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 79

13 diseases · 27 shared-gene connections
13 Diseases
49 Unique genes
0.176 Avg. similarity score
Generalized lipodystrophy Most-connected disease (8 links)
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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 ⇵
Generalized lipodystrophy 8 8 7
Lipodystrophy 8 8 18
Partial lipodystrophy 8 8 10
Berardinelli-seip congenital lipodystrophy 7 7 6
Congenital generalized lipodystrophy 5 5 6
congenital generalized lipodystrophy type 3 4 4 1
Carotid intima-media thickness 3 3 1
Central nervous system malformation 2 2 2
Epithelial ovarian carcinoma 2 2 28
LIPE-related familial partial lipodystrophy 2 2 1
PLIN1-related familial partial lipodystrophy 2 2 1
spondylometaphyseal dysplasia-cone-rod dystrophy syndrome 2 2 1
Intellectual developmental disorder speech ambulation 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CAV1 7 / 13 Berardinelli-seip congenital lipodystrophy, Congenital generalized lipodystrophy, congenital generalized lipodystrophy type 3, Epithelial ovarian carcinoma and 3 more
PPARG 5 / 13 Berardinelli-seip congenital lipodystrophy, Carotid intima-media thickness, Generalized lipodystrophy, Lipodystrophy and 1 more
AGPAT2 4 / 13 Berardinelli-seip congenital lipodystrophy, Congenital generalized lipodystrophy, Generalized lipodystrophy, Lipodystrophy
BSCL2 4 / 13 Berardinelli-seip congenital lipodystrophy, Congenital generalized lipodystrophy, Generalized lipodystrophy, Lipodystrophy
CAVIN1 4 / 13 Berardinelli-seip congenital lipodystrophy, Congenital generalized lipodystrophy, Generalized lipodystrophy, Lipodystrophy
FOS 3 / 13 Berardinelli-seip congenital lipodystrophy, Epithelial ovarian carcinoma, Generalized lipodystrophy
LIPE 3 / 13 LIPE-related familial partial lipodystrophy, Lipodystrophy, Partial lipodystrophy
LMNB2 3 / 13 Central nervous system malformation, Lipodystrophy, Partial lipodystrophy
PCYT1A 3 / 13 Generalized lipodystrophy, Lipodystrophy, spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
PLIN1 3 / 13 Lipodystrophy, Partial lipodystrophy, PLIN1-related familial partial lipodystrophy
ACTL6B 2 / 13 Congenital generalized lipodystrophy, Intellectual developmental disorder speech ambulation
ADRA2A 2 / 13 Lipodystrophy, Partial lipodystrophy
AKT2 2 / 13 Lipodystrophy, Partial lipodystrophy
CIDEC 2 / 13 Lipodystrophy, Partial lipodystrophy
LMNA 2 / 13 Lipodystrophy, Partial lipodystrophy
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 ⇵
Apoptosis
AKT2, FOS, RAF1, TP53, LMNB2, LMNA, PARP2
 KEGG 7 / 137 12.5× 1.24e-6 5.90e-5 ✓ sig.
Apelin signaling pathway
AKT2, CCN2, RAF1, GNG3, LIPE, PLIN1, NOTCH3
 KEGG 7 / 140 12.3× 1.44e-6 6.69e-5 ✓ sig.
Breast cancer
AKT2, FOS, ERBB2, RAF1, TP53, WNT4, NOTCH3
 KEGG 7 / 148 11.6× 2.09e-6 9.11e-5 ✓ sig.
Endocrine resistance
AKT2, FOS, ERBB2, RAF1, TP53, NOTCH3
 KEGG 6 / 99 14.9× 2.83e-6 1.18e-4 ✓ sig.
Regulation of lipolysis in adipocytes
AKT2, CIDEC, LIPE, PLIN1, PLAAT3
 KEGG 5 / 59 20.8× 3.89e-6 1.55e-4 ✓ sig.
Hepatocellular carcinoma
AKT2, GSTM1, GSTT1, RAF1, TP53, WNT4, ACTL6B
 KEGG 7 / 170 10.1× 5.24e-6 1.97e-4 ✓ sig.
Pathways in cancer
AKT2, FOS, PPARG, ERBB2, GSTM1, GSTT1, RAF1, TP53, WNT4, GNG3, NOTCH3
 KEGG 11 / 533 5.1× 7.44e-6 2.62e-4 ✓ sig.
Platinum drug resistance
AKT2, ERBB2, GSTM1, GSTT1, TP53
 KEGG 5 / 75 16.3× 1.28e-5 4.12e-4 ✓ sig.
Fluid shear stress and atherosclerosis
AKT2, CAV1, FOS, GSTM1, GSTT1, TP53
 KEGG 6 / 141 10.4× 2.17e-5 6.39e-4 ✓ sig.
Chemical carcinogenesis - receptor activation
AKT2, FOS, CYP3A4, GSTM1, GSTT1, KPNB1, RAF1
 KEGG 7 / 215 8.0× 2.42e-5 6.99e-4 ✓ sig.
Endometrial cancer
AKT2, ERBB2, RAF1, TP53
 KEGG 4 / 59 16.6× 9.44e-5 2.14e-3 ✓ sig.
Thyroid hormone signaling pathway
AKT2, RAF1, TP53, WNT4, NOTCH3
 KEGG 5 / 122 10.0× 1.33e-4 2.82e-3 ✓ sig.
Kaposi sarcoma-associated herpesvirus infection
AKT2, FOS, PPP3CA, RAF1, TP53, GNG3
 KEGG 6 / 196 7.5× 1.36e-4 2.88e-3 ✓ sig.
Proteoglycans in cancer
AKT2, CAV1, ERBB2, RAF1, TP53, WNT4
 KEGG 6 / 204 7.2× 1.70e-4 3.44e-3 ✓ sig.
Prolactin signaling pathway
AKT2, FOS, RAF1, SOCS7
 KEGG 4 / 71 13.8× 1.94e-4 3.82e-3 ✓ 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 ⇵
negative regulation of connective tissue replacement involved in inflammatory response wound healing
PPARG, AGER
 GO:1904597 2 / 2 381× 6.74e-6 3.80e-4 ✓ sig.
positive regulation of miRNA transcription
FOS, PPARG, TP53, NOTCH3
 GO:1902895 4 / 56 27.2× 1.39e-5 6.74e-4 ✓ sig.
negative regulation of miRNA processing
TP53, ZMPSTE24
 GO:1903799 2 / 3 254× 2.02e-5 9.04e-4 ✓ sig.
negative regulation of lipid catabolic process
BSCL2, ADRA2A, CIDEC
 GO:0050995 3 / 21 54.5× 2.18e-5 9.60e-4 ✓ sig.
nuclear envelope organization
LMNB2, LMNA, ZMPSTE24
 GO:0006998 3 / 24 47.7× 3.30e-5 1.31e-3 ✓ sig.
immature T cell proliferation in thymus
ERBB2, WNT4
 GO:0033080 2 / 5 153× 6.70e-5 2.24e-3 ✓ sig.
nuclear pore localization
LMNB2, LMNA
 GO:0051664 2 / 5 153× 6.70e-5 2.24e-3 ✓ sig.
lipid storage
BSCL2, CAV1, CIDEC
 GO:0019915 3 / 32 35.8× 7.97e-5 2.55e-3 ✓ sig.
positive regulation of DNA metabolic process
AGER, ATAD5
 GO:0051054 2 / 6 127× 1.00e-4 3.03e-3 ✓ sig.
ether lipid metabolic process
LIPE, PLAAT3
 GO:0046485 2 / 6 127× 1.00e-4 3.03e-3 ✓ sig.
positive regulation of cell migration
AKT2, CAV1, AGER, PPP3CA, SYNPO2, ADRA2A
 GO:0030335 6 / 292 7.8× 1.10e-4 3.24e-3 ✓ sig.
regulation of DNA damage response, signal transduction by p53 class mediator
TP53, ZMPSTE24
 GO:0043516 2 / 7 109× 1.40e-4 3.89e-3 ✓ sig.
protein localization to nuclear envelope
LMNB2, LMNA
 GO:0090435 2 / 8 95.3× 1.87e-4 4.82e-3 ✓ sig.
protein import into nucleus
KPNB1, PPP3CA, TP53, LMNA
 GO:0006606 4 / 110 13.9× 1.96e-4 4.99e-3 ✓ sig.
epidermis development
AGPAT2, CCN2, PPP3CA, ZMPSTE24
 GO:0008544 4 / 114 13.4× 2.25e-4 5.48e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Lipodystrophy Partial lipodystrophy 0.450 9 3.63e-27 1.05e-25 ✓ sig.
Berardinelli-seip congenital lipodystrophy Generalized lipodystrophy 0.750 6 3.79e-22 8.33e-21 ✓ sig.
Generalized lipodystrophy Lipodystrophy 0.300 6 7.02e-18 1.27e-16 ✓ sig.
Berardinelli-seip congenital lipodystrophy Lipodystrophy 0.250 5 7.13e-15 1.07e-13 ✓ sig.
Berardinelli-seip congenital lipodystrophy Congenital generalized lipodystrophy 0.444 4 9.61e-14 1.31e-12 ✓ sig.
Congenital generalized lipodystrophy Generalized lipodystrophy 0.400 4 2.24e-13 3.02e-12 ✓ sig.
Congenital generalized lipodystrophy Lipodystrophy 0.190 4 1.96e-11 2.21e-10 ✓ sig.
Berardinelli-seip congenital lipodystrophy Partial lipodystrophy 0.133 2 5.69e-6 3.09e-5 ✓ sig.
Generalized lipodystrophy Partial lipodystrophy 0.125 2 7.96e-6 4.23e-5 ✓ sig.
Berardinelli-seip congenital lipodystrophy Epithelial ovarian carcinoma 0.061 2 4.76e-5 2.28e-4 ✓ sig.
Epithelial ovarian carcinoma Generalized lipodystrophy 0.059 2 6.66e-5 2.40e-4 ✓ sig.
Congenital generalized lipodystrophy Intellectual developmental disorder speech ambulation 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Congenital generalized lipodystrophy congenital generalized lipodystrophy type 3 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Berardinelli-seip congenital lipodystrophy congenital generalized lipodystrophy type 3 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Berardinelli-seip congenital lipodystrophy Carotid intima-media thickness 0.143 1 3.90e-4 8.52e-4 ✓ sig.
congenital generalized lipodystrophy type 3 Generalized lipodystrophy 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Generalized lipodystrophy spondylometaphyseal dysplasia-cone-rod dystrophy syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Carotid intima-media thickness Generalized lipodystrophy 0.125 1 4.55e-4 9.55e-4 ✓ sig.
congenital generalized lipodystrophy type 3 Partial lipodystrophy 0.091 1 6.49e-4 1.22e-3 ✓ sig.
LIPE-related familial partial lipodystrophy Partial lipodystrophy 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Carotid intima-media thickness Partial lipodystrophy 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Partial lipodystrophy PLIN1-related familial partial lipodystrophy 0.091 1 6.49e-4 1.22e-3 ✓ sig.
LIPE-related familial partial lipodystrophy Lipodystrophy 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Lipodystrophy PLIN1-related familial partial lipodystrophy 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Lipodystrophy spondylometaphyseal dysplasia-cone-rod dystrophy syndrome 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Central nervous system malformation Partial lipodystrophy 0.083 1 1.30e-3 2.04e-3 ✓ sig.
Central nervous system malformation Lipodystrophy 0.050 1 2.34e-3 3.23e-3 ✓ sig.