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 352

6 diseases · 12 shared-gene connections
6 Diseases
10 Unique genes
0.250 Avg. similarity score
Cockayne syndrome Most-connected disease (5 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 ⇵
Cockayne syndrome 5 5 6
Uv-sensitive syndrome 5 5 5
Cerebrooculofacioskeletal syndrome 4 4 6
Cockayne spectrum with or without cerebrooculofacioskeletal syndrome 4 4 1
De sanctis-cacchione syndrome 4 4 2
Cockayne syndrome type 1 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ERCC6 5 / 6 Cerebrooculofacioskeletal syndrome, Cockayne spectrum with or without cerebrooculofacioskeletal syndrome, Cockayne syndrome, De sanctis-cacchione syndrome and 1 more
PGBD3 4 / 6 Cerebrooculofacioskeletal syndrome, Cockayne syndrome, De sanctis-cacchione syndrome, Uv-sensitive syndrome
ERCC8 3 / 6 Cockayne syndrome, Cockayne syndrome type 1, Uv-sensitive syndrome
ERCC1 2 / 6 Cerebrooculofacioskeletal syndrome, Cockayne syndrome
NDUFAF2 2 / 6 Cockayne syndrome, Uv-sensitive 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 ⇵
Nucleotide excision repair
ERCC1, ERCC2, ERCC5, ERCC6, BIVM-ERCC5, ERCC4, ERCC8, UVSSA
 KEGG 8 / 63 153× 1.61e-17 8.45e-15 ✓ sig.
Dual incision in TC-NER
ERCC1, ERCC2, ERCC5, ERCC6, ERCC4, ERCC8, UVSSA
 Reactome 7 / 66 127× 1.29e-14 3.93e-12 ✓ sig.
Dual Incision in GG-NER
ERCC1, ERCC2, ERCC5, ERCC4
 Reactome 4 / 41 117× 2.42e-8 1.91e-6 ✓ sig.
Formation of Incision Complex in GG-NER
ERCC1, ERCC2, ERCC5, ERCC4
 Reactome 4 / 43 112× 2.94e-8 2.26e-6 ✓ sig.
Transcription-Coupled Nucleotide Excision Repair (TC-NER)
ERCC2, ERCC6, ERCC8, UVSSA
 Reactome 4 / 45 107× 3.55e-8 2.65e-6 ✓ sig.
Formation of TC-NER Pre-Incision Complex
ERCC2, ERCC6, ERCC8, UVSSA
 Reactome 4 / 54 89.0× 7.51e-8 5.08e-6 ✓ sig.
Gap-filling DNA repair synthesis and ligation in TC-NER
ERCC2, ERCC6, ERCC8, UVSSA
 Reactome 4 / 65 73.9× 1.60e-7 9.84e-6 ✓ sig.
HDR through Single Strand Annealing (SSA)
ERCC1, ERCC4
 Reactome 2 / 37 64.9× 4.09e-4 6.83e-3 ✓ sig.
Fanconi Anemia Pathway
ERCC1, ERCC4
 Reactome 2 / 40 60.1× 4.79e-4 7.71e-3 ✓ sig.
RNA Polymerase I Transcription Initiation
ERCC2, ERCC6
 Reactome 2 / 45 53.4× 6.06e-4 9.26e-3 ✓ sig.
Fanconi anemia pathway
ERCC1, ERCC4
 KEGG 2 / 54 44.5× 8.73e-4 1.22e-2 ✓ sig.
RNA Pol II CTD phosphorylation and interaction with CE
ERCC2
 Reactome 1 / 27 44.5× 2.23e-2 1.09e-1
mRNA Capping
ERCC2
 Reactome 1 / 29 41.4× 2.39e-2 1.14e-1
RNA Polymerase I Transcription Termination
ERCC2
 Reactome 1 / 32 37.5× 2.63e-2 1.20e-1
Formation of the Early Elongation Complex
ERCC2
 Reactome 1 / 33 36.4× 2.71e-2 1.22e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
transcription-coupled nucleotide-excision repair
ERCC2, ERCC5, ERCC6, ERCC8, UVSSA
 GO:0006283 5 / 12 779× 1.05e-14 6.83e-12 ✓ sig.
response to UV
ERCC2, ERCC5, ERCC6, ERCC4, ERCC8, UVSSA
 GO:0009411 6 / 54 208× 9.10e-14 5.02e-11 ✓ sig.
DNA repair
ERCC1, ERCC2, ERCC5, ERCC6, ERCC4, ERCC8, UVSSA
 GO:0006281 7 / 420 31.1× 3.12e-10 7.93e-8 ✓ sig.
DNA damage response
ERCC1, ERCC2, ERCC5, ERCC6, ERCC4, ERCC8, UVSSA
 GO:0006974 7 / 577 22.7× 2.86e-9 5.66e-7 ✓ sig.
nucleotide-excision repair
ERCC1, ERCC2, ERCC5, ERCC4
 GO:0006289 4 / 42 178× 4.58e-9 8.63e-7 ✓ sig.
UV protection
ERCC1, ERCC2, ERCC4
 GO:0009650 3 / 12 467× 2.42e-8 3.67e-6 ✓ sig.
response to X-ray
ERCC1, ERCC6, ERCC8
 GO:0010165 3 / 19 295× 1.06e-7 1.27e-5 ✓ sig.
response to oxidative stress
ERCC1, ERCC2, ERCC6, ERCC8
 GO:0006979 4 / 146 51.2× 7.24e-7 6.40e-5 ✓ sig.
telomeric DNA-containing double minutes formation
ERCC1, ERCC4
 GO:0061819 2 / 3 1,246× 7.73e-7 6.73e-5 ✓ sig.
negative regulation of protection from non-homologous end joining at telomere
ERCC1, ERCC4
 GO:1905765 2 / 3 1,246× 7.73e-7 6.73e-5 ✓ sig.
negative regulation of telomere maintenance
ERCC1, ERCC4
 GO:0032205 2 / 5 747× 2.58e-6 1.76e-4 ✓ sig.
transcription elongation by RNA polymerase I
ERCC2, ERCC6
 GO:0006362 2 / 7 534× 5.40e-6 3.20e-4 ✓ sig.
double-strand break repair via classical nonhomologous end joining
ERCC6, ERCC8
 GO:0097680 2 / 11 340× 1.41e-5 6.84e-4 ✓ sig.
single strand break repair
ERCC6, ERCC8
 GO:0000012 2 / 12 311× 1.70e-5 7.89e-4 ✓ sig.
multicellular organism growth
ERCC1, ERCC2, ERCC6
 GO:0035264 3 / 115 48.7× 2.64e-5 1.11e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cockayne syndrome Uv-sensitive syndrome 0.500 4 3.20e-14 4.55e-13 ✓ sig.
Cerebrooculofacioskeletal syndrome Cockayne syndrome 0.300 3 6.57e-10 6.39e-9 ✓ sig.
De sanctis-cacchione syndrome Uv-sensitive syndrome 0.333 2 8.44e-8 6.27e-7 ✓ sig.
Cerebrooculofacioskeletal syndrome De sanctis-cacchione syndrome 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Cockayne syndrome De sanctis-cacchione syndrome 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Cerebrooculofacioskeletal syndrome Uv-sensitive syndrome 0.200 2 1.26e-6 7.70e-6 ✓ sig.
Cockayne spectrum with or without cerebrooculofacioskeletal syndrome De sanctis-cacchione syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cockayne spectrum with or without cerebrooculofacioskeletal syndrome Uv-sensitive syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Cockayne syndrome type 1 Uv-sensitive syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Cerebrooculofacioskeletal syndrome Cockayne spectrum with or without cerebrooculofacioskeletal syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Cockayne spectrum with or without cerebrooculofacioskeletal syndrome Cockayne syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Cockayne syndrome Cockayne syndrome type 1 0.143 1 3.90e-4 8.52e-4 ✓ sig.