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 273
7
Diseases
20
Unique genes
0.136
Avg. similarity score
Septo-optic dysplasia
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Septo-optic dysplasia
Combined pituitary hormone deficiency
Pituitary hormone deficiency
Growth hormone deficiency with pituitary anomalies
Winkelman bethge pfeiffer syndrome
Webb-dattani syndrome
hypogonadotropic hypogonadism 3 with or without anosmia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Septo-optic dysplasia | 5 | 5 | 10 |
| Combined pituitary hormone deficiency | 4 | 4 | 9 |
| Pituitary hormone deficiency | 4 | 4 | 9 |
| Growth hormone deficiency with pituitary anomalies | 3 | 3 | 1 |
| Winkelman bethge pfeiffer syndrome | 2 | 2 | 1 |
| Webb-dattani syndrome | 1 | 1 | 1 |
| hypogonadotropic hypogonadism 3 with or without anosmia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HESX1 | 4 / 7 | Combined pituitary hormone deficiency, Growth hormone deficiency with pituitary anomalies, Pituitary hormone deficiency, Septo-optic dysplasia |
| LHX3 | 3 / 7 | Combined pituitary hormone deficiency, Pituitary hormone deficiency, Winkelman bethge pfeiffer syndrome |
| OTX2 | 3 / 7 | Combined pituitary hormone deficiency, Pituitary hormone deficiency, Septo-optic dysplasia |
| ARNT2 | 2 / 7 | Septo-optic dysplasia, Webb-dattani syndrome |
| LHX4 | 2 / 7 | Combined pituitary hormone deficiency, Pituitary hormone deficiency |
| POU1F1 | 2 / 7 | Combined pituitary hormone deficiency, Pituitary hormone deficiency |
| PROKR2 | 2 / 7 | hypogonadotropic hypogonadism 3 with or without anosmia, Septo-optic dysplasia |
| PROP1 | 2 / 7 | Combined pituitary hormone deficiency, Pituitary hormone deficiency |
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 ⇵ |
|---|---|---|---|---|---|
| Deactivation of the beta-catenin transactivating complex | Reactome | 3 / 42 | 42.9× | 4.35e-5 | 1.14e-3 ✓ sig. |
| Basal cell carcinoma | KEGG | 3 / 63 | 28.6× | 1.47e-4 | 3.07e-3 ✓ sig. |
| Pathways in cancer | KEGG | 5 / 533 | 5.6× | 1.50e-3 | 1.85e-2 ✓ sig. |
| Signaling pathways regulating pluripotency of stem cells | KEGG | 3 / 144 | 12.5× | 1.66e-3 | 1.99e-2 ✓ sig. |
| Signaling by FGFR1 amplification mutants | Reactome | 1 / 1 | 601× | 1.67e-3 | 2.00e-2 ✓ sig. |
| Hippo signaling pathway | KEGG | 3 / 157 | 11.5× | 2.12e-3 | 2.38e-2 ✓ sig. |
| Hedgehog signaling pathway | KEGG | 2 / 56 | 21.4× | 3.84e-3 | 3.67e-2 ✓ sig. |
| Signaling by plasma membrane FGFR1 fusions | Reactome | 1 / 3 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| FGFR1c and Klotho ligand binding and activation | Reactome | 1 / 3 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| GLI proteins bind promoters of Hh responsive genes to promote transcription | Reactome | 1 / 3 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation | Reactome | 1 / 3 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Regulation of commissural axon pathfinding by SLIT and ROBO | Reactome | 1 / 3 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Role of ABL in ROBO-SLIT signaling | Reactome | 1 / 4 | 150× | 6.65e-3 | 5.28e-2 |
| HHAT G278V abrogates palmitoylation of Hh-Np | Reactome | 1 / 4 | 150× | 6.65e-3 | 5.28e-2 |
| SLIT2:ROBO1 increases RHOA activity | Reactome | 1 / 4 | 150× | 6.65e-3 | 5.28e-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 ⇵ |
|---|---|---|---|---|---|
| pituitary gland development | GO:0021983 | 6 / 30 | 187× | 3.83e-13 | 1.90e-10 ✓ sig. |
| regulation of DNA-templated transcription | GO:0006355 | 13 / 1,454 | 8.4× | 1.68e-10 | 4.59e-8 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 11 / 1,208 | 8.5× | 7.69e-9 | 1.36e-6 ✓ sig. |
| positive regulation of DNA-templated transcription | GO:0045893 | 9 / 778 | 10.8× | 3.99e-8 | 5.60e-6 ✓ sig. |
| adenohypophysis development | GO:0021984 | 3 / 9 | 311× | 8.77e-8 | 1.08e-5 ✓ sig. |
| regulation of transcription by RNA polymerase II | GO:0006357 | 11 / 1,602 | 6.4× | 1.44e-7 | 1.65e-5 ✓ sig. |
| brain development | GO:0007420 | 6 / 244 | 23.0× | 1.55e-7 | 1.75e-5 ✓ sig. |
| tube development | GO:0035295 | 3 / 13 | 216× | 2.98e-7 | 3.03e-5 ✓ sig. |
| negative regulation of transcription by RNA polymerase II | GO:0000122 | 9 / 1,002 | 8.4× | 3.47e-7 | 3.44e-5 ✓ sig. |
| medial motor column neuron differentiation | GO:0021526 | 2 / 2 | 934× | 1.09e-6 | 8.87e-5 ✓ sig. |
| forebrain development | GO:0030900 | 4 / 76 | 49.2× | 1.16e-6 | 9.37e-5 ✓ sig. |
| neuron differentiation | GO:0030182 | 5 / 222 | 21.0× | 3.03e-6 | 2.01e-4 ✓ sig. |
| ventral midline development | GO:0007418 | 2 / 3 | 623× | 3.26e-6 | 2.14e-4 ✓ sig. |
| dopaminergic neuron differentiation | GO:0071542 | 3 / 30 | 93.4× | 4.18e-6 | 2.60e-4 ✓ sig. |
| lung development | GO:0030324 | 4 / 108 | 34.6× | 4.76e-6 | 2.89e-4 ✓ sig. |