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 335
6
Diseases
12
Unique genes
0.146
Avg. similarity score
Immunodeficiency-centromeric instability-facial anomalies syndrome
Most-connected disease (5 links)
Disease
Searched: immunodeficiency-centromeric instability-facial anomalies syndrome 4
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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immunodeficiency-centromeric instability-facial anomalies syndrome 4
Immunodeficiency-centromeric instability-facial anomalies syndrome
Kabuki syndrome
immunodeficiency-centromeric instability-facial anomalies syndrome 1
immunodeficiency-centromeric instability-facial anomalies syndrome 2
immunodeficiency-centromeric instability-facial anomalies syndrome 3
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Immunodeficiency-centromeric instability-facial anomalies syndrome | 5 | 5 | 5 |
| Kabuki syndrome | 3 | 3 | 9 |
| immunodeficiency-centromeric instability-facial anomalies syndrome 1 | 2 | 2 | 1 |
| immunodeficiency-centromeric instability-facial anomalies syndrome 2 | 2 | 2 | 1 |
| immunodeficiency-centromeric instability-facial anomalies syndrome 3 | 1 | 1 | 1 |
| immunodeficiency-centromeric instability-facial anomalies syndrome 4 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| DNMT3B | 3 / 6 | Immunodeficiency-centromeric instability-facial anomalies syndrome, immunodeficiency-centromeric instability-facial anomalies syndrome 1, Kabuki syndrome |
| ZBTB24 | 3 / 6 | Immunodeficiency-centromeric instability-facial anomalies syndrome, immunodeficiency-centromeric instability-facial anomalies syndrome 2, Kabuki syndrome |
| CDCA7 | 2 / 6 | Immunodeficiency-centromeric instability-facial anomalies syndrome, immunodeficiency-centromeric instability-facial anomalies syndrome 3 |
| HELLS | 2 / 6 | Immunodeficiency-centromeric instability-facial anomalies syndrome, immunodeficiency-centromeric instability-facial anomalies syndrome 4 |
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 ⇵ |
|---|---|---|---|---|---|
| Lysine degradation | KEGG | 3 / 63 | 47.7× | 2.93e-5 | 8.62e-4 ✓ sig. |
| PKMTs methylate histone lysines | Reactome | 3 / 71 | 42.3× | 4.19e-5 | 1.16e-3 ✓ sig. |
| RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function | Reactome | 3 / 97 | 31.0× | 1.07e-4 | 2.45e-3 ✓ sig. |
| SUMOylation of DNA methylation proteins | Reactome | 1 / 4 | 250× | 3.99e-3 | 3.87e-2 ✓ sig. |
| ARMS-mediated activation | Reactome | 1 / 5 | 200× | 4.99e-3 | 4.51e-2 ✓ sig. |
| Cushing syndrome | KEGG | 2 / 155 | 12.9× | 1.00e-2 | 7.09e-2 |
| Transcriptional misregulation in cancer | KEGG | 2 / 198 | 10.1× | 1.60e-2 | 9.43e-2 |
| Cobalamin transport and metabolism | KEGG | 1 / 18 | 55.6× | 1.78e-2 | 1.00e-1 |
| Homologous DNA Pairing and Strand Exchange | Reactome | 1 / 25 | 40.0× | 2.47e-2 | 1.21e-1 |
| Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) | Reactome | 1 / 26 | 38.5× | 2.57e-2 | 1.23e-1 |
| Resolution of D-loop Structures through Holliday Junction Intermediates | Reactome | 1 / 33 | 30.3× | 3.25e-2 | 1.40e-1 |
| Presynaptic phase of homologous DNA pairing and strand exchange | Reactome | 1 / 39 | 25.7× | 3.83e-2 | 1.53e-1 |
| Homologous recombination | KEGG | 1 / 41 | 24.4× | 4.02e-2 | 1.57e-1 |
| Deactivation of the beta-catenin transactivating complex | Reactome | 1 / 42 | 23.8× | 4.12e-2 | 1.59e-1 |
| HDR through Homologous Recombination (HRR) | Reactome | 1 / 48 | 20.9× | 4.69e-2 | 1.70e-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 ⇵ |
|---|---|---|---|---|---|
| chromatin organization | GO:0006325 | 6 / 449 | 20.8× | 1.52e-7 | 1.76e-5 ✓ sig. |
| chromatin remodeling | GO:0006338 | 5 / 320 | 24.3× | 1.02e-6 | 8.60e-5 ✓ sig. |
| methylation | GO:0032259 | 4 / 191 | 32.6× | 4.91e-6 | 3.04e-4 ✓ sig. |
| heterochromatin formation | GO:0031507 | 3 / 70 | 66.7× | 1.08e-5 | 5.74e-4 ✓ sig. |
| negative regulation of gene expression via chromosomal CpG island methylation | GO:0044027 | 2 / 16 | 195× | 4.51e-5 | 1.72e-3 ✓ sig. |
| double-strand break repair via homologous recombination | GO:0000724 | 3 / 119 | 39.3× | 5.31e-5 | 1.95e-3 ✓ sig. |
| regulation of DNA-templated transcription | GO:0006355 | 6 / 1,454 | 6.4× | 1.35e-4 | 3.90e-3 ✓ sig. |
| beta-catenin-TCF complex assembly | GO:1904837 | 1 / 1 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| epigenetic regulation of gene expression | GO:0040029 | 2 / 62 | 50.2× | 7.00e-4 | 1.24e-2 ✓ sig. |
| positive regulation of DNA-templated transcription | GO:0045893 | 4 / 778 | 8.0× | 1.13e-3 | 1.69e-2 ✓ sig. |
| chromosomal DNA methylation maintenance following DNA replication | GO:0141119 | 1 / 2 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| mitotic recombination-dependent replication fork processing | GO:1990426 | 1 / 2 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| negative regulation of DNA methylation-dependent heterochromatin formation | GO:0090310 | 1 / 2 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| double-strand break repair | GO:0006302 | 2 / 87 | 35.8× | 1.37e-3 | 1.89e-2 ✓ sig. |
| regulation of gene expression | GO:0010468 | 3 / 402 | 11.6× | 1.88e-3 | 2.26e-2 ✓ sig. |