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 323

6 diseases · 11 shared-gene connections
6 Diseases
54 Unique genes
0.166 Avg. similarity score
Developmental regression Most-connected disease (5 links)
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Disease Searched: hypotonia, ataxia, and delayed development syndrome 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 ⇵
Developmental regression 5 5 18
Chromosome 10q deletion syndrome 4 4 1
Developmental delay with ataxia, hypotonia, and facial dysmorphism 4 4 1
Vesicoureteral reflux 4 4 38
hypotonia, ataxia, and delayed development syndrome 4 4 1
Hepatoencephalopathy due to combined oxidative phosphorylation defect 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
EBF3 5 / 6 Chromosome 10q deletion syndrome, Developmental delay with ataxia, hypotonia, and facial dysmorphism, Developmental regression, hypotonia, ataxia, and delayed development syndrome and 1 more
GFM1 2 / 6 Developmental regression, Hepatoencephalopathy due to combined oxidative phosphorylation defect
NDUFAF6 2 / 6 Developmental regression, Vesicoureteral reflux
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 ⇵
Complex I biogenesis
ND1, NDUFAF6, NDUFB3, NDUFS4
 Reactome 4 / 55 16.2× 1.05e-4 2.42e-3 ✓ sig.
Retrograde endocannabinoid signaling
GNB1, ND1, NDUFB3, NDUFS4
 KEGG 4 / 149 6.0× 4.45e-3 4.19e-2 ✓ sig.
Loss of MECP2 binding ability to 5hmC-DNA
MECP2
 Reactome 1 / 1 222× 4.50e-3 4.21e-2 ✓ sig.
Inhibition of PKR
EIF2AK2
 Reactome 1 / 1 222× 4.50e-3 4.21e-2 ✓ sig.
MPS IIIA - Sanfilippo syndrome A
SGSH
 Reactome 1 / 1 222× 4.50e-3 4.21e-2 ✓ sig.
Respiratory electron transport
ND1, NDUFB3, NDUFS4
 Reactome 3 / 83 8.0× 6.13e-3 5.19e-2
Loss of MECP2 binding ability to 5mC-DNA
MECP2
 Reactome 1 / 3 74.1× 1.34e-2 8.46e-2
Breakdown of the nuclear lamina
LMNA
 Reactome 1 / 3 74.1× 1.34e-2 8.46e-2
Regulation of commissural axon pathfinding by SLIT and ROBO
ROBO2
 Reactome 1 / 3 74.1× 1.34e-2 8.46e-2
MECP2 regulates neuronal receptors and channels
MECP2
 Reactome 1 / 4 55.6× 1.79e-2 1.00e-1
Chemical carcinogenesis - reactive oxygen species
ND1, NDUFB3, NDUFS4, MGST2
 KEGG 4 / 227 3.9× 1.88e-2 1.04e-1
Thermogenesis
ND1, NDUFAF6, NDUFB3, NDUFS4
 KEGG 4 / 234 3.8× 2.08e-2 1.09e-1
RUNX1 regulates transcription of genes involved in interleukin signaling
LIFR
 Reactome 1 / 5 44.5× 2.23e-2 1.14e-1
Oxidative phosphorylation
ND1, NDUFB3, NDUFS4
 KEGG 3 / 137 4.9× 2.36e-2 1.18e-1
Ca2+ pathway
GNB1, WNT5A
 Reactome 2 / 56 7.9× 2.62e-2 1.25e-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 ⇵
gallbladder development
SOX17, NIPBL
 GO:0061010 2 / 2 346× 8.20e-6 4.64e-4 ✓ sig.
olfactory bulb interneuron development
ROBO2, WNT5A
 GO:0021891 2 / 3 231× 2.45e-5 1.08e-3 ✓ sig.
outflow tract septum morphogenesis
ROBO2, ENG, ZFPM2
 GO:0003148 3 / 28 37.1× 7.10e-5 2.42e-3 ✓ sig.
negative regulation of mesenchymal cell proliferation
LMNA, WNT5A
 GO:0072201 2 / 6 115× 1.22e-4 3.61e-3 ✓ sig.
negative regulation of synapse assembly
ROBO2, WNT5A
 GO:0051964 2 / 6 115× 1.22e-4 3.61e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
MECP2, SOX17, BMP5, ENG, OTX1, PRKN, WNT5A, ZFPM2, IFNG, KAT6B, MED13L, NIPBL
 GO:0045944 12 / 1,208 3.4× 1.37e-4 3.94e-3 ✓ sig.
positive regulation of response to cytokine stimulus
IFIH1, WNT5A
 GO:0060760 2 / 7 98.9× 1.71e-4 4.64e-3 ✓ sig.
pericardium morphogenesis
BMP5, WNT5A
 GO:0003344 2 / 7 98.9× 1.71e-4 4.64e-3 ✓ sig.
metanephros development
ROBO2, SOX17, NIPBL
 GO:0001656 3 / 38 27.3× 1.79e-4 4.83e-3 ✓ sig.
mitochondrial respiratory chain complex I assembly
ND1, NDUFAF6, NDUFS4
 GO:0032981 3 / 40 26.0× 2.09e-4 5.39e-3 ✓ sig.
intracellular protein localization
LMNA, MECP2, DMD, WNT5A, NIPBL
 GO:0008104 5 / 194 8.9× 2.40e-4 5.93e-3 ✓ sig.
embryonic organ development
SOX17, WDPCP, ZFPM2
 GO:0048568 3 / 42 24.7× 2.42e-4 5.96e-3 ✓ sig.
mitochondrial electron transport, NADH to ubiquinone
ND1, NDUFB3, NDUFS4
 GO:0006120 3 / 47 22.1× 3.38e-4 7.53e-3 ✓ sig.
positive regulation of DNA-templated transcription
EBF3, MECP2, NMNAT1, SOX17, WNT5A, ZFPM2, AFAP1L2, AGTR2, KAT6B
 GO:0045893 9 / 778 4.0× 3.55e-4 7.80e-3 ✓ sig.
positive regulation of chemokine production
EIF2AK2, WNT5A, IFNG
 GO:0032722 3 / 49 21.2× 3.83e-4 8.21e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Chromosome 10q deletion syndrome Developmental delay with ataxia, hypotonia, and facial dysmorphism 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Chromosome 10q deletion syndrome hypotonia, ataxia, and delayed development syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Developmental delay with ataxia, hypotonia, and facial dysmorphism hypotonia, ataxia, and delayed development syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Developmental regression Vesicoureteral reflux 0.036 2 8.85e-4 1.57e-3 ✓ sig.
Chromosome 10q deletion syndrome Developmental regression 0.053 1 1.17e-3 1.90e-3 ✓ sig.
Developmental delay with ataxia, hypotonia, and facial dysmorphism Developmental regression 0.053 1 1.17e-3 1.90e-3 ✓ sig.
Developmental regression Hepatoencephalopathy due to combined oxidative phosphorylation defect 0.053 1 1.17e-3 1.90e-3 ✓ sig.
Developmental regression hypotonia, ataxia, and delayed development syndrome 0.053 1 1.17e-3 1.90e-3 ✓ sig.
Chromosome 10q deletion syndrome Vesicoureteral reflux 0.026 1 2.47e-3 3.37e-3 ✓ sig.
Developmental delay with ataxia, hypotonia, and facial dysmorphism Vesicoureteral reflux 0.026 1 2.47e-3 3.37e-3 ✓ sig.
hypotonia, ataxia, and delayed development syndrome Vesicoureteral reflux 0.026 1 2.47e-3 3.37e-3 ✓ sig.