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 251
8
Diseases
37
Unique genes
0.206
Avg. similarity score
Abnormality of the face
Most-connected disease (6 links)
Disease
Searched: Morphological abnormality of the central nervous system
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Morphological abnormality of the central nervous system
Abnormality of the face
Behavioral abnormality
Neurodevelopmental disorder with dysmorphic facies, sleep disturbance, and brain abnormalities
Oral cleft
Sleep disturbance
Short stature
Intellectual developmental disorder with short stature, facial anomalies, and speech delay
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Abnormality of the face | 6 | 6 | 7 |
| Behavioral abnormality | 5 | 5 | 14 |
| Neurodevelopmental disorder with dysmorphic facies, sleep disturbance, and brain abnormalities | 5 | 5 | 1 |
| Oral cleft | 5 | 5 | 1 |
| Sleep disturbance | 5 | 5 | 1 |
| Morphological abnormality of the central nervous system | 4 | 4 | 2 |
| Short stature | 3 | 3 | 21 |
| Intellectual developmental disorder with short stature, facial anomalies, and speech delay | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| KAT5 | 7 / 8 | Abnormality of the face, Behavioral abnormality, Morphological abnormality of the central nervous system, Neurodevelopmental disorder with dysmorphic facies, sleep disturbance, and brain abnormalities and 3 more |
| FBXL3 | 2 / 8 | Intellectual developmental disorder with short stature, facial anomalies, and speech delay, Short stature |
| HEATR3 | 2 / 8 | Abnormality of the face, Short stature |
| IQSEC1 | 2 / 8 | Behavioral abnormality, Short stature |
| PDZD8 | 2 / 8 | Abnormality of the face, Behavioral abnormality |
| PUS7 | 2 / 8 | Behavioral abnormality, Short stature |
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 ⇵ |
|---|---|---|---|---|---|
| Deadenylation of mRNA | Reactome | 2 / 24 | 27.0× | 2.44e-3 | 2.20e-2 ✓ sig. |
| Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | Reactome | 3 / 115 | 8.5× | 5.24e-3 | 3.76e-2 ✓ sig. |
| Nuclear import of Rev protein | Reactome | 1 / 4 | 81.1× | 1.23e-2 | 6.45e-2 |
| Hypusine synthesis from eIF5A-lysine | Reactome | 1 / 4 | 81.1× | 1.23e-2 | 6.45e-2 |
| TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation | Reactome | 1 / 5 | 64.9× | 1.53e-2 | 7.35e-2 |
| Long-term potentiation | KEGG | 2 / 67 | 9.7× | 1.80e-2 | 8.08e-2 |
| Sensing of DNA Double Strand Breaks | Reactome | 1 / 6 | 54.1× | 1.83e-2 | 8.16e-2 |
| CaMK IV-mediated phosphorylation of CREB | Reactome | 1 / 6 | 54.1× | 1.83e-2 | 8.16e-2 |
| CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde | Reactome | 1 / 6 | 54.1× | 1.83e-2 | 8.16e-2 |
| Transport and synthesis of PAPS | Reactome | 1 / 6 | 54.1× | 1.83e-2 | 8.16e-2 |
| RAS signaling downstream of NF1 loss-of-function variants | Reactome | 1 / 7 | 46.4× | 2.14e-2 | 8.91e-2 |
| RNA degradation | KEGG | 2 / 78 | 8.3× | 2.39e-2 | 9.50e-2 |
| Transport of nucleotide sugars | Reactome | 1 / 9 | 36.1× | 2.74e-2 | 1.03e-1 |
| SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion | Reactome | 1 / 10 | 32.5× | 3.04e-2 | 1.09e-1 |
| MET activates RAP1 and RAC1 | Reactome | 1 / 11 | 29.5× | 3.34e-2 | 1.15e-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 ⇵ |
|---|---|---|---|---|---|
| nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | GO:0000184 | 3 / 36 | 42.1× | 4.88e-5 | 1.81e-3 ✓ sig. |
| lipid droplet disassembly | GO:1905691 | 2 / 7 | 144× | 7.96e-5 | 2.61e-3 ✓ sig. |
| regulation of hematopoietic stem cell differentiation | GO:1902036 | 2 / 11 | 91.8× | 2.07e-4 | 5.22e-3 ✓ sig. |
| phosphatidylethanolamine biosynthetic process | GO:0006646 | 2 / 12 | 84.2× | 2.49e-4 | 5.92e-3 ✓ sig. |
| phosphatidylcholine biosynthetic process | GO:0006656 | 2 / 25 | 40.4× | 1.11e-3 | 1.55e-2 ✓ sig. |
| regulation of cell morphogenesis | GO:0022604 | 2 / 30 | 33.7× | 1.60e-3 | 1.88e-2 ✓ sig. |
| regulation of mesoderm development | GO:2000380 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |
| regulation of retrograde protein transport, ER to cytosol | GO:1904152 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |
| regulation of endoribonuclease activity | GO:0060699 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |
| regulation of eIF2 alpha phosphorylation by dsRNA | GO:0060735 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |
| regulation of mRNA stability involved in cellular response to UV | GO:1902629 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |
| regulation of translation by machinery localization | GO:0043143 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |
| cellular response to selenite ion | GO:0072715 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |
| negative regulation of selenocysteine incorporation | GO:1904570 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |
| spermidine metabolic process | GO:0008216 | 1 / 1 | 505× | 1.98e-3 | 2.11e-2 ✓ sig. |