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 19

25 diseases · 66 shared-gene connections
25 Diseases
86 Unique genes
0.289 Avg. similarity score
Lymphangioleiomyomatosis Most-connected disease (11 links)
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Disease Searched: Polycystic kidney disease 2 with or without polycystic liver disease 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 ⇵
Lymphangioleiomyomatosis 11 11 2
Fibroma 10 10 2
Polycystic kidney disease with tuberous sclerosis 10 10 2
Subependymal giant cell astrocytoma 9 9 3
Polycystic kidneys, severe infantile with tuberous sclerosis 8 8 2
Epithelioid type angiomyolipoma 7 7 1
Tuberous sclerosis 2 7 7 1
Tuberous sclerosis complex 7 7 6
Liver cyst 6 6 2
Lung lymphangioleiomyomatosis 6 6 3
Benign neoplasm of brain 5 5 13
Cortical dysplasia 5 5 8
Focal cortical dysplasia 5 5 8
Polycystic kidney disease 1 with or without polycystic liver disease 5 5 1
Tuberous sclerosis 1 5 5 1
Brain disease 4 4 42
Congenital kidney anomaly 4 4 3
Renovascular hypertension 4 4 2
Xanthinuria 4 4 4
Pineal parenchymal tumor of intermediate differentiation 3 3 2
Intracranial aneurysm 2 2 15
Polycystic kidney disease 2 with or without polycystic liver disease 2 2 1
Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 7 1 1 1
Encephalopathy, acute, infection-induced, susceptibility to, 6 1 1 1
Fliedner-zweier syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TSC2 14 / 25 Benign neoplasm of brain, Brain disease, Cortical dysplasia, Epithelioid type angiomyolipoma and 10 more
TSC1 11 / 25 Benign neoplasm of brain, Brain disease, Cortical dysplasia, Fibroma and 7 more
PKD1 9 / 25 Congenital kidney anomaly, Focal cortical dysplasia, Intracranial aneurysm, Liver cyst and 5 more
PKD2 3 / 25 Intracranial aneurysm, Liver cyst, Polycystic kidney disease 2 with or without polycystic liver disease
BRAF 2 / 25 Cortical dysplasia, Subependymal giant cell astrocytoma
IFNG 2 / 25 Brain disease, Tuberous sclerosis complex
IRF3 2 / 25 Brain disease, Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 7
MTOR 2 / 25 Cortical dysplasia, Focal cortical dysplasia
NTHL1 2 / 25 Focal cortical dysplasia, Tuberous sclerosis complex
SCAF4 2 / 25 Congenital kidney anomaly, Fliedner-zweier syndrome
TBR1 2 / 25 Cortical dysplasia, Focal cortical dysplasia
TICAM1 2 / 25 Brain disease, Encephalopathy, acute, infection-induced, susceptibility to, 6
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 ⇵
Herpes simplex virus 1 infection
TSC2, IFNB1, IFNG, IRF3, TBK1, TICAM1, TSC1, MTOR, RHEB, BCL2, IL6, PIK3CA
 KEGG 12 / 182 9.2× 5.88e-9 4.60e-7 ✓ sig.
Hepatitis B
IFNB1, IRF3, TBK1, TGFB1, TICAM1, BCL2, IL6, MMP9, BRAF, PIK3CA, EP300
 KEGG 11 / 163 9.4× 2.09e-8 1.42e-6 ✓ sig.
Lipid and atherosclerosis
CYP2A6, IFNB1, IRF3, TBK1, TICAM1, NOS3, BCL2, IL6, MMP9, NCF1, PIK3CA
 KEGG 11 / 216 7.1× 3.70e-7 1.76e-5 ✓ sig.
Human papillomavirus infection
TSC2, IFNB1, IRF3, LAMC3, PPP2R2B, TBK1, TICAM1, TSC1, MTOR, RHEB, COL1A2, PIK3CA
 KEGG 13 / 333 5.5× 6.37e-7 2.82e-5 ✓ sig.
Diabetic cardiomyopathy
CPT2, NDUFS4, TGFB1, MTOR, NOS3, COL1A2, MMP2, MMP9, NCF1, PIK3CA
 KEGG 10 / 205 6.8× 1.93e-6 7.34e-5 ✓ sig.
TRAF3-dependent IRF activation pathway
IFNB1, IRF3, TBK1, EP300
 Reactome 4 / 14 39.9× 2.32e-6 8.56e-5 ✓ sig.
Human cytomegalovirus infection
TSC2, CXCR2, IFNB1, IRF3, TBK1, TSC1, MTOR, RHEB, IL6, PIK3CA
 KEGG 10 / 226 6.2× 4.63e-6 1.54e-4 ✓ sig.
Prostate cancer
MTOR, BCL2, MMP9, SRD5A2, BRAF, PIK3CA, EP300
 KEGG 7 / 98 10.0× 6.16e-6 1.95e-4 ✓ sig.
Fluid shear stress and atherosclerosis
IFNG, NOS3, BCL2, MMP2, MMP9, NCF1, PIK3CA, BMPR1A
 KEGG 8 / 141 7.9× 7.26e-6 2.24e-4 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
TGFB1, NOS3, BCL2, COL1A2, IL6, MMP2, PIK3CA
 KEGG 7 / 101 9.7× 7.53e-6 2.31e-4 ✓ sig.
Chagas disease
IFNB1, IFNG, PPP2R2B, TGFB1, TICAM1, IL6, PIK3CA
 KEGG 7 / 103 9.5× 8.57e-6 2.57e-4 ✓ sig.
PI3K-Akt signaling pathway
TSC2, IFNB1, LAMC3, PPP2R2B, TSC1, MTOR, RHEB, NOS3, BCL2, COL1A2, IL6, PIK3CA
 KEGG 12 / 361 4.6× 9.35e-6 2.75e-4 ✓ sig.
HIF-1 signaling pathway
IFNG, MTOR, NOS3, BCL2, IL6, PIK3CA, EP300
 KEGG 7 / 110 8.9× 1.32e-5 3.67e-4 ✓ sig.
Hepatitis C
IFNB1, IFNG, IRF3, PPP2R2B, TBK1, TICAM1, BRAF, PIK3CA
 KEGG 8 / 159 7.0× 1.75e-5 4.67e-4 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
ALB, APP, CP, FAM20C, IL6, MMP2, VCAN
 Reactome 7 / 125 7.8× 3.04e-5 7.32e-4 ✓ 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
PKD1, APP, IFNB1, IFNG, IRF3, OGG1, TBK1, TGFB1, TBR1, ENG, IL6, KMT2D
 GO:0045944 22 / 1,208 4.0× 1.76e-8 2.88e-6 ✓ sig.
TORC1 signaling
TSC2, TBK1, TSC1, MTOR, RHEB, DEPDC5, EP300
 GO:0038202 7 / 67 22.7× 2.37e-8 3.74e-6 ✓ sig.
cell surface receptor signaling pathway via JAK-STAT
PKD1, IFNB1, IFNG, STAMBP, IL6, PKD2, EP300
 GO:0007259 7 / 67 22.7× 2.37e-8 3.74e-6 ✓ sig.
positive regulation of TORC1 signaling
TSC2, TBK1, TSC1, MTOR, RHEB, DEPDC5, EP300
 GO:1904263 7 / 71 21.4× 3.57e-8 5.32e-6 ✓ sig.
heart development
PKD1, TSC2, TGFB1, TH, ENG, MMP2, PKD2, SOX17, EP300, BMPR1A
 GO:0007507 10 / 273 8.0× 5.01e-7 4.88e-5 ✓ sig.
intracellular copper ion homeostasis
APP, CP, SCO1, SCO2
 GO:0006878 4 / 18 48.3× 1.22e-6 1.01e-4 ✓ sig.
positive regulation of translational initiation
TSC2, TBK1, MTOR, RHEB, DEPDC5
 GO:0045948 5 / 42 25.9× 1.37e-6 1.11e-4 ✓ sig.
defense response to virus
IFNB1, IFNG, IRF3, TBK1, TICAM1, TREX1, UNC93B1, BCL2, IL6
 GO:0051607 9 / 247 7.9× 2.02e-6 1.53e-4 ✓ sig.
response to xenobiotic stimulus
OTC, SLC1A1, TGFB1, BCL2, MMP2, SRD5A2, SS18, XPC, ABL1
 GO:0009410 9 / 248 7.9× 2.09e-6 1.57e-4 ✓ sig.
cellular response to nutrient levels
TSC2, TBK1, MTOR, RHEB, DEPDC5, EP300
 GO:0031669 6 / 83 15.7× 2.26e-6 1.68e-4 ✓ sig.
regulation of gene expression
PKD1, APP, IRF3, TBK1, TGFB1, TREX1, TBR1, BCL2, PIK3CA, TET2, ABL1
 GO:0010468 11 / 402 5.9× 2.29e-6 1.70e-4 ✓ sig.
regulation of cell cycle
PKD1, TSC2, NUP214, TGFB1, TSC1, RHEB, BCL2, PKD2, ABL1
 GO:0051726 9 / 262 7.5× 3.27e-6 2.25e-4 ✓ sig.
ephrin receptor signaling pathway
CDK5R1, MMP2, MMP9, SS18, ABL1
 GO:0048013 5 / 51 21.3× 3.65e-6 2.46e-4 ✓ sig.
positive regulation of autophagy
IFNB1, IFNG, TBK1, TICAM1, MTOR, DEPDC5
 GO:0010508 6 / 92 14.2× 4.14e-6 2.72e-4 ✓ sig.
positive regulation of interleukin-6 production
APP, IFNG, TGFB1, TICAM1, UNC93B1, IL6
 GO:0032755 6 / 103 12.7× 7.97e-6 4.57e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Focal cortical dysplasia Tuberous sclerosis complex 0.364 4 4.38e-13 4.82e-12 ✓ sig.
Cortical dysplasia Focal cortical dysplasia 0.364 4 4.38e-13 4.82e-12 ✓ sig.
Fibroma Lymphangioleiomyomatosis 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Fibroma Subependymal giant cell astrocytoma 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Polycystic kidney disease with tuberous sclerosis Polycystic kidneys, severe infantile with tuberous sclerosis 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Lymphangioleiomyomatosis Subependymal giant cell astrocytoma 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Fibroma Lung lymphangioleiomyomatosis 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Lung lymphangioleiomyomatosis Subependymal giant cell astrocytoma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Lung lymphangioleiomyomatosis Lymphangioleiomyomatosis 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Cortical dysplasia Fibroma 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Polycystic kidneys, severe infantile with tuberous sclerosis Tuberous sclerosis complex 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Polycystic kidney disease with tuberous sclerosis Tuberous sclerosis complex 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Cortical dysplasia Subependymal giant cell astrocytoma 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Cortical dysplasia Lymphangioleiomyomatosis 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Lymphangioleiomyomatosis Tuberous sclerosis complex 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Fibroma Tuberous sclerosis complex 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Focal cortical dysplasia Polycystic kidney disease with tuberous sclerosis 0.222 2 2.33e-7 1.55e-6 ✓ sig.
Focal cortical dysplasia Polycystic kidneys, severe infantile with tuberous sclerosis 0.222 2 2.33e-7 1.55e-6 ✓ sig.
Focal cortical dysplasia Lymphangioleiomyomatosis 0.222 2 2.33e-7 1.55e-6 ✓ sig.
Brain disease Tuberous sclerosis complex 0.065 3 3.69e-7 2.40e-6 ✓ sig.
Cortical dysplasia Lung lymphangioleiomyomatosis 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Benign neoplasm of brain Fibroma 0.143 2 6.50e-7 4.06e-6 ✓ sig.
Benign neoplasm of brain Lymphangioleiomyomatosis 0.143 2 6.50e-7 4.06e-6 ✓ sig.
Benign neoplasm of brain Subependymal giant cell astrocytoma 0.143 2 6.50e-7 4.06e-6 ✓ sig.
Intracranial aneurysm Liver cyst 0.125 2 8.76e-7 5.37e-6 ✓ sig.
Benign neoplasm of brain Lung lymphangioleiomyomatosis 0.133 2 1.95e-6 1.14e-5 ✓ sig.
Brain disease Lymphangioleiomyomatosis 0.047 2 7.18e-6 3.93e-5 ✓ sig.
Benign neoplasm of brain Tuberous sclerosis complex 0.111 2 9.74e-6 5.27e-5 ✓ sig.
Epithelioid type angiomyolipoma Tuberous sclerosis 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Polycystic kidney disease 1 with or without polycystic liver disease Polycystic kidney disease with tuberous sclerosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Polycystic kidneys, severe infantile with tuberous sclerosis Tuberous sclerosis 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Liver cyst Polycystic kidney disease 2 with or without polycystic liver disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Polycystic kidney disease 1 with or without polycystic liver disease Renovascular hypertension 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Polycystic kidney disease 1 with or without polycystic liver disease Polycystic kidneys, severe infantile with tuberous sclerosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lymphangioleiomyomatosis Tuberous sclerosis 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Subependymal giant cell astrocytoma Tuberous sclerosis 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Fibroma Tuberous sclerosis 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Subependymal giant cell astrocytoma Tuberous sclerosis 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Polycystic kidney disease with tuberous sclerosis Tuberous sclerosis 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epithelioid type angiomyolipoma Subependymal giant cell astrocytoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Pineal parenchymal tumor of intermediate differentiation Tuberous sclerosis 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lymphangioleiomyomatosis Tuberous sclerosis 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epithelioid type angiomyolipoma Polycystic kidney disease with tuberous sclerosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Liver cyst Polycystic kidney disease 1 with or without polycystic liver disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Fibroma Tuberous sclerosis 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epithelioid type angiomyolipoma Fibroma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epithelioid type angiomyolipoma Lymphangioleiomyomatosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epithelioid type angiomyolipoma Polycystic kidneys, severe infantile with tuberous sclerosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital kidney anomaly Fliedner-zweier syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital kidney anomaly Polycystic kidney disease 1 with or without polycystic liver disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Lung lymphangioleiomyomatosis Tuberous sclerosis 1 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Fibroma Pineal parenchymal tumor of intermediate differentiation 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Polycystic kidneys, severe infantile with tuberous sclerosis Renovascular hypertension 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Polycystic kidney disease with tuberous sclerosis Renovascular hypertension 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Liver cyst Polycystic kidney disease with tuberous sclerosis 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Liver cyst Renovascular hypertension 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Pineal parenchymal tumor of intermediate differentiation Subependymal giant cell astrocytoma 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Epithelioid type angiomyolipoma Xanthinuria 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Tuberous sclerosis 2 Xanthinuria 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Congenital kidney anomaly Liver cyst 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Congenital kidney anomaly Polycystic kidney disease with tuberous sclerosis 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Polycystic kidney disease with tuberous sclerosis Xanthinuria 0.167 1 5.16e-4 9.13e-4 ✓ sig.
Polycystic kidneys, severe infantile with tuberous sclerosis Xanthinuria 0.167 1 5.16e-4 9.13e-4 ✓ sig.
Intracranial aneurysm Polycystic kidney disease 2 with or without polycystic liver disease 0.063 1 9.68e-4 1.50e-3 ✓ sig.
Brain disease Encephalopathy, acute, infection-induced, susceptibility to, 6 0.023 1 2.71e-3 3.48e-3 ✓ sig.
Brain disease Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 7 0.023 1 2.71e-3 3.48e-3 ✓ sig.