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 115
10
Diseases
36
Unique genes
0.151
Avg. similarity score
Transposition of the great arteries
Most-connected disease (8 links)
Disease
Searched: immunodeficiency 114, folate-responsive
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immunodeficiency 114, folate-responsive
Transposition of the great arteries
Discordant ventriculoarterial connection
Double outlet right ventricle
Knobloch syndrome
Right atrial isomerism
Right isomerism
Down syndrome
Congenitally uncorrected transposition of the great arteries
microcornea-myopic chorioretinal atrophy
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Transposition of the great arteries | 8 | 8 | 11 |
| Discordant ventriculoarterial connection | 6 | 6 | 4 |
| Double outlet right ventricle | 4 | 4 | 8 |
| Knobloch syndrome | 4 | 4 | 4 |
| Right atrial isomerism | 4 | 4 | 3 |
| Right isomerism | 4 | 4 | 1 |
| immunodeficiency 114, folate-responsive | 4 | 4 | 1 |
| Down syndrome | 3 | 3 | 19 |
| Congenitally uncorrected transposition of the great arteries | 2 | 2 | 1 |
| microcornea-myopic chorioretinal atrophy | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GDF1 | 5 / 10 | Discordant ventriculoarterial connection, Double outlet right ventricle, Right atrial isomerism, Right isomerism and 1 more |
| SLC19A1 | 5 / 10 | Discordant ventriculoarterial connection, Down syndrome, immunodeficiency 114, folate-responsive, Knobloch syndrome and 1 more |
| CERS1 | 3 / 10 | Double outlet right ventricle, Right atrial isomerism, Transposition of the great arteries |
| CFC1 | 3 / 10 | Congenitally uncorrected transposition of the great arteries, Double outlet right ventricle, Transposition of the great arteries |
| MTHFR | 3 / 10 | Discordant ventriculoarterial connection, Down syndrome, Transposition of the great arteries |
| ADAMTS18 | 2 / 10 | Knobloch syndrome, microcornea-myopic chorioretinal atrophy |
| MED13L | 2 / 10 | Discordant ventriculoarterial connection, Transposition of the great arteries |
| UPF1 | 2 / 10 | Right atrial isomerism, Transposition of the great arteries |
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 ⇵ |
|---|---|---|---|---|---|
| Metabolism of folate and pterines | Reactome | 3 / 17 | 58.9× | 1.63e-5 | 5.13e-4 ✓ sig. |
| Folate transport and metabolism | KEGG | 3 / 31 | 32.3× | 1.05e-4 | 2.36e-3 ✓ sig. |
| Detoxification of Reactive Oxygen Species | Reactome | 3 / 34 | 29.4× | 1.39e-4 | 2.95e-3 ✓ sig. |
| Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) | Reactome | 2 / 7 | 95.3× | 1.82e-4 | 3.66e-3 ✓ sig. |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 3 / 51 | 19.6× | 4.67e-4 | 7.72e-3 ✓ sig. |
| Collagen degradation | Reactome | 3 / 52 | 19.2× | 4.94e-4 | 8.06e-3 ✓ sig. |
| Physiological factors | Reactome | 2 / 12 | 55.6× | 5.66e-4 | 8.95e-3 ✓ sig. |
| YAP1- and WWTR1 (TAZ)-stimulated gene expression | Reactome | 2 / 14 | 47.7× | 7.77e-4 | 1.15e-2 ✓ sig. |
| Factors involved in megakaryocyte development and platelet production | Reactome | 3 / 99 | 10.1× | 3.18e-3 | 3.25e-2 ✓ sig. |
| Antifolate resistance | KEGG | 2 / 30 | 22.2× | 3.60e-3 | 3.56e-2 ✓ sig. |
| Activation of Matrix Metalloproteinases | Reactome | 2 / 33 | 20.2× | 4.35e-3 | 4.06e-2 ✓ sig. |
| Signaling by SCF-KIT | Reactome | 2 / 37 | 18.0× | 5.45e-3 | 4.73e-2 ✓ sig. |
| Thyroid hormone signaling pathway | KEGG | 3 / 122 | 8.2× | 5.72e-3 | 4.89e-2 ✓ sig. |
| One carbon pool by folate | KEGG | 2 / 38 | 17.6× | 5.74e-3 | 4.90e-2 ✓ sig. |
| Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation | Reactome | 2 / 38 | 17.6× | 5.74e-3 | 4.90e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| heart development | GO:0007507 | 7 / 273 | 13.3× | 7.64e-7 | 6.72e-5 ✓ sig. |
| cardiac muscle tissue morphogenesis | GO:0055008 | 3 / 13 | 120× | 1.85e-6 | 1.38e-4 ✓ sig. |
| atrial septum morphogenesis | GO:0060413 | 3 / 13 | 120× | 1.85e-6 | 1.38e-4 ✓ sig. |
| right ventricular cardiac muscle tissue morphogenesis | GO:0003221 | 2 / 2 | 519× | 3.61e-6 | 2.35e-4 ✓ sig. |
| embryonic heart tube anterior/posterior pattern specification | GO:0035054 | 2 / 3 | 346× | 1.08e-5 | 5.62e-4 ✓ sig. |
| astrocyte differentiation | GO:0048708 | 3 / 25 | 62.3× | 1.47e-5 | 7.15e-4 ✓ sig. |
| outflow tract septum morphogenesis | GO:0003148 | 3 / 28 | 55.6× | 2.08e-5 | 9.41e-4 ✓ sig. |
| cardiac muscle cell differentiation | GO:0055007 | 3 / 30 | 51.9× | 2.57e-5 | 1.10e-3 ✓ sig. |
| atrioventricular node development | GO:0003162 | 2 / 6 | 173× | 5.39e-5 | 1.94e-3 ✓ sig. |
| methionine metabolic process | GO:0006555 | 2 / 6 | 173× | 5.39e-5 | 1.94e-3 ✓ sig. |
| positive regulation of interleukin-1 alpha production | GO:0032730 | 2 / 7 | 148× | 7.53e-5 | 2.51e-3 ✓ sig. |
| cell-cell signaling | GO:0007267 | 5 / 234 | 11.1× | 8.10e-5 | 2.65e-3 ✓ sig. |
| response to xenobiotic stimulus | GO:0009410 | 5 / 248 | 10.5× | 1.07e-4 | 3.24e-3 ✓ sig. |
| embryo implantation | GO:0007566 | 3 / 48 | 32.4× | 1.07e-4 | 3.25e-3 ✓ sig. |
| in utero embryonic development | GO:0001701 | 5 / 252 | 10.3× | 1.15e-4 | 3.42e-3 ✓ sig. |