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 268

8 diseases · 15 shared-gene connections
8 Diseases
70 Unique genes
0.221 Avg. similarity score
Developmental delay with immunodeficiency syndrome Most-connected disease (5 links)
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Disease Searched: Growth retardation 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 ⇵
Developmental delay with immunodeficiency syndrome 5 5 1
Endocrine system disease 5 5 14
Hepatic insufficiency 5 5 9
Immunodeficiency, developmental delay, and hypohomocysteinemia 5 5 1
Leukoencephalopathy, immune deficiency and hypohomocysteinemia 5 5 1
Growth retardation 3 3 2
Hepatomegaly 1 1 58
Multiple congenital anomalies-hypotonia-seizures syndrome 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
NFE2L2 7 / 8 Developmental delay with immunodeficiency syndrome, Endocrine system disease, Growth retardation, Hepatic insufficiency and 3 more
RELA 3 / 8 Endocrine system disease, Hepatic insufficiency, Hepatomegaly
ALB 2 / 8 Hepatic insufficiency, Hepatomegaly
CYGB 2 / 8 Hepatic insufficiency, Hepatomegaly
KEAP1 2 / 8 Hepatic insufficiency, Hepatomegaly
MAPK14 2 / 8 Hepatic insufficiency, Hepatomegaly
MTOR 2 / 8 Endocrine system disease, Hepatomegaly
NOS2 2 / 8 Hepatic insufficiency, Hepatomegaly
NOS3 2 / 8 Hepatic insufficiency, Hepatomegaly
PIGN 2 / 8 Endocrine system disease, Multiple congenital anomalies-hypotonia-seizures syndrome 1
TGFB1 2 / 8 Hepatic insufficiency, Hepatomegaly
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 ⇵
SUMOylation of intracellular receptors
NR1H2, NR1H4, NR1I2, NR5A2, PPARA, THRA
 Reactome 6 / 27 38.1× 8.47e-9 6.37e-7 ✓ sig.
Nuclear Receptor transcription pathway
NR1H2, NR1H4, NR1I2, NR1I3, NR5A2, PPARA, THRA
 Reactome 7 / 52 23.1× 1.83e-8 1.26e-6 ✓ sig.
Chemical carcinogenesis - reactive oxygen species
NFE2L2, RELA, KEAP1, MAPK14, AHR, AKT1, CYBA, CYP1A1, CYP1A2, CYP1B1, MET
 KEGG 11 / 227 8.3× 7.01e-8 4.09e-6 ✓ sig.
Chemical carcinogenesis - receptor activation
GNAS, MTOR, RELA, AHR, AKT1, CYP1A1, CYP1A2, CYP1B1, NR1I3, PPARA
 KEGG 10 / 215 8.0× 4.26e-7 1.99e-5 ✓ sig.
Lipid and atherosclerosis
NFE2L2, RELA, MAPK14, NOS3, AKT1, CAMK2A, CYBA, CYP1A1, IFNA2, LDLR
 KEGG 10 / 216 7.9× 4.45e-7 2.07e-5 ✓ sig.
Diabetic cardiomyopathy
MTOR, RELA, MAPK14, NOS3, TGFB1, AKT1, CAMK2A, CYBA, PPARA
 KEGG 9 / 205 7.5× 2.73e-6 9.85e-5 ✓ sig.
Adipocytokine signaling pathway
MTOR, RELA, AKT1, LEP, LEPR, PPARA
 KEGG 6 / 70 14.7× 3.08e-6 1.09e-4 ✓ sig.
Non-alcoholic fatty liver disease
ITCH, RELA, MAPK14, TGFB1, AKT1, LEP, LEPR, PPARA
 KEGG 8 / 157 8.7× 3.39e-6 1.18e-4 ✓ sig.
Relaxin signaling pathway
GNAS, RELA, MAPK14, NOS2, NOS3, TGFB1, AKT1
 KEGG 7 / 130 9.2× 1.01e-5 2.93e-4 ✓ sig.
Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET)
CYP1A1, CYP1A2, CYP1B1
 Reactome 3 / 8 64.3× 1.04e-5 3.01e-4 ✓ sig.
Ovarian steroidogenesis
GNAS, ACOT1, CYP1A1, CYP1B1, LDLR
 KEGG 5 / 52 16.5× 1.22e-5 3.44e-4 ✓ sig.
Longevity regulating pathway
MTOR, RELA, SIRT1, AKT1, ATG5, SESN2
 KEGG 6 / 90 11.4× 1.34e-5 3.70e-4 ✓ sig.
Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE)
CYP1A1, CYP1A2, CYP1B1
 Reactome 3 / 9 57.2× 1.55e-5 4.22e-4 ✓ sig.
Fluid shear stress and atherosclerosis
NFE2L2, RELA, KEAP1, MAPK14, NOS3, AKT1, CYBA
 KEGG 7 / 141 8.5× 1.71e-5 4.58e-4 ✓ sig.
Alcoholic liver disease
RELA, SIRT1, MAPK14, AKT1, ALDH1B1, IFNA2, PPARA
 KEGG 7 / 144 8.3× 1.96e-5 5.13e-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 ⇵
intracellular receptor signaling pathway
AHR, NR1H2, NR1H4, NR1I2, NR1I3, NR5A2, PPARA
 GO:0030522 7 / 39 47.9× 1.06e-10 3.24e-8 ✓ sig.
nitric oxide metabolic process
CYGB, NOS3, AKT1, CYP1A1, PPARA
 GO:0046209 5 / 12 111× 4.95e-10 1.28e-7 ✓ sig.
response to insulin
MTOR, RELA, SIRT1, MAPK14, LEP, PPARA, SESN2
 GO:0032868 7 / 83 22.5× 2.52e-8 3.95e-6 ✓ sig.
positive regulation of blood vessel endothelial cell migration
NFE2L2, SIRT1, MAPK14, NOS3, TGFB1, AKT1
 GO:0043536 6 / 51 31.4× 3.50e-8 5.23e-6 ✓ sig.
cellular response to starvation
MTOR, SIRT1, ALB, AKT1, ATG5, ATG7, PPARA
 GO:0009267 7 / 90 20.8× 4.44e-8 6.42e-6 ✓ sig.
cellular response to tumor necrosis factor
NFE2L2, RELA, SIRT1, MAPK14, AKT1, CYBA, GPER1
 GO:0071356 7 / 107 17.5× 1.47e-7 1.77e-5 ✓ sig.
olefinic compound metabolic process
CYP1A1, CYP1A2, CYP1B1
 GO:0120254 3 / 4 200× 2.01e-7 2.27e-5 ✓ sig.
xenobiotic metabolic process
ABCC3, AHR, CYP1A1, CYP1A2, CYP1B1, NR1I2, SLC29A3
 GO:0006805 7 / 120 15.6× 3.24e-7 3.40e-5 ✓ sig.
response to nutrient levels
MTOR, ALB, ATG7, CYBA, LEP, NR1H2
 GO:0031667 6 / 79 20.3× 4.98e-7 4.86e-5 ✓ sig.
inflammatory response
NFE2L2, ITCH, MTOR, RELA, NOS2, TGFB1, AKT1, CYBA, GPER1, IFNA2, NR1H4
 GO:0006954 11 / 467 6.3× 1.21e-6 1.00e-4 ✓ sig.
nitric oxide biosynthetic process
NOS2, NOS3, AKT1, CYP1B1
 GO:0006809 4 / 23 46.4× 1.51e-6 1.21e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
NFE2L2, EBF2, RELA, SIRT1, MAPK14, TGFB1, AHR, AKT1, GPER1, MET, NR1H2, NR1H4
 GO:0045944 17 / 1,208 3.8× 1.61e-6 1.27e-4 ✓ sig.
steroid catabolic process
CYP1A1, CYP1A2, CYP1B1
 GO:0006706 3 / 7 114× 1.74e-6 1.36e-4 ✓ sig.
hormone metabolic process
CYP1A1, CYP1A2, CYP1B1, LEP
 GO:0042445 4 / 25 42.7× 2.15e-6 1.61e-4 ✓ sig.
toxin metabolic process
CYP1A1, CYP1A2, CYP1B1
 GO:0009404 3 / 8 100× 2.78e-6 1.97e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hepatic insufficiency Hepatomegaly 0.153 9 7.55e-23 1.20e-21 ✓ sig.
Endocrine system disease Hepatic insufficiency 0.091 2 2.72e-5 1.41e-4 ✓ sig.
Developmental delay with immunodeficiency syndrome Immunodeficiency, developmental delay, and hypohomocysteinemia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Developmental delay with immunodeficiency syndrome Leukoencephalopathy, immune deficiency and hypohomocysteinemia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Immunodeficiency, developmental delay, and hypohomocysteinemia Leukoencephalopathy, immune deficiency and hypohomocysteinemia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Developmental delay with immunodeficiency syndrome Growth retardation 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Growth retardation Immunodeficiency, developmental delay, and hypohomocysteinemia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Growth retardation Leukoencephalopathy, immune deficiency and hypohomocysteinemia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Developmental delay with immunodeficiency syndrome Hepatic insufficiency 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Hepatic insufficiency Immunodeficiency, developmental delay, and hypohomocysteinemia 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Hepatic insufficiency Leukoencephalopathy, immune deficiency and hypohomocysteinemia 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Developmental delay with immunodeficiency syndrome Endocrine system disease 0.067 1 9.04e-4 1.41e-3 ✓ sig.
Endocrine system disease Immunodeficiency, developmental delay, and hypohomocysteinemia 0.067 1 9.04e-4 1.41e-3 ✓ sig.
Endocrine system disease Leukoencephalopathy, immune deficiency and hypohomocysteinemia 0.067 1 9.04e-4 1.41e-3 ✓ sig.
Endocrine system disease Multiple congenital anomalies-hypotonia-seizures syndrome 1 0.067 1 9.04e-4 1.41e-3 ✓ sig.