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 356

6 diseases · 8 shared-gene connections
6 Diseases
7 Unique genes
0.260 Avg. similarity score
Colorectal cancer susceptibility 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 ⇵
Colorectal cancer susceptibility 5 5 4
POLD1-related polyposis and colorectal cancer syndrome 3 3 1
mandibular hypoplasia-deafness-progeroid syndrome 3 3 1
non-severe combined immunodeficiency due to polymerase delta deficiency 3 3 2
Paraquat lung disease 1 1 3
colorectal cancer, susceptibility to, 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
POLD1 4 / 6 Colorectal cancer susceptibility, mandibular hypoplasia-deafness-progeroid syndrome, non-severe combined immunodeficiency due to polymerase delta deficiency, POLD1-related polyposis and colorectal cancer syndrome
GALNT12 2 / 6 Colorectal cancer susceptibility, colorectal cancer, susceptibility to, 1
SMAD7 2 / 6 Colorectal cancer susceptibility, Paraquat lung disease
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 ⇵
PCNA-Dependent Long Patch Base Excision Repair
POLD1, POLE, POLD2
 Reactome 3 / 21 245× 1.61e-7 9.86e-6 ✓ sig.
Gap-filling DNA repair synthesis and ligation in GG-NER
POLD1, POLE, POLD2
 Reactome 3 / 25 206× 2.77e-7 1.60e-5 ✓ sig.
Recognition of DNA damage by PCNA-containing replication complex
POLD1, POLE, POLD2
 Reactome 3 / 30 172× 4.89e-7 2.63e-5 ✓ sig.
Termination of translesion DNA synthesis
POLD1, POLE, POLD2
 Reactome 3 / 32 161× 5.97e-7 3.12e-5 ✓ sig.
DNA replication
POLD1, POLE, POLD2
 KEGG 3 / 36 143× 8.59e-7 4.28e-5 ✓ sig.
Dual Incision in GG-NER
POLD1, POLE, POLD2
 Reactome 3 / 41 126× 1.28e-6 6.06e-5 ✓ sig.
Base excision repair
POLD1, POLE, POLD2
 KEGG 3 / 44 117× 1.59e-6 7.25e-5 ✓ sig.
HDR through Homologous Recombination (HRR)
POLD1, POLE, POLD2
 Reactome 3 / 48 107× 2.07e-6 9.07e-5 ✓ sig.
Telomere C-strand (Lagging Strand) Synthesis
POLD1, POLD2
 Reactome 2 / 5 686× 2.91e-6 1.21e-4 ✓ sig.
Nucleotide excision repair
POLD1, POLE, POLD2
 KEGG 3 / 63 81.7× 4.74e-6 1.82e-4 ✓ sig.
Gap-filling DNA repair synthesis and ligation in TC-NER
POLD1, POLE, POLD2
 Reactome 3 / 65 79.2× 5.21e-6 1.96e-4 ✓ sig.
Dual incision in TC-NER
POLD1, POLE, POLD2
 Reactome 3 / 66 78.0× 5.46e-6 2.04e-4 ✓ sig.
Processive synthesis on the C-strand of the telomere
POLD1, POLD2
 Reactome 2 / 8 429× 8.14e-6 2.82e-4 ✓ sig.
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
POLD1, POLD2
 Reactome 2 / 10 343× 1.31e-5 4.19e-4 ✓ sig.
Processive synthesis on the lagging strand
POLD1, POLD2
 Reactome 2 / 10 343× 1.31e-5 4.19e-4 ✓ 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 ⇵
DNA biosynthetic process
POLD1, POLE, POLD2
 GO:0071897 3 / 32 250× 1.59e-7 1.78e-5 ✓ sig.
DNA-templated DNA replication
POLD1, POLE, POLD2
 GO:0006261 3 / 41 195× 3.41e-7 3.38e-5 ✓ sig.
DNA replication proofreading
POLD1, POLE
 GO:0045004 2 / 3 1,780× 3.61e-7 3.55e-5 ✓ sig.
nucleotide-excision repair, DNA gap filling
POLD1, POLE
 GO:0006297 2 / 6 890× 1.80e-6 1.33e-4 ✓ sig.
base-excision repair, gap-filling
POLD1, POLE
 GO:0006287 2 / 14 381× 1.09e-5 5.58e-4 ✓ sig.
DNA replication
POLD1, POLE, POLD2
 GO:0006260 3 / 131 61.1× 1.15e-5 5.82e-4 ✓ sig.
DNA synthesis involved in DNA repair
POLD1, POLE
 GO:0000731 2 / 23 232× 3.03e-5 1.23e-3 ✓ sig.
negative regulation of cell differentiation
SMAD7, SKIL
 GO:0045596 2 / 75 71.2× 3.29e-4 7.16e-3 ✓ sig.
negative regulation of BMP signaling pathway
SMAD7, SKIL
 GO:0030514 2 / 75 71.2× 3.29e-4 7.16e-3 ✓ sig.
DNA repair
POLD1, POLE, POLD2
 GO:0006281 3 / 420 19.1× 3.69e-4 7.73e-3 ✓ sig.
positive regulation of chondrocyte hypertrophy
SMAD7
 GO:1903043 1 / 1 2,670× 3.75e-4 7.81e-3 ✓ sig.
beta-catenin destruction complex disassembly
SMAD7
 GO:1904886 1 / 1 2,670× 3.75e-4 7.81e-3 ✓ sig.
transforming growth factor beta receptor signaling pathway
SMAD7, SKIL
 GO:0007179 2 / 112 47.7× 7.33e-4 1.24e-2 ✓ sig.
negative regulation of T-helper 17 type immune response
SMAD7
 GO:2000317 1 / 2 1,335× 7.49e-4 1.25e-2 ✓ sig.
DNA damage response
POLD1, POLE, POLD2
 GO:0006974 3 / 577 13.9× 9.34e-4 1.45e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
mandibular hypoplasia-deafness-progeroid syndrome POLD1-related polyposis and colorectal cancer syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
mandibular hypoplasia-deafness-progeroid syndrome non-severe combined immunodeficiency due to polymerase delta deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
non-severe combined immunodeficiency due to polymerase delta deficiency POLD1-related polyposis and colorectal cancer syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Colorectal cancer susceptibility colorectal cancer, susceptibility to, 1 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Colorectal cancer susceptibility POLD1-related polyposis and colorectal cancer syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Colorectal cancer susceptibility mandibular hypoplasia-deafness-progeroid syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Colorectal cancer susceptibility non-severe combined immunodeficiency due to polymerase delta deficiency 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Colorectal cancer susceptibility Paraquat lung disease 0.143 1 7.79e-4 1.39e-3 ✓ sig.