytopenia 5 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Benign kidney neoplasm Thrombocytopenia 5 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hematologic neoplasms Thrombocytopenia 5 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Benign renal pelvis neoplasm Rhabdomyosarcoma with mixed embryonal and alveolar features 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Benign kidney neoplasm Rhabdomyosarcoma with mixed embryonal and alveolar features 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Inclusion body fibromatosis Rhabdomyosarcoma with mixed embryonal and alveolar features 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Mixed epithelial stromal tumor of the kidney Rhabdomyosarcoma with mixed embryonal and alveolar features 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Hematologic neoplasms Mixed epithelial stromal tumor of the kidney 0.143 1 6.46e-4 1.09e-3 ✓ sig.
Benign renal pelvis neoplasm Hematologic neoplasms 0.143 1 6.46e-4 1.09e-3 ✓ sig.
Dopamine beta-hydroxylase deficiency Hematologic neoplasms 0.143 1 6.46e-4 1.09e-3 ✓ sig.