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 393

5 diseases · 7 shared-gene connections
5 Diseases
4 Unique genes
0.302 Avg. similarity score
Cataract-multisystem syndrome Most-connected disease (4 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 ⇵
Cataract-multisystem syndrome 4 4 3
Dkc1-related disorder 3 3 1
X-linked dyskeratosis congenita 3 3 2
dyskeratosis congenita, x-linked 3 3 1
pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 9 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
DKC1 4 / 5 Cataract-multisystem syndrome, Dkc1-related disorder, dyskeratosis congenita, x-linked, X-linked dyskeratosis congenita
NOP10 2 / 5 Cataract-multisystem syndrome, pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 9
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 ⇵
Telomere Extension By Telomerase
DKC1, NOP10, RTEL1
 Reactome 3 / 16 563× 7.75e-9 7.01e-7 ✓ sig.
rRNA modification in the nucleus and cytosol
DKC1, NOP10
 Reactome 2 / 12 500× 5.49e-6 2.05e-4 ✓ sig.
Ribosome biogenesis in eukaryotes
DKC1, NOP10
 KEGG 2 / 125 48.0× 6.36e-4 9.63e-3 ✓ sig.
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)
RTEL1
 Reactome 1 / 26 115× 8.63e-3 6.28e-2
Inflammatory bowel disease
MAF
 KEGG 1 / 66 45.5× 2.18e-2 1.08e-1
Th1 and Th2 cell differentiation
MAF
 KEGG 1 / 93 32.3× 3.06e-2 1.31e-1
Transcriptional misregulation in cancer
MAF
 KEGG 1 / 198 15.2× 6.43e-2 1.96e-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 ⇵
snRNA pseudouridine synthesis
DKC1, NOP10
 GO:0031120 2 / 3 3,115× 1.03e-7 1.24e-5 ✓ sig.
rRNA pseudouridine synthesis
DKC1, NOP10
 GO:0031118 2 / 4 2,336× 2.06e-7 2.23e-5 ✓ sig.
pseudouridine synthesis
DKC1, NOP10
 GO:0001522 2 / 16 584× 4.12e-6 2.57e-4 ✓ sig.
telomere maintenance via telomerase
DKC1, NOP10
 GO:0007004 2 / 24 389× 9.47e-6 5.01e-4 ✓ sig.
DNA strand displacement
RTEL1
 GO:0000732 1 / 1 4,672× 2.14e-4 5.28e-3 ✓ sig.
negative regulation of telomere maintenance in response to DNA damage
RTEL1
 GO:1904506 1 / 1 4,672× 2.14e-4 5.28e-3 ✓ sig.
positive regulation of telomeric loop disassembly
RTEL1
 GO:1904535 1 / 1 4,672× 2.14e-4 5.28e-3 ✓ sig.
box H/ACA sno(s)RNA metabolic process
DKC1
 GO:0033979 1 / 1 4,672× 2.14e-4 5.28e-3 ✓ sig.
ribosome biogenesis
DKC1, NOP10
 GO:0042254 2 / 122 76.6× 2.51e-4 5.95e-3 ✓ sig.
box H/ACA sno(s)RNA 3'-end processing
DKC1
 GO:0000495 1 / 2 2,336× 4.28e-4 8.59e-3 ✓ sig.
telomeric loop disassembly
RTEL1
 GO:0090657 1 / 2 2,336× 4.28e-4 8.59e-3 ✓ sig.
protein localization to Cajal body
DKC1
 GO:1904867 1 / 2 2,336× 4.28e-4 8.59e-3 ✓ sig.
rRNA processing
DKC1, NOP10
 GO:0006364 2 / 162 57.7× 4.43e-4 8.80e-3 ✓ sig.
mitotic telomere maintenance via semi-conservative replication
RTEL1
 GO:1902990 1 / 3 1,557× 6.42e-4 1.13e-2 ✓ sig.
negative regulation of t-circle formation
RTEL1
 GO:1904430 1 / 3 1,557× 6.42e-4 1.13e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Dkc1-related disorder dyskeratosis congenita, x-linked 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dkc1-related disorder X-linked dyskeratosis congenita 0.333 1 1.30e-4 3.90e-4 ✓ sig.
dyskeratosis congenita, x-linked X-linked dyskeratosis congenita 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cataract-multisystem syndrome Dkc1-related disorder 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cataract-multisystem syndrome dyskeratosis congenita, x-linked 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cataract-multisystem syndrome pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 9 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cataract-multisystem syndrome X-linked dyskeratosis congenita 0.200 1 3.90e-4 8.52e-4 ✓ sig.