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.
← Back to all clusters
Cluster 426
6
Diseases
19
Unique genes
0.177
Avg. similarity score
Macular telangiectasia
Most-connected disease (4 links)
Disease
Searched: Neurometabolic disorder
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) ·
drag a node to pin it in place · scroll/pinch to zoom.
Neurometabolic disorder
Macular telangiectasia
Neu-laxova syndrome
Phosphoserine phosphatase deficiency
Spastic paraplegia 77, autosomal recessive
Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Macular telangiectasia | 4 | 4 | 16 |
| Neurometabolic disorder | 4 | 4 | 5 |
| Neu-laxova syndrome | 3 | 3 | 3 |
| Phosphoserine phosphatase deficiency | 3 | 3 | 1 |
| Spastic paraplegia 77, autosomal recessive | 1 | 1 | 1 |
| Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PSPH | 4 / 6 | Macular telangiectasia, Neu-laxova syndrome, Neurometabolic disorder, Phosphoserine phosphatase deficiency |
| PHGDH | 3 / 6 | Macular telangiectasia, Neu-laxova syndrome, Neurometabolic disorder |
| FARS2 | 2 / 6 | Neurometabolic disorder, Spastic paraplegia 77, autosomal recessive |
| PSAT1 | 2 / 6 | Neu-laxova syndrome, Neurometabolic disorder |
| SLC1A4 | 2 / 6 | Macular telangiectasia, Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| Serine biosynthesis | Reactome | 3 / 9 | 211× | 2.80e-7 | 1.38e-5 ✓ sig. |
| Biosynthesis of amino acids | KEGG | 4 / 75 | 33.7× | 5.06e-6 | 1.66e-4 ✓ sig. |
| Carbon metabolism | KEGG | 4 / 115 | 22.0× | 2.77e-5 | 6.79e-4 ✓ sig. |
| Glycine, serine and threonine metabolism | KEGG | 3 / 40 | 47.4× | 3.20e-5 | 7.64e-4 ✓ sig. |
| Sphingolipid signaling pathway | KEGG | 3 / 122 | 15.5× | 8.80e-4 | 1.03e-2 ✓ sig. |
| Amino acid transport across the plasma membrane | Reactome | 2 / 33 | 38.3× | 1.22e-3 | 1.32e-2 ✓ sig. |
| Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG) | Reactome | 1 / 1 | 632× | 1.58e-3 | 1.60e-2 ✓ sig. |
| Sphingolipid de novo biosynthesis | Reactome | 2 / 43 | 29.4× | 2.06e-3 | 1.94e-2 ✓ sig. |
| Cysteine and methionine metabolism | KEGG | 2 / 52 | 24.3× | 3.00e-3 | 2.54e-2 ✓ sig. |
| Sphingolipid metabolism | KEGG | 2 / 54 | 23.4× | 3.23e-3 | 2.69e-2 ✓ sig. |
| Vitamin B6 metabolism | KEGG | 1 / 6 | 105× | 9.46e-3 | 5.49e-2 |
| Urea cycle | Reactome | 1 / 10 | 63.2× | 1.57e-2 | 7.46e-2 |
| Fatty acyl-CoA biosynthesis | Reactome | 1 / 12 | 52.7× | 1.88e-2 | 8.28e-2 |
| Mitochondrial tRNA aminoacylation | Reactome | 1 / 14 | 45.2× | 2.19e-2 | 9.03e-2 |
| APC truncation mutants have impaired AXIN binding | Reactome | 1 / 14 | 45.2× | 2.19e-2 | 9.03e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| L-serine biosynthetic process | GO:0006564 | 3 / 6 | 492× | 1.78e-8 | 2.91e-6 ✓ sig. |
| L-serine metabolic process | GO:0006563 | 3 / 10 | 295× | 1.06e-7 | 1.34e-5 ✓ sig. |
| amino acid biosynthetic process | GO:0008652 | 3 / 27 | 109× | 2.57e-6 | 1.85e-4 ✓ sig. |
| proline transport | GO:0015824 | 2 / 11 | 179× | 5.36e-5 | 1.94e-3 ✓ sig. |
| glutamine metabolic process | GO:0006541 | 2 / 15 | 131× | 1.02e-4 | 3.14e-3 ✓ sig. |
| intracellular glucose homeostasis | GO:0001678 | 2 / 27 | 72.9× | 3.39e-4 | 7.30e-3 ✓ sig. |
| ceramide biosynthetic process | GO:0046513 | 2 / 41 | 48.0× | 7.84e-4 | 1.27e-2 ✓ sig. |
| sphingolipid biosynthetic process | GO:0030148 | 2 / 45 | 43.7× | 9.45e-4 | 1.42e-2 ✓ sig. |
| carbamoyl phosphate biosynthetic process | GO:0070409 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| threonine metabolic process | GO:0006566 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| regulation of fat cell apoptotic process | GO:1904649 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| threonine transport | GO:0015826 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| hydroxyproline transport | GO:0034589 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| serine import across plasma membrane | GO:0098718 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| mitochondrial citrate transmembrane transport | GO:0006843 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Neu-laxova syndrome | Neurometabolic disorder | 0.500 | 3 | 1.62e-11 | 1.61e-10 ✓ sig. |
| Macular telangiectasia | Neu-laxova syndrome | 0.111 | 2 | 3.00e-6 | 1.72e-5 ✓ sig. |
| Macular telangiectasia | Neurometabolic disorder | 0.100 | 2 | 9.99e-6 | 5.40e-5 ✓ sig. |
| Neu-laxova syndrome | Phosphoserine phosphatase deficiency | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Neurometabolic disorder | Phosphoserine phosphatase deficiency | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Neurometabolic disorder | Spastic paraplegia 77, autosomal recessive | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Macular telangiectasia | Phosphoserine phosphatase deficiency | 0.059 | 1 | 1.03e-3 | 1.57e-3 ✓ sig. |
| Macular telangiectasia | Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome | 0.059 | 1 | 1.03e-3 | 1.57e-3 ✓ sig. |