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 230

7 diseases · 13 shared-gene connections
7 Diseases
8 Unique genes
0.301 Avg. similarity score
Preaxial polydactyly with upper back hypertrichosis Most-connected disease (5 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 ⇵
Preaxial polydactyly with upper back hypertrichosis 5 5 1
Skeletal system disorder 5 5 1
holoprosencephaly 3 5 5 1
Schizencephaly 4 4 5
Partial agenesis of corpus callosum 3 3 3
Triphalangeal thumb-polysyndactyly syndrome 3 3 2
Congenital hypogonadotropic hypogonadism 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SHH 6 / 7 holoprosencephaly 3, Partial agenesis of corpus callosum, Preaxial polydactyly with upper back hypertrichosis, Schizencephaly and 2 more
EMX2 2 / 7 Congenital hypogonadotropic hypogonadism, Schizencephaly
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 ⇵
AGE-RAGE signaling pathway in diabetic complications
COL4A1, AGER
 KEGG 2 / 101 29.7× 1.90e-3 2.19e-2 ✓ sig.
Caspase activation via Dependence Receptors in the absence of ligand
DCC
 Reactome 1 / 4 375× 2.66e-3 2.83e-2 ✓ sig.
HHAT G278V abrogates palmitoylation of Hh-Np
SHH
 Reactome 1 / 4 375× 2.66e-3 2.83e-2 ✓ sig.
Pathways in cancer
SHH, DCC, COL4A1
 KEGG 3 / 533 8.4× 4.12e-3 3.85e-2 ✓ sig.
Release of Hh-Np from the secreting cell
SHH
 Reactome 1 / 7 214× 4.65e-3 4.18e-2 ✓ sig.
Ligand-receptor interactions
SHH
 Reactome 1 / 7 214× 4.65e-3 4.18e-2 ✓ sig.
Netrin-1 signaling
DCC
 Reactome 1 / 8 188× 5.32e-3 4.56e-2 ✓ sig.
Advanced glycosylation endproduct receptor signaling
AGER
 Reactome 1 / 8 188× 5.32e-3 4.56e-2 ✓ sig.
Axon guidance
SHH, DCC
 KEGG 2 / 183 16.4× 6.09e-3 4.98e-2 ✓ sig.
DCC mediated attractive signaling
DCC
 Reactome 1 / 11 136× 7.31e-3 5.62e-2
Extracellular matrix organization
COL4A1
 Reactome 1 / 15 100× 9.95e-3 6.82e-2
Anchoring fibril formation
COL4A1
 Reactome 1 / 15 100× 9.95e-3 6.82e-2
Activation of SMO
SHH
 Reactome 1 / 18 83.4× 1.19e-2 7.61e-2
Crosslinking of collagen fibrils
COL4A1
 Reactome 1 / 18 83.4× 1.19e-2 7.61e-2
NCAM1 interactions
COL4A1
 Reactome 1 / 21 71.5× 1.39e-2 8.31e-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 ⇵
telencephalon regionalization
SHH, SIX3
 GO:0021978 2 / 7 667× 3.36e-6 2.19e-4 ✓ sig.
cell proliferation in forebrain
EMX2, SIX3
 GO:0021846 2 / 14 334× 1.46e-5 7.00e-4 ✓ sig.
thyroid gland development
SHH, SIX3
 GO:0030878 2 / 30 156× 6.93e-5 2.30e-3 ✓ sig.
branching involved in blood vessel morphogenesis
SHH, COL4A1
 GO:0001569 2 / 33 142× 8.41e-5 2.66e-3 ✓ sig.
brain development
EMX2, COL4A1, SIX3
 GO:0007420 3 / 244 28.7× 1.17e-4 3.42e-3 ✓ sig.
embryonic digit morphogenesis
SHH, LMBR1
 GO:0042733 2 / 57 82.0× 2.53e-4 5.97e-3 ✓ sig.
negative regulation of Wnt signaling pathway
SHH, SIX3
 GO:0030178 2 / 61 76.6× 2.90e-4 6.55e-3 ✓ sig.
negative regulation of neuron differentiation
SHH, SIX3
 GO:0045665 2 / 63 74.2× 3.09e-4 6.87e-3 ✓ sig.
camera-type eye development
SHH, SIX3
 GO:0043010 2 / 74 63.1× 4.27e-4 8.59e-3 ✓ sig.
regulation of CD4-positive, alpha-beta T cell activation
AGER
 GO:2000514 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
polarity specification of anterior/posterior axis
SHH
 GO:0009949 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
cell proliferation in external granule layer
SHH
 GO:0021924 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
right lung development
SHH
 GO:0060458 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
left lung development
SHH
 GO:0060459 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
primary prostatic bud elongation
SHH
 GO:0060516 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
holoprosencephaly 3 Preaxial polydactyly with upper back hypertrichosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
holoprosencephaly 3 Skeletal system disorder 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Preaxial polydactyly with upper back hypertrichosis Skeletal system disorder 0.500 1 6.49e-5 2.34e-4 ✓ sig.
holoprosencephaly 3 Triphalangeal thumb-polysyndactyly syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Preaxial polydactyly with upper back hypertrichosis Triphalangeal thumb-polysyndactyly syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Skeletal system disorder Triphalangeal thumb-polysyndactyly syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
holoprosencephaly 3 Partial agenesis of corpus callosum 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Partial agenesis of corpus callosum Preaxial polydactyly with upper back hypertrichosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Partial agenesis of corpus callosum Skeletal system disorder 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital hypogonadotropic hypogonadism Schizencephaly 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Preaxial polydactyly with upper back hypertrichosis Schizencephaly 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Schizencephaly Skeletal system disorder 0.167 1 3.25e-4 7.58e-4 ✓ sig.
holoprosencephaly 3 Schizencephaly 0.167 1 3.25e-4 7.58e-4 ✓ sig.