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 585
5
Diseases
9
Unique genes
0.334
Avg. similarity score
Berardinelli-seip congenital lipodystrophy
Most-connected disease (3 links)
Disease
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Berardinelli-seip congenital lipodystrophy
Congenital generalized lipodystrophy
Generalized lipodystrophy
Carotid intima-media thickness
Intellectual developmental disorder speech ambulation
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Berardinelli-seip congenital lipodystrophy | 3 | 3 | 6 |
| Congenital generalized lipodystrophy | 3 | 3 | 6 |
| Generalized lipodystrophy | 3 | 3 | 7 |
| Carotid intima-media thickness | 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 |
|---|---|---|
| AGPAT2 | 3 / 5 | Berardinelli-seip congenital lipodystrophy, Congenital generalized lipodystrophy, Generalized lipodystrophy |
| BSCL2 | 3 / 5 | Berardinelli-seip congenital lipodystrophy, Congenital generalized lipodystrophy, Generalized lipodystrophy |
| CAV1 | 3 / 5 | Berardinelli-seip congenital lipodystrophy, Congenital generalized lipodystrophy, Generalized lipodystrophy |
| CAVIN1 | 3 / 5 | Berardinelli-seip congenital lipodystrophy, Congenital generalized lipodystrophy, Generalized lipodystrophy |
| PPARG | 3 / 5 | Berardinelli-seip congenital lipodystrophy, Carotid intima-media thickness, Generalized lipodystrophy |
| ACTL6B | 2 / 5 | Congenital generalized lipodystrophy, Intellectual developmental disorder speech ambulation |
| FOS | 2 / 5 | Berardinelli-seip congenital lipodystrophy, Generalized 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 ⇵ |
|---|---|---|---|---|---|
| Extra-nuclear estrogen signaling | Reactome | 2 / 58 | 46.0× | 8.07e-4 | 9.62e-3 ✓ sig. |
| Circadian entrainment | KEGG | 2 / 97 | 27.5× | 2.24e-3 | 2.07e-2 ✓ sig. |
| Choline metabolism in cancer | KEGG | 2 / 99 | 27.0× | 2.33e-3 | 2.13e-2 ✓ sig. |
| Glycerophospholipid metabolism | KEGG | 2 / 102 | 26.2× | 2.47e-3 | 2.22e-2 ✓ sig. |
| Cholinergic synapse | KEGG | 2 / 115 | 23.2× | 3.13e-3 | 2.63e-2 ✓ sig. |
| NOSTRIN mediated eNOS trafficking | Reactome | 1 / 5 | 267× | 3.74e-3 | 2.98e-2 ✓ sig. |
| Relaxin signaling pathway | KEGG | 2 / 130 | 20.5× | 3.98e-3 | 3.12e-2 ✓ sig. |
| Dopaminergic synapse | KEGG | 2 / 132 | 20.2× | 4.10e-3 | 3.18e-2 ✓ sig. |
| Phosphonate and phosphinate metabolism | KEGG | 1 / 6 | 222× | 4.49e-3 | 3.39e-2 ✓ sig. |
| Fluid shear stress and atherosclerosis | KEGG | 2 / 141 | 18.9× | 4.67e-3 | 3.48e-2 ✓ sig. |
| Osteoclast differentiation | KEGG | 2 / 142 | 18.8× | 4.73e-3 | 3.52e-2 ✓ sig. |
| Non-alcoholic fatty liver disease | KEGG | 2 / 157 | 17.0× | 5.76e-3 | 4.01e-2 ✓ sig. |
| Pathways in cancer | KEGG | 3 / 533 | 7.5× | 5.97e-3 | 4.10e-2 ✓ sig. |
| Activation of the AP-1 family of transcription factors | Reactome | 1 / 10 | 133× | 7.47e-3 | 4.73e-2 ✓ sig. |
| FOXO-mediated transcription of cell cycle genes | Reactome | 1 / 11 | 121× | 8.22e-3 | 5.04e-2 |
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 cholesterol efflux | GO:0010875 | 2 / 27 | 154× | 7.19e-5 | 2.42e-3 ✓ sig. |
| response to progesterone | GO:0032570 | 2 / 31 | 134× | 9.52e-5 | 2.98e-3 ✓ sig. |
| lipid storage | GO:0019915 | 2 / 32 | 130× | 1.02e-4 | 3.13e-3 ✓ sig. |
| positive regulation of miRNA transcription | GO:1902895 | 2 / 56 | 74.2× | 3.13e-4 | 7.00e-3 ✓ sig. |
| phospholipid biosynthetic process | GO:0008654 | 2 / 58 | 71.6× | 3.36e-4 | 7.27e-3 ✓ sig. |
| negative regulation of MAPK cascade | GO:0043409 | 2 / 64 | 64.9× | 4.09e-4 | 8.31e-3 ✓ sig. |
| cellular response to transforming growth factor beta stimulus | GO:0071560 | 2 / 67 | 62.0× | 4.49e-4 | 8.83e-3 ✓ sig. |
| medium-term memory | GO:0072375 | 1 / 1 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| cellular response to prolactin | GO:1990646 | 1 / 1 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| negative regulation of BMP signaling pathway | GO:0030514 | 2 / 75 | 55.4× | 5.62e-4 | 1.03e-2 ✓ sig. |
| negative regulation of connective tissue replacement involved in inflammatory response wound healing | GO:1904597 | 1 / 2 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| regulation of the force of heart contraction by chemical signal | GO:0003057 | 1 / 2 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| response to forskolin | GO:1904321 | 1 / 2 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| positive regulation of cold-induced thermogenesis | GO:0120162 | 2 / 102 | 40.7× | 1.04e-3 | 1.50e-2 ✓ sig. |
| protein localization to basolateral plasma membrane | GO:1903361 | 1 / 3 | 692× | 1.44e-3 | 1.79e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Berardinelli-seip congenital lipodystrophy | Generalized lipodystrophy | 0.750 | 6 | 3.65e-22 | 5.71e-21 ✓ sig. |
| Berardinelli-seip congenital lipodystrophy | Congenital generalized lipodystrophy | 0.444 | 4 | 9.39e-14 | 1.06e-12 ✓ sig. |
| Congenital generalized lipodystrophy | Generalized lipodystrophy | 0.400 | 4 | 2.19e-13 | 2.45e-12 ✓ sig. |
| Berardinelli-seip congenital lipodystrophy | Carotid intima-media thickness | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Congenital generalized lipodystrophy | Intellectual developmental disorder speech ambulation | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Carotid intima-media thickness | Generalized lipodystrophy | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |