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 114

10 diseases · 14 shared-gene connections
10 Diseases
265 Unique genes
0.072 Avg. similarity score
Colitis Most-connected disease (6 links)
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Disease Searched: macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly 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 ⇵
Colitis 6 6 33
Brain ischemia 5 5 70
Status epilepticus 4 4 70
Brain injuries 3 3 80
Necrosis 3 3 55
Sepsis 2 2 34
thrombocytopenia 6 2 2 1
Developmental delay with overweight and facial dysmorphism 1 1 1
inflammatory skin and bowel disease, neonatal, 1 1 1 1
macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
NOS2 6 / 10 Brain injuries, Brain ischemia, Colitis, Necrosis and 2 more
TNF 6 / 10 Brain injuries, Brain ischemia, Colitis, Necrosis and 2 more
IL1B 5 / 10 Brain injuries, Brain ischemia, Colitis, Necrosis and 1 more
IL6 5 / 10 Brain injuries, Brain ischemia, Colitis, Necrosis and 1 more
IL1RN 4 / 10 Brain injuries, Brain ischemia, Necrosis, Status epilepticus
PTGS2 4 / 10 Brain injuries, Brain ischemia, Colitis, Status epilepticus
BDNF 3 / 10 Brain injuries, Brain ischemia, Status epilepticus
CASP3 3 / 10 Brain ischemia, Sepsis, Status epilepticus
CAT 3 / 10 Brain ischemia, Necrosis, Status epilepticus
CCL2 3 / 10 Brain injuries, Brain ischemia, Status epilepticus
CSF3 3 / 10 Brain injuries, Brain ischemia, Sepsis
IFNG 3 / 10 Colitis, Necrosis, Sepsis
IL10 3 / 10 Brain injuries, Colitis, Sepsis
IL17A 3 / 10 Brain ischemia, Colitis, Necrosis
JUN 3 / 10 Brain injuries, Brain ischemia, Status epilepticus
MMP9 3 / 10 Brain injuries, Brain ischemia, Sepsis
MPO 3 / 10 Brain injuries, Brain ischemia, Colitis
RELA 3 / 10 Brain injuries, Brain ischemia, Colitis
SOD2 3 / 10 Brain injuries, Brain ischemia, Necrosis
SRC 3 / 10 Colitis, Status epilepticus, thrombocytopenia 6
ADAM17 2 / 10 Colitis, inflammatory skin and bowel disease, neonatal, 1
AHR 2 / 10 Colitis, Necrosis
ALB 2 / 10 Brain injuries, Brain ischemia
ANGPT1 2 / 10 Brain ischemia, Sepsis
ASIC1 2 / 10 Brain injuries, Brain ischemia
BECN1 2 / 10 Brain injuries, Status epilepticus
CCL3 2 / 10 Brain ischemia, Status epilepticus
CDC42 2 / 10 macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome, Necrosis
CEBPB 2 / 10 Brain injuries, Brain ischemia
CXCL10 2 / 10 Brain injuries, Brain ischemia
DMD 2 / 10 Necrosis, Status epilepticus
EPO 2 / 10 Brain injuries, Status epilepticus
FOS 2 / 10 Brain injuries, Status epilepticus
HMGB1 2 / 10 Necrosis, Sepsis
HMOX1 2 / 10 Colitis, Status epilepticus
ICAM1 2 / 10 Brain injuries, Brain ischemia
IGF1 2 / 10 Brain ischemia, Colitis
IL1A 2 / 10 Brain injuries, Brain ischemia
MAPK1 2 / 10 Brain ischemia, Sepsis
MAPK3 2 / 10 Brain ischemia, Sepsis
MIF 2 / 10 Colitis, Sepsis
MTHFR 2 / 10 Brain ischemia, Necrosis
PARP1 2 / 10 Brain injuries, Brain ischemia
SOD1 2 / 10 Brain ischemia, Necrosis
SRRM2 2 / 10 Developmental delay with overweight and facial dysmorphism, Status epilepticus
TLR4 2 / 10 Brain injuries, Sepsis
TNFRSF1A 2 / 10 Brain injuries, Brain ischemia
UCP2 2 / 10 Brain injuries, Brain ischemia
VEGFA 2 / 10 Brain injuries, Status epilepticus
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 ⇵
Lipid and atherosclerosis
CCL2, CD14, FOS, GSK3B, HSPA1A, IL1B, IL6, JUN, MMP9, PPP3CA, SOD2, TICAM2
 KEGG 49 / 216 10.3× 3.66e-36 1.64e-32 ✓ sig.
Cytokine-cytokine receptor interaction
CCL2, CSF3, CXCL10, EPO, IFNL3, IL10, IL12RB2, IL13RA2, IL18R1, IL1A, IL1B, IL1R1
 KEGG 53 / 298 8.1× 2.09e-33 6.85e-30 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
CCL2, FGF2, FOS, IL10, IL13RA2, IL1A, IL1B, IL6, MMP9, PTGS2, TNF, VEGFA
 Reactome 31 / 108 13.0× 1.92e-26 3.68e-23 ✓ sig.
TNF signaling pathway
CCL2, CEBPB, CXCL10, FOS, IL18R1, IL1B, IL6, IRF1, JUN, MMP9, PTGS2, TNF
 KEGG 30 / 119 11.4× 8.87e-24 1.22e-20 ✓ sig.
Toxoplasmosis
HSPA1A, IL10, TLR2, TLR4, TNF, TNFRSF1A, ITGB1, LAMA1, NOS2, RELA, CASP3, CASP9
 KEGG 28 / 112 11.3× 3.81e-22 4.07e-19 ✓ sig.
IL-17 signaling pathway
CCL2, CEBPB, CSF3, CXCL10, FOS, GSK3B, IL1B, IL6, JUN, MMP9, PTGS2, TNF
 KEGG 26 / 94 12.5× 7.25e-22 7.07e-19 ✓ sig.
Interleukin-10 signaling
CCL2, CSF3, CXCL10, IL10, IL1A, IL1B, IL1R1, IL1RN, IL6, PTGS2, TNF, TNFRSF1A
 Reactome 20 / 47 19.3× 2.09e-21 1.89e-18 ✓ sig.
Tuberculosis
CD14, CEBPB, CLEC4E, IL10, IL1A, IL1B, IL6, PPP3CA, TLR1, TLR2, TLR4, TLR9
 KEGG 33 / 181 8.3× 2.80e-21 2.45e-18 ✓ sig.
Kaposi sarcoma-associated herpesvirus infection
BECN1, FGF2, FOS, GSK3B, IL6, JUN, PPP3CA, PTGS2, TNFRSF1A, VEGFA, ICAM1, RELA
 KEGG 34 / 196 7.9× 3.58e-21 3.06e-18 ✓ sig.
Viral protein interaction with cytokine and cytokine receptor
CCL2, CXCL10, IL10, IL18R1, IL2, IL6, TNF, TNFRSF14, TNFRSF1A, TNFSF10, CCL11, CCL13
 KEGG 26 / 100 11.8× 4.15e-21 3.52e-18 ✓ sig.
Apoptosis
FOS, JUN, PARP1, TNF, TNFRSF1A, TNFSF10, RELA, BBC3, CASP3, CASP9, CYCS, DIABLO
 KEGG 28 / 137 9.3× 1.37e-19 9.51e-17 ✓ sig.
Chagas disease
CCL2, FOS, IL10, IL1B, IL2, IL6, JUN, TLR2, TLR4, TLR9, TNF, TNFRSF1A
 KEGG 25 / 103 11.0× 1.54e-19 1.06e-16 ✓ sig.
Measles
FOS, GSK3B, HSPA1A, IL1A, IL1B, IL2, IL6, JUN, TLR2, TLR4, TLR9, RELA
 KEGG 28 / 139 9.1× 2.07e-19 1.38e-16 ✓ sig.
Pathways in cancer
EPO, FGF2, FOS, GSK3B, IL12RB2, IL2, IL6, IL7, JUN, MMP9, PTGS2, TRAF4
 KEGG 51 / 533 4.3× 2.30e-19 1.53e-16 ✓ sig.
Human cytomegalovirus infection
CCL2, GSK3B, IL1B, IL1R1, IL6, PPP3CA, PTGS2, TNF, TNFRSF1A, VEGFA, RELA, CASP3
 KEGG 34 / 226 6.8× 3.91e-19 2.56e-16 ✓ 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 ⇵
inflammatory response
CCL2, CD14, CEBPB, CXCL10, FOS, IL18R1, IL1A, IL1B, IL1R1, IL1RN, IL6, LY86
 GO:0006954 57 / 467 8.6× 7.43e-37 5.83e-33 ✓ sig.
response to lipopolysaccharide
CEBPB, CXCL10, EPO, FOS, IL10, IL12RB2, IL1B, MPO, SOD2, TLR4, TNF, NOS2
 GO:0032496 33 / 161 14.5× 6.22e-29 2.97e-25 ✓ sig.
immune response
CCL2, CEBPB, CLEC4E, CSF3, CXCL10, IL10, IL18R1, IL1A, IL1B, IL1R1, IL1RN, IL2
 GO:0006955 50 / 543 6.5× 1.78e-26 6.68e-23 ✓ sig.
negative regulation of apoptotic process
BECN1, EPO, GSK3B, HSPA1A, IL10, IL2, IL31RA, IL6, IL7, JUN, MMP9, MPO
 GO:0043066 49 / 524 6.6× 3.00e-26 1.08e-22 ✓ sig.
cellular response to lipopolysaccharide
CCL2, CD14, CEBPB, CSF3, CXCL10, IL10, IL1A, IL1B, IL6, MMP9, TICAM2, TLR4
 GO:0071222 31 / 187 11.7× 2.87e-24 8.46e-21 ✓ sig.
positive regulation of chemokine production
IL1B, IL6, IL7, TLR2, TLR4, TLR9, TNF, EGR1, HIF1A, IL18, ADAM17, HMOX1
 GO:0032722 19 / 49 27.3× 5.14e-23 1.27e-19 ✓ sig.
positive regulation of gene expression
CCL2, CEBPB, FGF2, GSK3B, HSPA1A, IL1A, IL1B, IL6, IL7, PPP3CA, TLR2, TLR4
 GO:0010628 44 / 504 6.2× 2.20e-22 4.92e-19 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
BECN1, CSF3, FGF2, GSK3B, IL1B, IL1R1, NOX4, TNF, VEGFA, ITGB1, ANGPT1, CAT
 GO:0051897 31 / 217 10.1× 2.93e-22 6.44e-19 ✓ sig.
apoptotic process
BECN1, CD14, EPO, IL1A, IL1B, IRF1, JUN, MMP9, PARP1, TLR2, TNFRSF1A, TNFSF10
 GO:0006915 52 / 747 4.9× 6.99e-22 1.45e-18 ✓ sig.
response to xenobiotic stimulus
BECN1, ENO2, FOS, GABRB3, GABRG3, IL10, JUN, SOD2, TNF, RELA, ADD3, CASP3
 GO:0009410 32 / 248 9.1× 1.46e-21 2.89e-18 ✓ sig.
positive regulation of inflammatory response
CEBPB, IL1B, IL2, TLR2, TLR4, TLR9, TNF, TNFRSF1A, CCL3, IL17RA, IL18, MDK
 GO:0050729 24 / 122 13.9× 7.53e-21 1.34e-17 ✓ sig.
positive regulation of ERK1 and ERK2 cascade
CHRNA7, EPO, FGF2, IL1B, JUN, NOX4, TLR4, TNF, VEGFA, ICAM1, ANGPT1, CCL3
 GO:0070374 28 / 201 9.8× 6.81e-20 1.04e-16 ✓ sig.
positive regulation of MAPK cascade
CHRNA7, FGF2, IL1B, IL6, TLR9, TNF, VEGFA, NMNAT1, FGF1, IGF1, MAP2K1, SOD1
 GO:0043410 29 / 224 9.1× 1.15e-19 1.71e-16 ✓ sig.
positive regulation of interleukin-6 production
IL1A, IL1B, IL6, TLR1, TLR2, TLR4, TLR9, TNF, NOS2, RELA, IL17A, IL17RA
 GO:0032755 21 / 103 14.4× 1.00e-18 1.27e-15 ✓ sig.
response to hypoxia
BECN1, CHRNA7, EPO, SOD2, TNF, UCP2, VEGFA, NOS2, CASP3, CASP9, CAT, EGR1
 GO:0001666 25 / 176 10.0× 4.41e-18 5.14e-15 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Brain injuries Brain ischemia 0.180 23 1.33e-36 5.12e-35 ✓ sig.
Brain ischemia Sepsis 0.105 10 2.32e-16 3.63e-15 ✓ sig.
Brain ischemia Colitis 0.095 9 1.72e-14 2.36e-13 ✓ sig.
Brain ischemia Necrosis 0.086 10 4.80e-14 6.37e-13 ✓ sig.
Brain injuries Status epilepticus 0.079 11 6.17e-14 8.12e-13 ✓ sig.
Colitis Sepsis 0.115 7 5.43e-13 6.71e-12 ✓ sig.
Brain ischemia Status epilepticus 0.076 10 6.18e-13 7.57e-12 ✓ sig.
Brain injuries Colitis 0.075 8 4.64e-12 5.22e-11 ✓ sig.
Colitis Necrosis 0.085 7 1.99e-11 2.12e-10 ✓ sig.
Colitis inflammatory skin and bowel disease, neonatal, 1 0.029 1 2.14e-3 3.04e-3 ✓ sig.
Colitis thrombocytopenia 6 0.029 1 2.14e-3 3.04e-3 ✓ sig.
macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome Necrosis 0.018 1 3.57e-3 4.59e-3 ✓ sig.
Developmental delay with overweight and facial dysmorphism Status epilepticus 0.014 1 4.55e-3 5.67e-3 ✓ sig.
Status epilepticus thrombocytopenia 6 0.014 1 4.55e-3 5.67e-3 ✓ sig.