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 180

10 diseases · 26 shared-gene connections
10 Diseases
8 Unique genes
0.274 Avg. similarity score
Cold paroxysmal hemoglobinuria Most-connected disease (8 links)
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Disease Searched: Multiple congenital anomalies-hypotonia-seizures syndrome 3 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 ⇵
Cold paroxysmal hemoglobinuria 8 8 6
Hemoglobinuria paroxysmal 8 8 6
Multiple congenital anomalies-hypotonia-seizures syndrome 8 8 3
Paroxysmal nocturnal hemoglobinuria 6 6 7
Multiple congenital anomalies-hypotonia-seizures syndrome 2 5 5 1
Neurodevelopmental disorder with epilepsy and hemochromatosis 5 5 1
Intellectual developmental disorder seizures dysmorphic skeletal 4 4 1
Multiple congenital anomalies-hypotonia-seizures syndrome 3 4 4 1
C5 deficiency 3 3 1
Developmental and epileptic encephalopathy, 55 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PIGA 6 / 10 Cold paroxysmal hemoglobinuria, Hemoglobinuria paroxysmal, Multiple congenital anomalies-hypotonia-seizures syndrome, Multiple congenital anomalies-hypotonia-seizures syndrome 2 and 2 more
PIGT 6 / 10 Cold paroxysmal hemoglobinuria, Hemoglobinuria paroxysmal, Intellectual developmental disorder seizures dysmorphic skeletal, Multiple congenital anomalies-hypotonia-seizures syndrome and 2 more
C5 4 / 10 C5 deficiency, Cold paroxysmal hemoglobinuria, Hemoglobinuria paroxysmal, Paroxysmal nocturnal hemoglobinuria
C3 3 / 10 Cold paroxysmal hemoglobinuria, Hemoglobinuria paroxysmal, Paroxysmal nocturnal hemoglobinuria
HLA-DQA1 3 / 10 Cold paroxysmal hemoglobinuria, Hemoglobinuria paroxysmal, Paroxysmal nocturnal hemoglobinuria
HLA-DQB1 3 / 10 Cold paroxysmal hemoglobinuria, Hemoglobinuria paroxysmal, Paroxysmal nocturnal hemoglobinuria
PIGP 2 / 10 Developmental and epileptic encephalopathy, 55, Multiple congenital anomalies-hypotonia-seizures syndrome
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 ⇵
Staphylococcus aureus infection
C3, C5, HLA-DQA1, HLA-DQB1
 KEGG 4 / 99 60.7× 2.96e-7 1.45e-5 ✓ sig.
Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
PIGA, PIGT, PIGP
 KEGG 3 / 30 150× 7.81e-7 3.35e-5 ✓ sig.
Systemic lupus erythematosus
C3, C5, HLA-DQA1, HLA-DQB1
 KEGG 4 / 140 42.9× 1.19e-6 4.86e-5 ✓ sig.
Regulation of Complement cascade
C3, C5, CD59
 Reactome 3 / 47 95.8× 3.10e-6 1.10e-4 ✓ sig.
Herpes simplex virus 1 infection
C3, C5, HLA-DQA1, HLA-DQB1
 KEGG 4 / 182 33.0× 3.41e-6 1.19e-4 ✓ sig.
Activation of C3 and C5
C3, C5
 Reactome 2 / 8 375× 1.08e-5 3.12e-4 ✓ sig.
Leishmaniasis
C3, HLA-DQA1, HLA-DQB1
 KEGG 3 / 78 57.7× 1.44e-5 3.95e-4 ✓ sig.
Complement and coagulation cascades
C3, C5, CD59
 KEGG 3 / 88 51.2× 2.07e-5 5.37e-4 ✓ sig.
Hematopoietic cell lineage
HLA-DQA1, HLA-DQB1, CD59
 KEGG 3 / 100 45.0× 3.04e-5 7.33e-4 ✓ sig.
Synthesis of glycosylphosphatidylinositol (GPI)
PIGA, PIGP
 Reactome 2 / 17 177× 5.25e-5 1.13e-3 ✓ sig.
Translocation of ZAP-70 to Immunological synapse
HLA-DQA1, HLA-DQB1
 Reactome 2 / 19 158× 6.60e-5 1.36e-3 ✓ sig.
Phosphorylation of CD3 and TCR zeta chains
HLA-DQA1, HLA-DQB1
 Reactome 2 / 22 136× 8.91e-5 1.73e-3 ✓ sig.
PD-1 signaling
HLA-DQA1, HLA-DQB1
 Reactome 2 / 23 131× 9.75e-5 1.86e-3 ✓ sig.
Phagosome
C3, HLA-DQA1, HLA-DQB1
 KEGG 3 / 155 29.1× 1.13e-4 2.09e-3 ✓ sig.
Tuberculosis
C3, HLA-DQA1, HLA-DQB1
 KEGG 3 / 181 24.9× 1.78e-4 3.00e-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 ⇵
GPI anchor biosynthetic process
PIGA, PIGT, PIGP
 GO:0006506 3 / 31 226× 2.30e-7 2.54e-5 ✓ sig.
complement activation
C3, C5, CD59
 GO:0006956 3 / 35 200× 3.35e-7 3.49e-5 ✓ sig.
complement activation, GZMK pathway
C3, C5
 GO:0160257 2 / 12 389× 1.06e-5 5.67e-4 ✓ sig.
complement activation, lectin pathway
C3, C5
 GO:0001867 2 / 13 359× 1.25e-5 6.46e-4 ✓ sig.
antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
HLA-DQA1, HLA-DQB1
 GO:0002504 2 / 15 311× 1.68e-5 8.10e-4 ✓ sig.
complement activation, alternative pathway
C3, C5
 GO:0006957 2 / 16 292× 1.92e-5 8.97e-4 ✓ sig.
peptide antigen assembly with MHC class II protein complex
HLA-DQA1, HLA-DQB1
 GO:0002503 2 / 16 292× 1.92e-5 8.97e-4 ✓ sig.
leukocyte chemotaxis
C3, C5
 GO:0030595 2 / 16 292× 1.92e-5 8.97e-4 ✓ sig.
antigen processing and presentation of exogenous peptide antigen via MHC class II
HLA-DQA1, HLA-DQB1
 GO:0019886 2 / 31 151× 7.41e-5 2.48e-3 ✓ sig.
positive regulation of vascular endothelial growth factor production
C3, C5
 GO:0010575 2 / 32 146× 7.90e-5 2.60e-3 ✓ sig.
complement activation, classical pathway
C3, C5
 GO:0006958 2 / 37 126× 1.06e-4 3.23e-3 ✓ sig.
positive regulation of immune response
HLA-DQA1, HLA-DQB1
 GO:0050778 2 / 40 117× 1.24e-4 3.61e-3 ✓ sig.
positive regulation of T cell activation
HLA-DQA1, HLA-DQB1
 GO:0050870 2 / 45 104× 1.57e-4 4.29e-3 ✓ sig.
antigen processing and presentation
HLA-DQA1, HLA-DQB1
 GO:0019882 2 / 48 97.3× 1.79e-4 4.70e-3 ✓ sig.
immune system process
C3, C5, HLA-DQA1, HLA-DQB1
 GO:0002376 4 / 943 9.9× 3.83e-4 7.94e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cold paroxysmal hemoglobinuria Hemoglobinuria paroxysmal 0.857 6 5.22e-23 8.37e-22 ✓ sig.
Cold paroxysmal hemoglobinuria Paroxysmal nocturnal hemoglobinuria 0.750 6 3.65e-22 5.71e-21 ✓ sig.
Hemoglobinuria paroxysmal Paroxysmal nocturnal hemoglobinuria 0.750 6 3.65e-22 5.71e-21 ✓ sig.
Cold paroxysmal hemoglobinuria Multiple congenital anomalies-hypotonia-seizures syndrome 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Hemoglobinuria paroxysmal Multiple congenital anomalies-hypotonia-seizures syndrome 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Multiple congenital anomalies-hypotonia-seizures syndrome Paroxysmal nocturnal hemoglobinuria 0.222 2 5.25e-7 3.32e-6 ✓ sig.
Multiple congenital anomalies-hypotonia-seizures syndrome 2 Neurodevelopmental disorder with epilepsy and hemochromatosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder seizures dysmorphic skeletal Multiple congenital anomalies-hypotonia-seizures syndrome 3 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Multiple congenital anomalies-hypotonia-seizures syndrome Multiple congenital anomalies-hypotonia-seizures syndrome 2 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Multiple congenital anomalies-hypotonia-seizures syndrome Multiple congenital anomalies-hypotonia-seizures syndrome 3 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Multiple congenital anomalies-hypotonia-seizures syndrome Neurodevelopmental disorder with epilepsy and hemochromatosis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Intellectual developmental disorder seizures dysmorphic skeletal Multiple congenital anomalies-hypotonia-seizures syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Developmental and epileptic encephalopathy, 55 Multiple congenital anomalies-hypotonia-seizures syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cold paroxysmal hemoglobinuria Intellectual developmental disorder seizures dysmorphic skeletal 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Hemoglobinuria paroxysmal Intellectual developmental disorder seizures dysmorphic skeletal 0.143 1 3.87e-4 7.33e-4 ✓ sig.
C5 deficiency Cold paroxysmal hemoglobinuria 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cold paroxysmal hemoglobinuria Multiple congenital anomalies-hypotonia-seizures syndrome 2 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Hemoglobinuria paroxysmal Multiple congenital anomalies-hypotonia-seizures syndrome 2 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cold paroxysmal hemoglobinuria Multiple congenital anomalies-hypotonia-seizures syndrome 3 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Hemoglobinuria paroxysmal Multiple congenital anomalies-hypotonia-seizures syndrome 3 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cold paroxysmal hemoglobinuria Neurodevelopmental disorder with epilepsy and hemochromatosis 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Hemoglobinuria paroxysmal Neurodevelopmental disorder with epilepsy and hemochromatosis 0.143 1 3.87e-4 7.33e-4 ✓ sig.
C5 deficiency Hemoglobinuria paroxysmal 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Multiple congenital anomalies-hypotonia-seizures syndrome 2 Paroxysmal nocturnal hemoglobinuria 0.125 1 4.52e-4 8.26e-4 ✓ sig.
C5 deficiency Paroxysmal nocturnal hemoglobinuria 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Neurodevelopmental disorder with epilepsy and hemochromatosis Paroxysmal nocturnal hemoglobinuria 0.125 1 4.52e-4 8.26e-4 ✓ sig.