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 608
5
Diseases
3
Unique genes
0.375
Avg. similarity score
Lissencephaly 2 (norman-roberts type)
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Lissencephaly 2 (norman-roberts type)
Lissencephaly with cerebellar hypoplasia
Roberts syndrome
Sacroiliac arthritis
Sacroiliac joint synovitis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Lissencephaly 2 (norman-roberts type) | 4 | 4 | 1 |
| Lissencephaly with cerebellar hypoplasia | 4 | 4 | 2 |
| Roberts syndrome | 4 | 4 | 2 |
| Sacroiliac arthritis | 4 | 4 | 1 |
| Sacroiliac joint synovitis | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| RELN | 5 / 5 | Lissencephaly 2 (norman-roberts type), Lissencephaly with cerebellar hypoplasia, Roberts syndrome, Sacroiliac arthritis and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| Reelin signalling pathway | Reactome | 1 / 5 | 801× | 1.25e-3 | 1.34e-2 ✓ sig. |
| Establishment of Sister Chromatid Cohesion | Reactome | 1 / 11 | 364× | 2.75e-3 | 2.39e-2 ✓ sig. |
| Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models | Reactome | 1 / 16 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| CRMPs in Sema3A signaling | Reactome | 1 / 16 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| DARPP-32 events | Reactome | 1 / 19 | 211× | 4.74e-3 | 3.52e-2 ✓ sig. |
| Cocaine addiction | KEGG | 1 / 49 | 81.7× | 1.22e-2 | 6.42e-2 |
| ECM-receptor interaction | KEGG | 1 / 89 | 45.0× | 2.21e-2 | 9.07e-2 |
| Regulation of TP53 Activity through Phosphorylation | Reactome | 1 / 92 | 43.5× | 2.28e-2 | 9.23e-2 |
| Spinocerebellar ataxia | KEGG | 1 / 144 | 27.8× | 3.55e-2 | 1.19e-1 |
| Cell cycle | KEGG | 1 / 158 | 25.3× | 3.90e-2 | 1.26e-1 |
| Axon guidance | KEGG | 1 / 183 | 21.9× | 4.50e-2 | 1.36e-1 |
| Focal adhesion | KEGG | 1 / 203 | 19.7× | 4.99e-2 | 1.45e-1 |
| Human papillomavirus infection | KEGG | 1 / 333 | 12.0× | 8.09e-2 | 1.91e-1 |
| PI3K-Akt signaling pathway | KEGG | 1 / 361 | 11.1× | 8.75e-2 | 2.00e-1 |
| Alzheimer disease | KEGG | 1 / 388 | 10.3× | 9.38e-2 | 2.08e-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 ⇵ |
|---|---|---|---|---|---|
| layer formation in cerebral cortex | GO:0021819 | 2 / 18 | 692× | 2.63e-6 | 1.89e-4 ✓ sig. |
| protein localization to synapse | GO:0035418 | 2 / 19 | 656× | 2.94e-6 | 2.06e-4 ✓ sig. |
| associative learning | GO:0008306 | 2 / 40 | 311× | 1.34e-5 | 6.82e-4 ✓ sig. |
| hippocampus development | GO:0021766 | 2 / 74 | 168× | 4.63e-5 | 1.75e-3 ✓ sig. |
| forebrain development | GO:0030900 | 2 / 76 | 164× | 4.88e-5 | 1.81e-3 ✓ sig. |
| cerebral cortex development | GO:0021987 | 2 / 88 | 142× | 6.56e-5 | 2.26e-3 ✓ sig. |
| neuron migration | GO:0001764 | 2 / 132 | 94.4× | 1.48e-4 | 4.09e-3 ✓ sig. |
| spinal cord patterning | GO:0021511 | 1 / 1 | 6,229× | 1.61e-4 | 4.34e-3 ✓ sig. |
| positive regulation of lateral motor column neuron migration | GO:1902078 | 1 / 1 | 6,229× | 1.61e-4 | 4.34e-3 ✓ sig. |
| positive regulation of presynaptic cytosolic calcium concentration | GO:0099533 | 1 / 1 | 6,229× | 1.61e-4 | 4.34e-3 ✓ sig. |
| negative regulation of calcium ion-dependent exocytosis of neurotransmitter | GO:1903234 | 1 / 1 | 6,229× | 1.61e-4 | 4.34e-3 ✓ sig. |
| regulation of synaptic vesicle recycling | GO:1903421 | 1 / 2 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| lateral motor column neuron migration | GO:0097477 | 1 / 3 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| cerebellar cortex formation | GO:0021697 | 1 / 3 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| post-translational protein acetylation | GO:0034421 | 1 / 3 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Lissencephaly 2 (norman-roberts type) | Sacroiliac arthritis | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Lissencephaly 2 (norman-roberts type) | Sacroiliac joint synovitis | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Sacroiliac arthritis | Sacroiliac joint synovitis | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Lissencephaly 2 (norman-roberts type) | Lissencephaly with cerebellar hypoplasia | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Lissencephaly 2 (norman-roberts type) | Roberts syndrome | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Lissencephaly with cerebellar hypoplasia | Sacroiliac arthritis | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Lissencephaly with cerebellar hypoplasia | Sacroiliac joint synovitis | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Roberts syndrome | Sacroiliac arthritis | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Roberts syndrome | Sacroiliac joint synovitis | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Lissencephaly with cerebellar hypoplasia | Roberts syndrome | 0.250 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |