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 338

6 diseases · 10 shared-gene connections
6 Diseases
14 Unique genes
0.256 Avg. similarity score
Microcephalic dwarfism Most-connected disease (4 links)
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Disease 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.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Microcephalic dwarfism 4 4 1
Specific learning disability 4 4 12
Tatton-Brown-Rahman overgrowth syndrome 4 4 1
heyn-sproul-jackson syndrome 4 4 1
Clonal cytopenia of undetermined significance 3 3 3
Developmental delay with behavioral abnormalities 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
DNMT3A 5 / 6 Clonal cytopenia of undetermined significance, heyn-sproul-jackson syndrome, Microcephalic dwarfism, Specific learning disability and 1 more
ADGRL1 2 / 6 Developmental delay with behavioral abnormalities, Specific learning disability
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 ⇵
Gastrin-CREB signalling pathway via PKC and MAPK
MAPK1, RPS6KA3
 Reactome 2 / 9 191× 4.52e-5 1.18e-3 ✓ sig.
MAPK1 (ERK2) activation
MAPK1, PTPN11
 Reactome 2 / 9 191× 4.52e-5 1.18e-3 ✓ sig.
Chronic myeloid leukemia
RUNX1, MAPK1, PTPN11
 KEGG 3 / 77 33.4× 8.77e-5 2.02e-3 ✓ sig.
ERK/MAPK targets
MAPK1, RPS6KA3
 Reactome 2 / 14 123× 1.14e-4 2.49e-3 ✓ sig.
Growth hormone receptor signaling
GHR, MAPK1
 Reactome 2 / 14 123× 1.14e-4 2.49e-3 ✓ sig.
Regulation of RUNX1 Expression and Activity
RUNX1, PTPN11
 Reactome 2 / 16 107× 1.50e-4 3.11e-3 ✓ sig.
Spry regulation of FGF signaling
MAPK1, PTPN11
 Reactome 2 / 16 107× 1.50e-4 3.11e-3 ✓ sig.
Negative regulation of FGFR3 signaling
MAPK1, PTPN11
 Reactome 2 / 22 78.0× 2.88e-4 5.19e-3 ✓ sig.
Neurotrophin signaling pathway
MAPK1, PTPN11, RPS6KA3
 KEGG 3 / 120 21.4× 3.27e-4 5.74e-3 ✓ sig.
Negative regulation of FGFR4 signaling
MAPK1, PTPN11
 Reactome 2 / 24 71.5× 3.43e-4 5.96e-3 ✓ sig.
Negative regulation of FGFR1 signaling
MAPK1, PTPN11
 Reactome 2 / 26 66.0× 4.04e-4 6.76e-3 ✓ sig.
Negative regulation of FGFR2 signaling
MAPK1, PTPN11
 Reactome 2 / 27 63.5× 4.36e-4 7.15e-3 ✓ sig.
Oocyte meiosis
MAPK1, RPS6KA3, YWHAG
 KEGG 3 / 138 18.6× 4.92e-4 7.88e-3 ✓ sig.
Efferocytosis
DNMT3A, MAPK1, PTPN11
 KEGG 3 / 157 16.4× 7.18e-4 1.06e-2 ✓ sig.
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
ARID1A, RUNX1
 Reactome 2 / 38 45.2× 8.66e-4 1.22e-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 ⇵
ERBB signaling pathway
MAPK1, PTPN11
 GO:0038127 2 / 4 667× 3.12e-6 2.06e-4 ✓ sig.
Bergmann glial cell differentiation
MAPK1, PTPN11
 GO:0060020 2 / 11 243× 2.86e-5 1.18e-3 ✓ sig.
positive regulation of cell differentiation
ARID1A, GHR, RPS6KA3
 GO:0045597 3 / 83 48.2× 2.97e-5 1.21e-3 ✓ sig.
hormone metabolic process
GHR, PTPN11
 GO:0042445 2 / 25 107× 1.55e-4 4.20e-3 ✓ sig.
insulin-like growth factor receptor signaling pathway
GHR, MAPK1
 GO:0048009 2 / 33 80.9× 2.72e-4 6.26e-3 ✓ sig.
hormone-mediated signaling pathway
GHR, PTPN11
 GO:0009755 2 / 42 63.6× 4.41e-4 8.77e-3 ✓ sig.
regulation of response to nutrient levels
GHR
 GO:0032107 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
negative regulation of cortisol secretion
PTPN11
 GO:0051463 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
negative regulation of growth hormone secretion
PTPN11
 GO:0060125 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
intestinal epithelial cell migration
PTPN11
 GO:0061582 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
cellular response to amino acid starvation
MAPK1, YWHAG
 GO:0034198 2 / 60 44.5× 9.00e-4 1.41e-2 ✓ sig.
epidermal growth factor receptor signaling pathway
MAPK1, PTPN11
 GO:0007173 2 / 64 41.7× 1.02e-3 1.53e-2 ✓ sig.
TORC1 signaling
RPS6KA3, YWHAG
 GO:0038202 2 / 67 39.8× 1.12e-3 1.62e-2 ✓ sig.
cytosine metabolic process
MAPK1
 GO:0019858 1 / 2 667× 1.50e-3 1.91e-2 ✓ sig.
microvillus organization
PTPN11
 GO:0032528 1 / 2 667× 1.50e-3 1.91e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
heyn-sproul-jackson syndrome Microcephalic dwarfism 0.500 1 6.49e-5 2.34e-4 ✓ sig.
heyn-sproul-jackson syndrome Tatton-Brown-Rahman overgrowth syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Microcephalic dwarfism Tatton-Brown-Rahman overgrowth syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Clonal cytopenia of undetermined significance Microcephalic dwarfism 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Clonal cytopenia of undetermined significance heyn-sproul-jackson syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Clonal cytopenia of undetermined significance Tatton-Brown-Rahman overgrowth syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Developmental delay with behavioral abnormalities Specific learning disability 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Microcephalic dwarfism Specific learning disability 0.077 1 7.79e-4 1.39e-3 ✓ sig.
heyn-sproul-jackson syndrome Specific learning disability 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Specific learning disability Tatton-Brown-Rahman overgrowth syndrome 0.077 1 7.79e-4 1.39e-3 ✓ sig.