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 80
12
Diseases
23
Unique genes
0.143
Avg. similarity score
Xeroderma pigmentosum
Most-connected disease (8 links)
Disease
Searched: Trichothiodystrophy
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Trichothiodystrophy
Xeroderma pigmentosum
Xeroderma pigmentosum-cockayne syndrome
Cerebrooculofacioskeletal syndrome
xeroderma pigmentosum group B
xeroderma pigmentosum group D
xeroderma pigmentosum group G
Amish brittle hair brain syndrome
Trichorrhexis nodosa syndrome
xeroderma pigmentosum group C
xeroderma pigmentosum group E
xeroderma pigmentosum variant type
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Xeroderma pigmentosum | 8 | 8 | 12 |
| Trichothiodystrophy | 6 | 6 | 11 |
| Xeroderma pigmentosum-cockayne syndrome | 6 | 6 | 5 |
| Cerebrooculofacioskeletal syndrome | 4 | 4 | 6 |
| xeroderma pigmentosum group B | 3 | 3 | 1 |
| xeroderma pigmentosum group D | 3 | 3 | 1 |
| xeroderma pigmentosum group G | 3 | 3 | 1 |
| Amish brittle hair brain syndrome | 1 | 1 | 1 |
| Trichorrhexis nodosa syndrome | 1 | 1 | 1 |
| xeroderma pigmentosum group C | 1 | 1 | 1 |
| xeroderma pigmentosum group E | 1 | 1 | 1 |
| xeroderma pigmentosum variant type | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ERCC2 | 5 / 12 | Cerebrooculofacioskeletal syndrome, Trichothiodystrophy, Xeroderma pigmentosum, xeroderma pigmentosum group D and 1 more |
| ERCC3 | 4 / 12 | Trichothiodystrophy, Xeroderma pigmentosum, xeroderma pigmentosum group B, Xeroderma pigmentosum-cockayne syndrome |
| ERCC5 | 4 / 12 | Cerebrooculofacioskeletal syndrome, Xeroderma pigmentosum, xeroderma pigmentosum group G, Xeroderma pigmentosum-cockayne syndrome |
| BIVM-ERCC5 | 3 / 12 | Cerebrooculofacioskeletal syndrome, Xeroderma pigmentosum, Xeroderma pigmentosum-cockayne syndrome |
| DDB2 | 2 / 12 | Xeroderma pigmentosum, xeroderma pigmentosum group E |
| ERCC1 | 2 / 12 | Cerebrooculofacioskeletal syndrome, Xeroderma pigmentosum |
| ERCC4 | 2 / 12 | Xeroderma pigmentosum, Xeroderma pigmentosum-cockayne syndrome |
| MPLKIP | 2 / 12 | Trichorrhexis nodosa syndrome, Trichothiodystrophy |
| POLH | 2 / 12 | Xeroderma pigmentosum, xeroderma pigmentosum variant type |
| RNF113A | 2 / 12 | Amish brittle hair brain syndrome, Trichothiodystrophy |
| XPC | 2 / 12 | Xeroderma pigmentosum, xeroderma pigmentosum group C |
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 | KEGG | 11 / 63 | 91.2× | 4.24e-20 | 2.96e-17 ✓ sig. |
| Formation of Incision Complex in GG-NER | Reactome | 9 / 43 | 109× | 3.11e-17 | 1.38e-14 ✓ sig. |
| Dual Incision in GG-NER | Reactome | 8 / 41 | 102× | 4.22e-15 | 1.33e-12 ✓ sig. |
| Dual incision in TC-NER | Reactome | 8 / 66 | 63.3× | 2.46e-13 | 5.60e-11 ✓ sig. |
| Formation of TC-NER Pre-Incision Complex | Reactome | 5 / 54 | 48.3× | 4.81e-8 | 3.44e-6 ✓ sig. |
| Cytosolic tRNA aminoacylation | Reactome | 4 / 24 | 87.0× | 1.06e-7 | 6.88e-6 ✓ sig. |
| Basal transcription factors | KEGG | 4 / 44 | 47.5× | 1.32e-6 | 6.18e-5 ✓ sig. |
| Transcription-Coupled Nucleotide Excision Repair (TC-NER) | Reactome | 4 / 45 | 46.4× | 1.45e-6 | 6.71e-5 ✓ sig. |
| RNA Polymerase I Transcription Initiation | Reactome | 4 / 45 | 46.4× | 1.45e-6 | 6.71e-5 ✓ sig. |
| RNA Polymerase II Promoter Escape | Reactome | 4 / 47 | 44.4× | 1.73e-6 | 7.80e-5 ✓ sig. |
| RNA Polymerase II Transcription Pre-Initiation And Promoter Opening | Reactome | 4 / 47 | 44.4× | 1.73e-6 | 7.80e-5 ✓ sig. |
| RNA Polymerase II Transcription Initiation | Reactome | 4 / 47 | 44.4× | 1.73e-6 | 7.80e-5 ✓ sig. |
| RNA Polymerase II Transcription Initiation And Promoter Clearance | Reactome | 4 / 47 | 44.4× | 1.73e-6 | 7.80e-5 ✓ sig. |
| TP53 Regulates Transcription of DNA Repair Genes | Reactome | 4 / 65 | 32.1× | 6.40e-6 | 2.36e-4 ✓ sig. |
| Gap-filling DNA repair synthesis and ligation in TC-NER | Reactome | 4 / 65 | 32.1× | 6.40e-6 | 2.36e-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 ⇵ |
|---|---|---|---|---|---|
| nucleotide-excision repair | GO:0006289 | 9 / 42 | 174× | 4.66e-19 | 6.36e-16 ✓ sig. |
| DNA repair | GO:0006281 | 12 / 420 | 23.2× | 1.54e-14 | 9.49e-12 ✓ sig. |
| response to UV | GO:0009411 | 7 / 54 | 105× | 2.66e-13 | 1.33e-10 ✓ sig. |
| DNA damage response | GO:0006974 | 12 / 577 | 16.9× | 6.65e-13 | 3.08e-10 ✓ sig. |
| UV protection | GO:0009650 | 5 / 12 | 339× | 1.40e-12 | 6.10e-10 ✓ sig. |
| UV-damage excision repair | GO:0070914 | 4 / 11 | 295× | 5.72e-10 | 1.33e-7 ✓ sig. |
| regulation of mitotic cell cycle phase transition | GO:1901990 | 4 / 11 | 295× | 5.72e-10 | 1.33e-7 ✓ sig. |
| transcription-coupled nucleotide-excision repair | GO:0006283 | 4 / 12 | 271× | 8.57e-10 | 1.89e-7 ✓ sig. |
| pyrimidine dimer repair | GO:0006290 | 3 / 4 | 609× | 6.51e-9 | 1.15e-6 ✓ sig. |
| transcription elongation by RNA polymerase I | GO:0006362 | 3 / 7 | 348× | 5.68e-8 | 7.53e-6 ✓ sig. |
| tRNA aminoacylation for protein translation | GO:0006418 | 4 / 36 | 90.3× | 1.00e-7 | 1.22e-5 ✓ sig. |
| transcription initiation at RNA polymerase II promoter | GO:0006367 | 4 / 48 | 67.7× | 3.27e-7 | 3.31e-5 ✓ sig. |
| response to oxidative stress | GO:0006979 | 5 / 146 | 27.8× | 8.16e-7 | 7.10e-5 ✓ sig. |
| nucleotide-excision repair involved in interstrand cross-link repair | GO:1901255 | 2 / 2 | 812× | 1.45e-6 | 1.13e-4 ✓ sig. |
| telomeric DNA-containing double minutes formation | GO:0061819 | 2 / 3 | 542× | 4.34e-6 | 2.74e-4 ✓ sig. |