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 493

6 diseases · 8 shared-gene connections
6 Diseases
4 Unique genes
0.313 Avg. similarity score
Congenital cystic kidney disease 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 ⇵
Congenital cystic kidney disease 5 5 4
Lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome 3 3 1
Meckel syndrome 12 3 3 1
Severe microcephaly and short stature 3 3 1
Joubert syndrome 20 (includes developmental delay) 1 1 1
Meckel syndrome 14 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
KIF14 4 / 6 Congenital cystic kidney disease, Lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome, Meckel syndrome 12, Severe microcephaly and short stature
TMEM231 2 / 6 Congenital cystic kidney disease, Joubert syndrome 20 (includes developmental delay)
TXNDC15 2 / 6 Congenital cystic kidney disease, Meckel syndrome 14
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 ⇵
RHO GTPases activate CIT
KIF14
 Reactome 1 / 8 375× 2.66e-3 2.34e-2 ✓ sig.
Anchoring of the basal body to the plasma membrane
B9D1
 Reactome 1 / 98 30.6× 3.22e-2 1.13e-1
Motor proteins
KIF14
 KEGG 1 / 194 15.5× 6.31e-2 1.65e-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 ⇵
neuroepithelial cell differentiation
B9D1, TMEM231
 GO:0060563 2 / 12 779× 2.27e-6 1.68e-4 ✓ sig.
cell projection organization
B9D1, TMEM231, TXNDC15
 GO:0030030 3 / 214 65.5× 5.87e-6 3.60e-4 ✓ sig.
cilium assembly
B9D1, TMEM231, TXNDC15
 GO:0060271 3 / 237 59.1× 7.98e-6 4.57e-4 ✓ sig.
vasculature development
B9D1, TMEM231
 GO:0001944 2 / 33 283× 1.81e-5 8.59e-4 ✓ sig.
embryonic digit morphogenesis
B9D1, TMEM231
 GO:0042733 2 / 57 164× 5.46e-5 1.97e-3 ✓ sig.
camera-type eye development
B9D1, TMEM231
 GO:0043010 2 / 74 126× 9.23e-5 2.92e-3 ✓ sig.
regulation of protein localization
B9D1, TMEM231
 GO:0032880 2 / 89 105× 1.34e-4 3.80e-3 ✓ sig.
smoothened signaling pathway
B9D1, TMEM231
 GO:0007224 2 / 94 99.4× 1.49e-4 4.12e-3 ✓ sig.
cerebellar granular layer structural organization
KIF14
 GO:0021685 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
regulation of cell maturation
KIF14
 GO:1903429 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
cerebellar Purkinje cell layer structural organization
KIF14
 GO:0021693 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
negative regulation of integrin activation
KIF14
 GO:0033624 1 / 3 1,557× 6.42e-4 1.11e-2 ✓ sig.
regulation of Rap protein signal transduction
KIF14
 GO:0032487 1 / 4 1,168× 8.56e-4 1.33e-2 ✓ sig.
in utero embryonic development
B9D1, TMEM231
 GO:0001701 2 / 252 37.1× 1.07e-3 1.51e-2 ✓ sig.
cerebellar cortex development
KIF14
 GO:0021695 1 / 8 584× 1.71e-3 1.96e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome Severe microcephaly and short stature 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome Meckel syndrome 12 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Meckel syndrome 12 Severe microcephaly and short stature 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital cystic kidney disease Joubert syndrome 20 (includes developmental delay) 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Congenital cystic kidney disease Severe microcephaly and short stature 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Congenital cystic kidney disease Meckel syndrome 12 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Congenital cystic kidney disease Lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Congenital cystic kidney disease Meckel syndrome 14 0.200 1 2.58e-4 5.38e-4 ✓ sig.