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 264

7 diseases · 11 shared-gene connections
7 Diseases
14 Unique genes
0.240 Avg. similarity score
Specific learning disability Most-connected disease (5 links)
Log in to save this analysis

Save This Analysis

Disease Searched: Developmental delay with behavioral abnormalities 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 ⇵
Specific learning disability 5 5 12
Microcephalic dwarfism 4 4 1
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
coffin-lowry syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
DNMT3A 5 / 7 Clonal cytopenia of undetermined significance, heyn-sproul-jackson syndrome, Microcephalic dwarfism, Specific learning disability and 1 more
ADGRL1 2 / 7 Developmental delay with behavioral abnormalities, Specific learning disability
RPS6KA3 2 / 7 coffin-lowry syndrome, 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 ⇵
Toxoplasmosis
IL10, IL10RA, IL10RB, TGFB1
 KEGG 4 / 112 71.5× 1.06e-7 6.89e-6 ✓ sig.
Tuberculosis
IL10, IL10RA, IL10RB, TGFB1
 KEGG 4 / 181 44.2× 7.31e-7 3.71e-5 ✓ sig.
Interleukin-10 signaling
IL10, IL10RA, IL10RB
 Reactome 3 / 47 128× 1.11e-6 5.37e-5 ✓ sig.
Cytokine-cytokine receptor interaction
IL10, IL10RA, IL10RB, TGFB1
 KEGG 4 / 298 26.9× 5.36e-6 2.01e-4 ✓ sig.
Viral protein interaction with cytokine and cytokine receptor
IL10, IL10RA, IL10RB
 KEGG 3 / 100 60.1× 1.10e-5 3.63e-4 ✓ sig.
JAK-STAT signaling pathway
IL10, IL10RA, IL10RB
 KEGG 3 / 168 35.7× 5.21e-5 1.32e-3 ✓ sig.
Human cytomegalovirus infection
RIPK1, IL10RA, IL10RB
 KEGG 3 / 226 26.6× 1.26e-4 2.70e-3 ✓ sig.
Intestinal immune network for IgA production
IL10, TGFB1
 KEGG 2 / 50 80.1× 2.52e-4 4.68e-3 ✓ sig.
Malaria
IL10, TGFB1
 KEGG 2 / 50 80.1× 2.52e-4 4.68e-3 ✓ sig.
Inflammatory bowel disease
IL10, TGFB1
 KEGG 2 / 66 60.7× 4.40e-4 7.21e-3 ✓ sig.
Leishmaniasis
IL10, TGFB1
 KEGG 2 / 78 51.3× 6.14e-4 9.37e-3 ✓ sig.
Influenza Virus Induced Apoptosis
TGFB1
 Reactome 1 / 2 1,001× 9.99e-4 1.35e-2 ✓ sig.
The IPAF inflammasome
NLRC4
 Reactome 1 / 2 1,001× 9.99e-4 1.35e-2 ✓ sig.
TGFBR2 MSI Frameshift Mutants in Cancer
TGFB1
 Reactome 1 / 2 1,001× 9.99e-4 1.35e-2 ✓ sig.
Chagas disease
IL10, TGFB1
 KEGG 2 / 103 38.9× 1.07e-3 1.43e-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 2.10e-4 ✓ sig.
Bergmann glial cell differentiation
MAPK1, PTPN11
 GO:0060020 2 / 11 243× 2.86e-5 1.19e-3 ✓ sig.
positive regulation of cell differentiation
ARID1A, GHR, RPS6KA3
 GO:0045597 3 / 83 48.2× 2.97e-5 1.23e-3 ✓ sig.
hormone metabolic process
GHR, PTPN11
 GO:0042445 2 / 25 107× 1.55e-4 4.28e-3 ✓ sig.
insulin-like growth factor receptor signaling pathway
GHR, MAPK1
 GO:0048009 2 / 33 80.9× 2.72e-4 6.37e-3 ✓ sig.
hormone-mediated signaling pathway
GHR, PTPN11
 GO:0009755 2 / 42 63.6× 4.41e-4 8.96e-3 ✓ sig.
regulation of response to nutrient levels
GHR
 GO:0032107 1 / 1 1,335× 7.49e-4 1.28e-2 ✓ sig.
negative regulation of cortisol secretion
PTPN11
 GO:0051463 1 / 1 1,335× 7.49e-4 1.28e-2 ✓ sig.
negative regulation of growth hormone secretion
PTPN11
 GO:0060125 1 / 1 1,335× 7.49e-4 1.28e-2 ✓ sig.
intestinal epithelial cell migration
PTPN11
 GO:0061582 1 / 1 1,335× 7.49e-4 1.28e-2 ✓ sig.
cellular response to amino acid starvation
MAPK1, YWHAG
 GO:0034198 2 / 60 44.5× 9.00e-4 1.45e-2 ✓ sig.
epidermal growth factor receptor signaling pathway
MAPK1, PTPN11
 GO:0007173 2 / 64 41.7× 1.02e-3 1.56e-2 ✓ sig.
TORC1 signaling
RPS6KA3, YWHAG
 GO:0038202 2 / 67 39.8× 1.12e-3 1.66e-2 ✓ sig.
cytosine metabolic process
MAPK1
 GO:0019858 1 / 2 667× 1.50e-3 1.95e-2 ✓ sig.
microvillus organization
PTPN11
 GO:0032528 1 / 2 667× 1.50e-3 1.95e-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 2.32e-4 ✓ sig.
heyn-sproul-jackson syndrome Tatton-Brown-Rahman overgrowth syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Microcephalic dwarfism Tatton-Brown-Rahman overgrowth syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Clonal cytopenia of undetermined significance Microcephalic dwarfism 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Clonal cytopenia of undetermined significance heyn-sproul-jackson syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Clonal cytopenia of undetermined significance Tatton-Brown-Rahman overgrowth syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
coffin-lowry syndrome Specific learning disability 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Developmental delay with behavioral abnormalities Specific learning disability 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Microcephalic dwarfism Specific learning disability 0.077 1 7.79e-4 1.40e-3 ✓ sig.
heyn-sproul-jackson syndrome Specific learning disability 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Specific learning disability Tatton-Brown-Rahman overgrowth syndrome 0.077 1 7.79e-4 1.40e-3 ✓ sig.