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 329

7 diseases · 13 shared-gene connections
7 Diseases
10 Unique genes
0.282 Avg. similarity score
Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis Most-connected disease (5 links)
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Disease Searched: Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis 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 ⇵
Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis 5 5 1
Joubert syndrome 1 5 5 1
Mental retardation, truncal obesity, retinal dystrophy, and micropenis 5 5 1
Congenital hemivertebra 4 4 5
Coach syndrome 3 3 5
Congenital hypoplasia of femur 3 3 2
Ficus syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
INPP5E 6 / 7 Coach syndrome, Congenital hemivertebra, Congenital hypoplasia of femur, Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis and 2 more
LSM1 2 / 7 Congenital hemivertebra, Ficus syndrome
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 ⇵
Anchoring of the basal body to the plasma membrane
CC2D2A, OFD1, RPGRIP1L, TMEM67
 Reactome 4 / 98 49.0× 8.43e-7 3.59e-5 ✓ sig.
Hedgehog 'off' state
OFD1, RPGRIP1L
 Reactome 2 / 56 42.9× 9.38e-4 1.08e-2 ✓ sig.
ARL13B-mediated ciliary trafficking of INPP5E
INPP5E
 Reactome 1 / 3 400× 2.50e-3 2.23e-2 ✓ sig.
mRNA decay by 5' to 3' exoribonuclease
LSM1
 Reactome 1 / 14 85.8× 1.16e-2 6.22e-2
Synthesis of PIPs at the Golgi membrane
INPP5E
 Reactome 1 / 18 66.7× 1.49e-2 7.22e-2
VxPx cargo-targeting to cilium
PKD1
 Reactome 1 / 21 57.2× 1.74e-2 7.88e-2
Notch signaling pathway
DLL3
 KEGG 1 / 62 19.4× 5.05e-2 1.46e-1
Lysine degradation
PLOD2
 KEGG 1 / 63 19.1× 5.13e-2 1.47e-1
Collagen biosynthesis and modifying enzymes
PLOD2
 Reactome 1 / 67 17.9× 5.44e-2 1.52e-1
Loss of Nlp from mitotic centrosomes
OFD1
 Reactome 1 / 70 17.2× 5.68e-2 1.56e-1
Loss of proteins required for interphase microtubule organization from the centrosome
OFD1
 Reactome 1 / 70 17.2× 5.68e-2 1.56e-1
Inositol phosphate metabolism
INPP5E
 KEGG 1 / 73 16.5× 5.92e-2 1.59e-1
AURKA Activation by TPX2
OFD1
 Reactome 1 / 73 16.5× 5.92e-2 1.59e-1
RNA degradation
LSM1
 KEGG 1 / 78 15.4× 6.31e-2 1.65e-1
Recruitment of mitotic centrosome proteins and complexes
OFD1
 Reactome 1 / 82 14.6× 6.62e-2 1.70e-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 ⇵
cilium assembly
CC2D2A, INPP5E, OFD1, RPGRIP1L, TMEM67
 GO:0060271 5 / 237 39.4× 7.53e-8 1.00e-5 ✓ sig.
kidney development
CC2D2A, RPGRIP1L, PKD1
 GO:0001822 3 / 146 38.4× 5.39e-5 1.95e-3 ✓ sig.
axoneme assembly
CC2D2A, OFD1
 GO:0035082 2 / 33 113× 1.35e-4 3.83e-3 ✓ sig.
cell projection organization
CC2D2A, OFD1, TMEM67
 GO:0030030 3 / 214 26.2× 1.67e-4 4.47e-3 ✓ sig.
non-motile cilium assembly
CC2D2A, RPGRIP1L
 GO:1905515 2 / 57 65.6× 4.05e-4 8.24e-3 ✓ sig.
metanephric distal tubule morphogenesis
PKD1
 GO:0072287 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
camera-type eye development
CC2D2A, RPGRIP1L
 GO:0043010 2 / 74 50.5× 6.82e-4 1.17e-2 ✓ sig.
determination of left/right symmetry
CC2D2A, RPGRIP1L
 GO:0007368 2 / 83 45.0× 8.57e-4 1.33e-2 ✓ sig.
liver development
RPGRIP1L, PKD1
 GO:0001889 2 / 87 43.0× 9.41e-4 1.42e-2 ✓ sig.
nitrogen cycle metabolic process
PKD1
 GO:0071941 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
hydroxylysine biosynthetic process
PLOD2
 GO:0046947 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation
OFD1
 GO:2000314 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
lymph vessel morphogenesis
PKD1
 GO:0036303 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
metanephric proximal tubule development
PKD1
 GO:0072237 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
negative regulation of protein localization to cilium
INPP5E
 GO:1903565 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis Joubert syndrome 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis Mental retardation, truncal obesity, retinal dystrophy, and micropenis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Joubert syndrome 1 Mental retardation, truncal obesity, retinal dystrophy, and micropenis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital hypoplasia of femur Joubert syndrome 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital hypoplasia of femur Mental retardation, truncal obesity, retinal dystrophy, and micropenis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital hypoplasia of femur Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital hemivertebra Ficus syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Coach syndrome Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital hemivertebra Intellectual development disorder, truncal obesity, retinal dystrophy, and micropenis 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Coach syndrome Joubert syndrome 1 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital hemivertebra Joubert syndrome 1 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Coach syndrome Mental retardation, truncal obesity, retinal dystrophy, and micropenis 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital hemivertebra Mental retardation, truncal obesity, retinal dystrophy, and micropenis 0.167 1 3.23e-4 6.41e-4 ✓ sig.