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 73

14 diseases · 46 shared-gene connections
14 Diseases
30 Unique genes
0.418 Avg. similarity score
Spindle cell lipoma Most-connected disease (13 links)
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Disease Searched: Giant cell tumor of soft tissue 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 ⇵
Spindle cell lipoma 13 13 3
Keloid 11 11 4
Angiolipoma 8 8 3
Low grade fibromyxoid sarcoma with giant collagen rosettes 8 8 2
Parachordoma 8 8 2
Giant cell tumor of soft tissue 7 7 2
Amyotrophic lateral sclerosis type 6 5 5 1
Cutaneous fibrous histiocytoma 5 5 9
Epithelioid hemangioendothelioma 5 5 6
Myoepithelial tumor 5 5 7
Myxoma 5 5 9
Ossifying fibroma 5 5 9
Congenital fibrosarcoma 4 4 7
Nodular fasciitis 3 3 9

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

Gene ⇵ Member diseases ⇵ Linked diseases
FUS 14 / 14 Amyotrophic lateral sclerosis type 6, Angiolipoma, Congenital fibrosarcoma, Cutaneous fibrous histiocytoma and 10 more
CREB3L2 13 / 14 Angiolipoma, Congenital fibrosarcoma, Cutaneous fibrous histiocytoma, Epithelioid hemangioendothelioma and 9 more
CREB3L1 9 / 14 Angiolipoma, Congenital fibrosarcoma, Cutaneous fibrous histiocytoma, Keloid and 5 more
COL1A1 3 / 14 Congenital fibrosarcoma, Cutaneous fibrous histiocytoma, Nodular fasciitis
EWSR1 3 / 14 Cutaneous fibrous histiocytoma, Myoepithelial tumor, Myxoma
PDGFB 3 / 14 Congenital fibrosarcoma, Cutaneous fibrous histiocytoma, Nodular fasciitis
DDIT3 2 / 14 Cutaneous fibrous histiocytoma, Myxoma
ETV6 2 / 14 Congenital fibrosarcoma, Nodular fasciitis
NTRK3 2 / 14 Congenital fibrosarcoma, Nodular fasciitis
TP53 2 / 14 Keloid, Ossifying fibroma
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 ⇵
PI3K-Akt signaling pathway
CREB3L1, CREB3L2, TP53, ERBB4, PDGFB, COL1A1, KRAS, CREB1, PTEN, KIT, TSC2, MET
 KEGG 13 / 361 14.4× 9.96e-13 1.90e-10 ✓ sig.
Prostate cancer
CREB3L1, CREB3L2, TP53, PDGFB, KRAS, CREB1, PTEN, PIK3CA, CREBBP
 KEGG 9 / 98 36.8× 1.37e-12 2.52e-10 ✓ sig.
Human papillomavirus infection
CREB3L1, CREB3L2, TP53, COL1A1, KRAS, CREB1, PTEN, APC, TSC2, GNAS, PIK3CA, CREBBP
 KEGG 12 / 333 14.4× 9.37e-12 1.43e-9 ✓ sig.
Central carbon metabolism in cancer
NTRK3, TP53, KRAS, PTEN, KIT, MET, PIK3CA
 KEGG 7 / 71 39.5× 3.41e-10 3.53e-8 ✓ sig.
Longevity regulating pathway
CREB3L1, CREB3L2, TP53, KRAS, CREB1, TSC2, PIK3CA
 KEGG 7 / 90 31.1× 1.85e-9 1.62e-7 ✓ sig.
Melanogenesis
CREB3L1, CREB3L2, KRAS, CREB1, KIT, GNAS, CREBBP
 KEGG 7 / 101 27.7× 4.19e-9 3.40e-7 ✓ sig.
Growth hormone synthesis, secretion and action
CREB3L1, CREB3L2, KRAS, CREB1, GNAS, PIK3CA, CREBBP
 KEGG 7 / 122 23.0× 1.57e-8 1.11e-6 ✓ sig.
Transcriptional misregulation in cancer
FUS, EWSR1, TP53, DDIT3, PBX1, ETV6, ATF1, MET
 KEGG 8 / 198 16.2× 2.03e-8 1.38e-6 ✓ sig.
Melanoma
TP53, PDGFB, KRAS, PTEN, MET, PIK3CA
 KEGG 6 / 73 32.9× 2.16e-8 1.46e-6 ✓ sig.
Relaxin signaling pathway
CREB3L1, CREB3L2, COL1A1, KRAS, CREB1, GNAS, PIK3CA
 KEGG 7 / 130 21.6× 2.45e-8 1.63e-6 ✓ sig.
Human T-cell leukemia virus 1 infection
CREB3L1, CREB3L2, TP53, KRAS, CREB1, PTEN, PIK3CA, CREBBP
 KEGG 8 / 224 14.3× 5.31e-8 3.21e-6 ✓ sig.
Human cytomegalovirus infection
CREB3L1, CREB3L2, TP53, KRAS, CREB1, TSC2, GNAS, PIK3CA
 KEGG 8 / 226 14.2× 5.69e-8 3.41e-6 ✓ sig.
Hepatitis B
CREB3L1, CREB3L2, TP53, KRAS, CREB1, PIK3CA, CREBBP
 KEGG 7 / 163 17.2× 1.17e-7 6.40e-6 ✓ sig.
Hepatocellular carcinoma
TP53, KRAS, PTEN, APC, SMARCB1, MET, PIK3CA
 KEGG 7 / 170 16.5× 1.56e-7 8.24e-6 ✓ sig.
Endometrial cancer
TP53, KRAS, PTEN, APC, PIK3CA
 KEGG 5 / 59 33.9× 3.12e-7 1.51e-5 ✓ 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 transcription by RNA polymerase II
CREB3L1, CREB3L2, TP53, DDIT3, PBX1, CREB1, ETV6, PTEN, ATF1, POU5F1, SMARCB1, CDC73
 GO:0045944 14 / 1,208 7.2× 1.13e-9 2.57e-7 ✓ sig.
heart development
NTRK3, TP53, ERBB4, PDGFB, PRKAR1A, PTEN, TSC2
 GO:0007507 7 / 273 16.0× 2.01e-7 2.27e-5 ✓ sig.
negative regulation of cell population proliferation
TP53, ERBB4, PTEN, NF2, APC, TSC2, SMARCB1, CDC73
 GO:0008285 8 / 444 11.2× 3.53e-7 3.63e-5 ✓ sig.
regulation of transcription by RNA polymerase II
FUS, CREB3L1, CREB3L2, TP53, DDIT3, CREB1, ETV6, PRKAR1A, ATF1, POU5F1, SMARCB1, CDC73
 GO:0006357 13 / 1,602 5.1× 3.84e-7 3.89e-5 ✓ sig.
regulation of DNA-templated transcription
FUS, EWSR1, CREB3L1, CREB3L2, TP53, DDIT3, PBX1, CREB1, ETV6, ATF1, POU5F1, CREBBP
 GO:0006355 12 / 1,454 5.1× 1.08e-6 9.19e-5 ✓ sig.
cell surface receptor protein tyrosine kinase signaling pathway
NTRK3, ERBB4, PDGFB, KIT, MET
 GO:0007169 5 / 120 26.0× 1.26e-6 1.04e-4 ✓ sig.
positive regulation of DNA-templated transcription
FUS, CREB3L2, TP53, ERBB4, DDIT3, PDGFB, COL1A1, CREB1, CREBBP
 GO:0045893 9 / 778 7.2× 2.33e-6 1.72e-4 ✓ sig.
cell migration
CDH11, ERBB4, PTEN, APC, KIT, PIK3CA
 GO:0016477 6 / 303 12.3× 7.40e-6 4.31e-4 ✓ sig.
negative regulation of gene expression
CREB3L1, TP53, PDGFB, CREB1, PRKAR1A, PIK3CA
 GO:0010629 6 / 339 11.0× 1.40e-5 7.08e-4 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
NTRK3, ERBB4, PDGFB, KIT, PIK3CA
 GO:0051897 5 / 217 14.4× 2.27e-5 1.02e-3 ✓ sig.
positive regulation of RNA polymerase II transcription preinitiation complex assembly
TP53, CREB1
 GO:0045899 2 / 5 249× 2.48e-5 1.09e-3 ✓ sig.
response to purine-containing compound
CREB1, ATF1
 GO:0014074 2 / 7 178× 5.21e-5 1.90e-3 ✓ sig.
regulation of cell cycle
TP53, DDIT3, PTEN, NF2, TSC2
 GO:0051726 5 / 262 11.9× 5.58e-5 2.00e-3 ✓ sig.
positive chemotaxis
PDGFB, TSC2, MET
 GO:0050918 3 / 51 36.6× 7.38e-5 2.47e-3 ✓ sig.
visual learning
KRAS, CREB1, KIT
 GO:0008542 3 / 54 34.6× 8.76e-5 2.81e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital fibrosarcoma Nodular fasciitis 0.700 7 8.50e-25 1.45e-23 ✓ sig.
Congenital fibrosarcoma Cutaneous fibrous histiocytoma 0.417 5 3.56e-16 4.52e-15 ✓ sig.
Cutaneous fibrous histiocytoma Myxoma 0.385 5 9.50e-16 1.19e-14 ✓ sig.
Cutaneous fibrous histiocytoma Nodular fasciitis 0.357 5 2.14e-15 2.62e-14 ✓ sig.
Myoepithelial tumor Myxoma 0.333 4 1.02e-12 1.10e-11 ✓ sig.
Keloid Spindle cell lipoma 0.750 3 1.62e-12 1.71e-11 ✓ sig.
Angiolipoma Spindle cell lipoma 0.750 3 1.62e-12 1.71e-11 ✓ sig.
Angiolipoma Keloid 0.750 3 1.62e-12 1.71e-11 ✓ sig.
Cutaneous fibrous histiocytoma Myoepithelial tumor 0.308 4 1.84e-12 1.94e-11 ✓ sig.
Myoepithelial tumor Spindle cell lipoma 0.375 3 5.65e-11 5.40e-10 ✓ sig.
Congenital fibrosarcoma Spindle cell lipoma 0.375 3 5.65e-11 5.40e-10 ✓ sig.
Congenital fibrosarcoma Keloid 0.375 3 5.65e-11 5.40e-10 ✓ sig.
Ossifying fibroma Spindle cell lipoma 0.375 3 5.65e-11 5.40e-10 ✓ sig.
Keloid Ossifying fibroma 0.375 3 5.65e-11 5.40e-10 ✓ sig.
Angiolipoma Ossifying fibroma 0.375 3 5.65e-11 5.40e-10 ✓ sig.
Angiolipoma Myoepithelial tumor 0.375 3 5.65e-11 5.40e-10 ✓ sig.
Keloid Myoepithelial tumor 0.375 3 5.65e-11 5.40e-10 ✓ sig.
Angiolipoma Myxoma 0.333 3 9.05e-11 8.46e-10 ✓ sig.
Keloid Myxoma 0.333 3 9.05e-11 8.46e-10 ✓ sig.
Myxoma Spindle cell lipoma 0.333 3 9.05e-11 8.46e-10 ✓ sig.
Cutaneous fibrous histiocytoma Spindle cell lipoma 0.300 3 1.36e-10 1.25e-9 ✓ sig.
Nodular fasciitis Spindle cell lipoma 0.300 3 1.36e-10 1.25e-9 ✓ sig.
Giant cell tumor of soft tissue Parachordoma 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Giant cell tumor of soft tissue Low grade fibromyxoid sarcoma with giant collagen rosettes 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Low grade fibromyxoid sarcoma with giant collagen rosettes Parachordoma 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Low grade fibromyxoid sarcoma with giant collagen rosettes Spindle cell lipoma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Keloid Low grade fibromyxoid sarcoma with giant collagen rosettes 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Parachordoma Spindle cell lipoma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Giant cell tumor of soft tissue Keloid 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Angiolipoma Parachordoma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Angiolipoma Low grade fibromyxoid sarcoma with giant collagen rosettes 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Angiolipoma Giant cell tumor of soft tissue 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Giant cell tumor of soft tissue Spindle cell lipoma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Keloid Parachordoma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Epithelioid hemangioendothelioma Giant cell tumor of soft tissue 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Epithelioid hemangioendothelioma Low grade fibromyxoid sarcoma with giant collagen rosettes 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Epithelioid hemangioendothelioma Parachordoma 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Ossifying fibroma Parachordoma 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Low grade fibromyxoid sarcoma with giant collagen rosettes Ossifying fibroma 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Epithelioid hemangioendothelioma Spindle cell lipoma 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Epithelioid hemangioendothelioma Keloid 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Amyotrophic lateral sclerosis type 6 Giant cell tumor of soft tissue 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Amyotrophic lateral sclerosis type 6 Low grade fibromyxoid sarcoma with giant collagen rosettes 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Amyotrophic lateral sclerosis type 6 Parachordoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Amyotrophic lateral sclerosis type 6 Keloid 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Amyotrophic lateral sclerosis type 6 Spindle cell lipoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.