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 362

5 diseases · 9 shared-gene connections
5 Diseases
22 Unique genes
0.247 Avg. similarity score
Chromosome 15q24 deletion syndrome 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 ⇵
Chromosome 15q24 deletion syndrome 4 4 1
SIN3A-related intellectual disability syndrome 4 4 1
Witteveen-kolk syndrome 4 4 2
15q24 microdeletion 3 3 2
Congenital diaphragmatic hernia 3 3 20

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

Gene ⇵ Member diseases ⇵ Linked diseases
SIN3A 5 / 5 15q24 microdeletion, Chromosome 15q24 deletion syndrome, Congenital diaphragmatic hernia, SIN3A-related intellectual disability syndrome and 1 more
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 ⇵
ECM-receptor interaction
FRAS1, FREM1, FREM2
 KEGG 3 / 89 18.4× 5.47e-4 8.53e-3 ✓ sig.
Regulation of lipid metabolism by PPARalpha
SIN3A, SIN3B
 Reactome 2 / 20 54.6× 5.97e-4 9.15e-3 ✓ sig.
Transcriptional misregulation in cancer
SIN3A, MET, PAX3
 KEGG 3 / 198 8.3× 5.39e-3 4.60e-2 ✓ sig.
Loss of MECP2 binding ability to 5mC-DNA
SIN3A
 Reactome 1 / 3 182× 5.49e-3 4.65e-2 ✓ sig.
GLI proteins bind promoters of Hh responsive genes to promote transcription
GLI3
 Reactome 1 / 3 182× 5.49e-3 4.65e-2 ✓ sig.
MET activates STAT3
MET
 Reactome 1 / 3 182× 5.49e-3 4.65e-2 ✓ sig.
MECP2 regulates neuronal receptors and channels
MET
 Reactome 1 / 4 136× 7.31e-3 5.62e-2
MET activates PTPN11
MET
 Reactome 1 / 5 109× 9.13e-3 6.50e-2
MET interacts with TNS proteins
MET
 Reactome 1 / 5 109× 9.13e-3 6.50e-2
MET Receptor Activation
MET
 Reactome 1 / 6 91.0× 1.09e-2 7.25e-2
MET activates PI3K/AKT signaling
MET
 Reactome 1 / 6 91.0× 1.09e-2 7.25e-2
Regulation of MECP2 expression and activity
SIN3A
 Reactome 1 / 6 91.0× 1.09e-2 7.25e-2
InlB-mediated entry of Listeria monocytogenes into host cell
MET
 Reactome 1 / 7 78.0× 1.28e-2 7.89e-2
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
SIN3A, SIN3B
 Reactome 2 / 97 11.3× 1.34e-2 8.14e-2
Factors involved in megakaryocyte development and platelet production
GATA6, ZFPM2
 Reactome 2 / 99 11.0× 1.40e-2 8.34e-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 ⇵
anatomical structure morphogenesis
FRAS1, FREM1, FREM2, GATA6, GLI3, PAX3
 GO:0009653 6 / 160 31.9× 2.39e-8 3.64e-6 ✓ sig.
positive regulation of cardiac muscle myoblast proliferation
MEIS2, GATA6
 GO:0110024 2 / 3 566× 3.97e-6 2.49e-4 ✓ sig.
pancreas development
MEIS2, GATA6, MET
 GO:0031016 3 / 30 84.9× 5.63e-6 3.30e-4 ✓ sig.
metanephros development
FBN1, GLI3, NIPBL
 GO:0001656 3 / 38 67.1× 1.16e-5 5.86e-4 ✓ sig.
heart development
FBN1, FREM2, GLI3, NIPBL, ZFPM2
 GO:0007507 5 / 273 15.6× 1.38e-5 6.71e-4 ✓ sig.
ventricular septum morphogenesis
FGFRL1, SLIT3, ZFPM2
 GO:0060412 3 / 41 62.2× 1.47e-5 7.04e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
MEIS2, CDK8, GATA6, GLI3, MET, NIPBL, PAX3, ZFPM2
 GO:0045944 8 / 1,208 5.6× 4.21e-5 1.58e-3 ✓ sig.
negative regulation of transcription by RNA polymerase II
MEIS2, SIN3A, GATA6, GLI3, NIPBL, ZFPM2, SIN3B
 GO:0000122 7 / 1,002 5.9× 1.05e-4 3.12e-3 ✓ sig.
cell communication
FRAS1, FREM1, FREM2
 GO:0007154 3 / 80 31.9× 1.10e-4 3.24e-3 ✓ sig.
response to growth factor
MEIS2, GATA6
 GO:0070848 2 / 14 121× 1.19e-4 3.46e-3 ✓ sig.
regulation of DNA-templated transcription
MEIS2, SIN3A, GATA6, GLI3, MN1, MYRF, PAX3, SIN3B
 GO:0006355 8 / 1,454 4.7× 1.57e-4 4.23e-3 ✓ sig.
in utero embryonic development
SIN3A, GATA6, GLI3, ZFPM2
 GO:0001701 4 / 252 13.5× 1.95e-4 4.96e-3 ✓ sig.
embryonic digestive tract morphogenesis
GLI3, NIPBL
 GO:0048557 2 / 18 94.4× 2.00e-4 5.05e-3 ✓ sig.
animal organ development
FRAS1, GATA6, MET
 GO:0048513 3 / 102 25.0× 2.25e-4 5.48e-3 ✓ sig.
lung development
FBN1, GLI3, ZFPM2
 GO:0030324 3 / 108 23.6× 2.67e-4 6.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Chromosome 15q24 deletion syndrome SIN3A-related intellectual disability syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
15q24 microdeletion Chromosome 15q24 deletion syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
15q24 microdeletion SIN3A-related intellectual disability syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Chromosome 15q24 deletion syndrome Witteveen-kolk syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
SIN3A-related intellectual disability syndrome Witteveen-kolk syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
15q24 microdeletion Witteveen-kolk syndrome 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Chromosome 15q24 deletion syndrome Congenital diaphragmatic hernia 0.048 1 1.30e-3 2.04e-3 ✓ sig.
Congenital diaphragmatic hernia SIN3A-related intellectual disability syndrome 0.048 1 1.30e-3 2.04e-3 ✓ sig.
Congenital diaphragmatic hernia Witteveen-kolk syndrome 0.045 1 2.60e-3 3.50e-3 ✓ sig.