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 275

8 diseases · 18 shared-gene connections
8 Diseases
23 Unique genes
0.231 Avg. similarity score
Bestrophinopathy Most-connected disease (7 links)
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Disease Searched: Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma 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 ⇵
Bestrophinopathy 7 7 4
Iron overload 6 6 7
Vitreoretinochoroidopathy 6 6 2
Hemochromatosis type 5 4 4 1
Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma 4 4 1
Neurodegeneration with brain iron accumulation 9 4 4 1
Neurodegeneration with brain iron accumulation 3 3 14
Vitelliform macular dystrophy 2 2 5

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

Gene ⇵ Member diseases ⇵ Linked diseases
BEST1 6 / 8 Bestrophinopathy, Iron overload, Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma, Neurodegeneration with brain iron accumulation and 2 more
FTH1 6 / 8 Bestrophinopathy, Hemochromatosis type 5, Iron overload, Neurodegeneration with brain iron accumulation and 2 more
CP 2 / 8 Iron overload, Neurodegeneration with brain iron accumulation
PRPH2 2 / 8 Bestrophinopathy, Vitelliform macular dystrophy
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 ⇵
Iron uptake and transport
FTH1, CP, SLC40A1, TF, FTL
 Reactome 5 / 28 93.2× 1.54e-9 1.38e-7 ✓ sig.
Ferroptosis
FTH1, CP, SLC40A1, TF, FTL
 KEGG 5 / 42 62.2× 1.31e-8 9.46e-7 ✓ sig.
Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages)
CP, SLC40A1
 Reactome 2 / 2 522× 3.51e-6 1.22e-4 ✓ sig.
Defective CP causes aceruloplasminemia (ACERULOP)
CP, SLC40A1
 Reactome 2 / 2 522× 3.51e-6 1.22e-4 ✓ sig.
Mineral absorption
FTH1, SLC40A1, TF, FTL
 KEGG 4 / 61 34.2× 4.96e-6 1.63e-4 ✓ sig.
Porphyrin metabolism
FTH1, CP, FTL
 KEGG 3 / 46 34.1× 8.83e-5 1.72e-3 ✓ sig.
Coenzyme A biosynthesis
COASY, PANK2
 Reactome 2 / 8 131× 9.75e-5 1.86e-3 ✓ sig.
Metal ion SLC transporters
CP, SLC40A1
 Reactome 2 / 9 116× 1.25e-4 2.26e-3 ✓ sig.
Pantothenate and CoA biosynthesis
COASY, PANK2
 KEGG 2 / 21 49.7× 7.21e-4 8.84e-3 ✓ sig.
TGF-beta signaling pathway
BMP6, HAMP, TF
 KEGG 3 / 108 14.5× 1.10e-3 1.22e-2 ✓ sig.
Defective SLC40A1 causes hemochromatosis 4 (HFE4) (duodenum)
SLC40A1
 Reactome 1 / 2 261× 3.83e-3 3.03e-2 ✓ sig.
Golgi Associated Vesicle Biogenesis
FTH1, FTL
 Reactome 2 / 56 18.6× 5.07e-3 3.68e-2 ✓ sig.
Beta-oxidation of pristanoyl-CoA
CRAT
 Reactome 1 / 9 58.0× 1.71e-2 7.84e-2
Cargo recognition for clathrin-mediated endocytosis
TF, REPS1
 Reactome 2 / 106 9.9× 1.73e-2 7.88e-2
Post-translational protein phosphorylation
CP, TF
 Reactome 2 / 108 9.7× 1.79e-2 8.05e-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 ⇵
intracellular iron ion homeostasis
FTH1, BMP6, CP, HAMP, SLC40A1, TF, FTL, ATP13A2
 GO:0006879 8 / 71 91.5× 1.35e-14 9.05e-12 ✓ sig.
iron ion export across plasma membrane
HAMP, SLC40A1, TF
 GO:1903988 3 / 3 812× 1.63e-9 3.55e-7 ✓ sig.
multicellular organismal-level iron ion homeostasis
BMP6, HAMP, SLC40A1, TF
 GO:0060586 4 / 28 116× 3.50e-8 5.23e-6 ✓ sig.
iron ion transport
FTH1, SLC40A1, TF, FTL
 GO:0006826 4 / 31 105× 5.37e-8 7.54e-6 ✓ sig.
detection of light stimulus involved in visual perception
BEST1, CRB1, PRPH2
 GO:0050908 3 / 24 102× 3.24e-6 2.23e-4 ✓ sig.
visual perception
BEST1, CRB1, PRPH2, IMPG1, IMPG2
 GO:0007601 5 / 215 18.9× 5.47e-6 3.40e-4 ✓ sig.
cellular response to iron ion
BMP6, TF
 GO:0071281 2 / 7 232× 3.03e-5 1.26e-3 ✓ sig.
coenzyme A biosynthetic process
COASY, PANK2
 GO:0015937 2 / 10 162× 6.48e-5 2.24e-3 ✓ sig.
retina morphogenesis in camera-type eye
CRB1, IMPG2
 GO:0060042 2 / 14 116× 1.31e-4 3.74e-3 ✓ sig.
photoreceptor cell outer segment organization
CRB1, PRPH2
 GO:0035845 2 / 15 108× 1.51e-4 4.16e-3 ✓ sig.
response to iron ion
BMP6, HAMP
 GO:0010039 2 / 18 90.3× 2.19e-4 5.40e-3 ✓ sig.
response to low light intensity stimulus
PRPH2
 GO:0009645 1 / 1 812× 1.23e-3 1.64e-2 ✓ sig.
negative regulation of iron ion transmembrane transport
HAMP
 GO:0034760 1 / 1 812× 1.23e-3 1.64e-2 ✓ sig.
negative regulation of iron export across plasma membrane
HAMP
 GO:1904039 1 / 1 812× 1.23e-3 1.64e-2 ✓ sig.
negative regulation of intestinal absorption
HAMP
 GO:1904479 1 / 1 812× 1.23e-3 1.64e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Iron overload Neurodegeneration with brain iron accumulation 0.158 3 2.05e-8 1.59e-7 ✓ sig.
Bestrophinopathy Vitreoretinochoroidopathy 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Iron overload Vitreoretinochoroidopathy 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Bestrophinopathy Vitelliform macular dystrophy 0.250 2 5.00e-7 3.18e-6 ✓ sig.
Neurodegeneration with brain iron accumulation Vitreoretinochoroidopathy 0.133 2 7.59e-7 4.67e-6 ✓ sig.
Bestrophinopathy Iron overload 0.200 2 1.05e-6 6.38e-6 ✓ sig.
Bestrophinopathy Neurodegeneration with brain iron accumulation 0.118 2 4.55e-6 2.54e-5 ✓ sig.
Hemochromatosis type 5 Neurodegeneration with brain iron accumulation 9 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma Vitreoretinochoroidopathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neurodegeneration with brain iron accumulation 9 Vitreoretinochoroidopathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hemochromatosis type 5 Vitreoretinochoroidopathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Bestrophinopathy Hemochromatosis type 5 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Bestrophinopathy Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Bestrophinopathy Neurodegeneration with brain iron accumulation 9 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma Vitelliform macular dystrophy 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Iron overload Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Hemochromatosis type 5 Iron overload 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Iron overload Neurodegeneration with brain iron accumulation 9 0.125 1 4.52e-4 8.26e-4 ✓ sig.