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 55

15 diseases · 47 shared-gene connections
15 Diseases
29 Unique genes
0.291 Avg. similarity score
Alpha thalassemia x-linked intellectual disability Most-connected disease (12 links)
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Disease Searched: Pineocytoma 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 ⇵
Alpha thalassemia x-linked intellectual disability 12 12 1
Atr-x syndrome 12 12 1
Lung pecoma 11 11 1
X-linked alpha-thalassemia-intellectual disability syndrome 11 11 1
Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type 8 8 1
Intellectual developmental disorder hypotonic x-linked 6 6 2
Choroid plexus carcinoma 5 5 7
Extra-adrenal sympathetic paraganglioma 5 5 3
Peritoneal well differentiated papillary mesothelioma 5 5 3
Pineocytoma 5 5 3
Thoracic disease 5 5 3
Penile disease 4 4 6
Placental site trophoblastic tumor 3 3 6
Astroblastoma 1 1 7
Say meyer syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ATRX 14 / 15 Alpha thalassemia x-linked intellectual disability, Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type, Astroblastoma, Atr-x syndrome and 10 more
FAT1 2 / 15 Astroblastoma, Extra-adrenal sympathetic paraganglioma
HUWE1 2 / 15 Intellectual developmental disorder hypotonic x-linked, Say meyer syndrome
RHOA 2 / 15 Peritoneal well differentiated papillary mesothelioma, Placental site trophoblastic tumor
TP53 2 / 15 Astroblastoma, Choroid plexus 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 ⇵
Endometrial cancer
TP53, ILK, BRAF, APC
 KEGG 4 / 59 28.1× 1.14e-5 3.24e-4 ✓ sig.
Hepatocellular carcinoma
TP53, SMARCB1, BRAF, APC, ARID2
 KEGG 5 / 170 12.2× 4.83e-5 1.06e-3 ✓ sig.
Colorectal cancer
TP53, BRAF, APC, RHOA
 KEGG 4 / 87 19.0× 5.31e-5 1.14e-3 ✓ sig.
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
EP300, KMT2C, H3-3A, KMT2D
 Reactome 4 / 97 17.1× 8.13e-5 1.61e-3 ✓ sig.
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
SMARCB1, EP300, ARID2
 Reactome 3 / 38 32.7× 1.01e-4 1.91e-3 ✓ sig.
Ovarian tumor domain proteases
TP53, APC, RHOA
 Reactome 3 / 38 32.7× 1.01e-4 1.91e-3 ✓ sig.
PI5P Regulates TP53 Acetylation
TP53, EP300
 Reactome 2 / 9 92.0× 2.01e-4 3.29e-3 ✓ sig.
Cushing syndrome
POMC, BRAF, APC, KMT2D
 KEGG 4 / 155 10.7× 4.93e-4 6.61e-3 ✓ sig.
Cell cycle
ATRX, TP53, EP300, STAG2
 KEGG 4 / 158 10.5× 5.30e-4 6.98e-3 ✓ sig.
Central carbon metabolism in cancer
TP53, IDH2, IDH1
 KEGG 3 / 71 17.5× 6.48e-4 8.17e-3 ✓ sig.
Wnt signaling pathway
TP53, EP300, APC, RHOA
 KEGG 4 / 174 9.5× 7.62e-4 9.20e-3 ✓ sig.
TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest
TP53, EP300
 Reactome 2 / 18 46.0× 8.41e-4 9.92e-3 ✓ sig.
Regulation of TP53 Activity through Methylation
TP53, EP300
 Reactome 2 / 19 43.6× 9.39e-4 1.08e-2 ✓ sig.
Formation of the beta-catenin:TCF transactivating complex
EP300, H3-3A, KMT2D
 Reactome 3 / 88 14.1× 1.21e-3 1.31e-2 ✓ sig.
Focal adhesion
ILK, BRAF, RHOA, KDR
 KEGG 4 / 203 8.2× 1.35e-3 1.42e-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 ⇵
chromatin remodeling
ATRX, HUWE1, SMARCB1, EP300, KMT2C, ARID2, BRD4
 GO:0006338 7 / 320 14.1× 4.57e-7 4.51e-5 ✓ sig.
multicellular organism growth
ATRX, TP53, IFT80, EP300, H3-3A
 GO:0035264 5 / 115 28.0× 8.53e-7 7.52e-5 ✓ sig.
glyoxylate cycle
IDH2, IDH1
 GO:0006097 2 / 2 644× 2.33e-6 1.72e-4 ✓ sig.
canonical NF-kappaB signal transduction
HUWE1, IFT80, EP300, TRAF7
 GO:0007249 4 / 62 41.6× 2.45e-6 1.79e-4 ✓ sig.
response to inositol
INPP5E, IFT80
 GO:1902140 2 / 4 322× 1.39e-5 7.04e-4 ✓ sig.
isocitrate metabolic process
IDH2, IDH1
 GO:0006102 2 / 5 258× 2.32e-5 1.03e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
TP53, SMARCB1, EP300
 GO:0045815 3 / 41 47.1× 3.44e-5 1.39e-3 ✓ sig.
embryonic organ development
TP53, POLE, ARID2
 GO:0048568 3 / 42 46.0× 3.70e-5 1.47e-3 ✓ sig.
substrate adhesion-dependent cell spreading
ILK, BRAF, RHOA
 GO:0034446 3 / 46 42.0× 4.88e-5 1.81e-3 ✓ sig.
chromatin organization
ATRX, SMARCB1, KMT2C, ARID2, KMT2D, BRD4
 GO:0006325 6 / 449 8.6× 5.53e-5 1.99e-3 ✓ sig.
positive regulation of T-helper 17 cell lineage commitment
EP300, BRD4
 GO:2000330 2 / 8 161× 6.47e-5 2.24e-3 ✓ sig.
stem cell proliferation
TP53, IFT80, KDR
 GO:0072089 3 / 54 35.8× 7.90e-5 2.60e-3 ✓ sig.
subtelomeric heterochromatin formation
ATRX, H3-3A
 GO:0031509 2 / 11 117× 1.27e-4 3.66e-3 ✓ sig.
negative regulation of glial cell proliferation
TP53, IDH2
 GO:0060253 2 / 11 117× 1.27e-4 3.66e-3 ✓ sig.
NADP+ metabolic process
IDH2, IDH1
 GO:0006739 2 / 14 92.1× 2.09e-4 5.24e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Peritoneal well differentiated papillary mesothelioma Placental site trophoblastic tumor 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Astroblastoma Extra-adrenal sympathetic paraganglioma 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Alpha thalassemia x-linked intellectual disability X-linked alpha-thalassemia-intellectual disability syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Lung pecoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type Atr-x syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type X-linked alpha-thalassemia-intellectual disability syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type Lung pecoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atr-x syndrome X-linked alpha-thalassemia-intellectual disability syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atr-x syndrome Lung pecoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lung pecoma X-linked alpha-thalassemia-intellectual disability syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Atr-x syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder hypotonic x-linked Lung pecoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intellectual developmental disorder hypotonic x-linked Say meyer syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intellectual developmental disorder hypotonic x-linked X-linked alpha-thalassemia-intellectual disability syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Intellectual developmental disorder hypotonic x-linked 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Atr-x syndrome Intellectual developmental disorder hypotonic x-linked 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type Intellectual developmental disorder hypotonic x-linked 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Peritoneal well differentiated papillary mesothelioma X-linked alpha-thalassemia-intellectual disability syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type Thoracic disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Lung pecoma Thoracic disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Thoracic disease X-linked alpha-thalassemia-intellectual disability syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Atr-x syndrome Thoracic disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Thoracic disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type Pineocytoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Lung pecoma Pineocytoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Pineocytoma X-linked alpha-thalassemia-intellectual disability syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Atr-x syndrome Pineocytoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Pineocytoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Lung pecoma Peritoneal well differentiated papillary mesothelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Peritoneal well differentiated papillary mesothelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Extra-adrenal sympathetic paraganglioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Atr-x syndrome Extra-adrenal sympathetic paraganglioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Extra-adrenal sympathetic paraganglioma X-linked alpha-thalassemia-intellectual disability syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Extra-adrenal sympathetic paraganglioma Lung pecoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Atr-x syndrome Peritoneal well differentiated papillary mesothelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Atr-x syndrome Choroid plexus carcinoma 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Choroid plexus carcinoma Lung pecoma 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Alpha-thalassemia intellectual developmental disorder syndrome non-deletion type Choroid plexus carcinoma 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Choroid plexus carcinoma 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Choroid plexus carcinoma X-linked alpha-thalassemia-intellectual disability syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Placental site trophoblastic tumor 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Atr-x syndrome Placental site trophoblastic tumor 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Alpha thalassemia x-linked intellectual disability Penile disease 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Atr-x syndrome Penile disease 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Penile disease X-linked alpha-thalassemia-intellectual disability syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Lung pecoma Penile disease 0.143 1 3.87e-4 7.33e-4 ✓ sig.