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 124

10 diseases · 31 shared-gene connections
10 Diseases
87 Unique genes
0.322 Avg. similarity score
Congenital brain malformation Most-connected disease (9 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 brain malformation 9 9 17
Congenital hypoplasia of part of brain 9 9 17
Microgyria 8 8 17
Hydranencephaly 7 7 22
Macrogyria 7 7 29
Lissencephaly 6 6 50
joubert syndrome 36 5 5 1
Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay 4 4 36
joubert syndrome 14 4 4 1
ciliopathy-IFT74 3 3 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CASK 7 / 10 Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay, Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly and 3 more
FAM149B1 7 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, joubert syndrome 36 and 3 more
IFT74 7 / 10 ciliopathy-IFT74, Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly and 3 more
KIAA0586 7 / 10 Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay, Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly and 3 more
SEPSECS 7 / 10 Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay, Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly and 3 more
TMEM237 7 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, joubert syndrome 14 and 3 more
AMPD2 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
ARL3 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
B9D2 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
CHMP1A 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
INPP5E 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
KIAA0753 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
TMEM216 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
TMEM218 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
TOE1 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
TOGARAM1 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
TUBB3 6 / 10 Congenital brain malformation, Congenital hypoplasia of part of brain, Hydranencephaly, Lissencephaly and 2 more
NDE1 3 / 10 Hydranencephaly, Lissencephaly, Macrogyria
TUBA1A 3 / 10 Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay, Lissencephaly, Macrogyria
CTNNA2 2 / 10 Lissencephaly, Macrogyria
DYNC1H1 2 / 10 Lissencephaly, Macrogyria
LAMB1 2 / 10 Lissencephaly, Macrogyria
MACF1 2 / 10 Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay, Lissencephaly
PAFAH1B1 2 / 10 Lissencephaly, Macrogyria
POMGNT1 2 / 10 Lissencephaly, Macrogyria
POMT1 2 / 10 Lissencephaly, Macrogyria
POMT2 2 / 10 Lissencephaly, Macrogyria
TMTC3 2 / 10 Lissencephaly, Macrogyria
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 ⇵
Recruitment of NuMA to mitotic centrosomes
TUBA1A, TUBB2A, PAFAH1B1, TUBB3, NDE1, DYNC1H1, MZT2B, TUBA3E, TUBB, TUBB2B, TUBG1, TUBGCP2
 Reactome 12 / 94 17.6× 2.82e-12 5.62e-10 ✓ sig.
Recycling pathway of L1
KIF4A, L1CAM, TUBA1A, TUBB2A, TUBB3, ACTG1, TUBA3E, TUBB2B
 Reactome 8 / 40 27.6× 3.48e-10 4.43e-8 ✓ sig.
COPI-independent Golgi-to-ER retrograde traffic
PLA2G6, TUBA1A, TUBB2A, PAFAH1B1, TUBB3, DYNC1H1, TUBA3E, TUBB2B
 Reactome 8 / 51 21.7× 2.70e-9 2.71e-7 ✓ sig.
Motor proteins
KIF4A, TUBA1A, TUBB2A, TUBB3, ACTG1, DYNC1H1, MYH11, TUBA3E, TUBB, TUBB2B, TUBG1, KIF21B
 KEGG 12 / 194 8.5× 1.38e-8 1.15e-6 ✓ sig.
RHO GTPases Activate Formins
TUBA1A, TUBB2A, PAFAH1B1, B9D2, TUBB3, NDE1, ACTG1, DYNC1H1, TUBA3E, TUBB2B
 Reactome 10 / 140 9.9× 6.25e-8 4.36e-6 ✓ sig.
RHO GTPases activate IQGAPs
TUBA1A, TUBB2A, TUBB3, ACTG1, TUBA3E, TUBB2B
 Reactome 6 / 32 25.9× 9.45e-8 6.23e-6 ✓ sig.
Mitotic Prometaphase
TUBA1A, TUBB2A, PAFAH1B1, B9D2, TUBB3, NDE1, DYNC1H1, TUBA3E, TUBB2B
 Reactome 9 / 113 11.0× 1.16e-7 7.49e-6 ✓ sig.
Recruitment of mitotic centrosome proteins and complexes
TUBA1A, PAFAH1B1, NDE1, DYNC1H1, MZT2B, TUBB, TUBG1, TUBGCP2
 Reactome 8 / 82 13.5× 1.26e-7 8.00e-6 ✓ sig.
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane
TUBA1A, TUBB2A, TUBB3, TUBA3E, TUBB2B
 Reactome 5 / 18 38.3× 1.41e-7 8.82e-6 ✓ sig.
EML4 and NUDC in mitotic spindle formation
TUBA1A, TUBB2A, PAFAH1B1, B9D2, TUBB3, NDE1, DYNC1H1, TUBA3E, TUBB2B
 Reactome 9 / 117 10.6× 1.57e-7 9.70e-6 ✓ sig.
Cilium Assembly
TUBA1A, TUBB2A, TUBB3, TUBA3E, TUBB2B
 Reactome 5 / 19 36.3× 1.91e-7 1.15e-5 ✓ sig.
Kinesins
KIF4A, TUBA1A, TUBB2A, TUBB3, TUBA3E, TUBB2B, KIF21B
 Reactome 7 / 59 16.4× 2.06e-7 1.23e-5 ✓ sig.
Resolution of Sister Chromatid Cohesion
TUBA1A, TUBB2A, PAFAH1B1, B9D2, TUBB3, NDE1, DYNC1H1, TUBA3E, TUBB2B
 Reactome 9 / 126 9.9× 2.97e-7 1.70e-5 ✓ sig.
Aggrephagy
TUBA1A, TUBB2A, TUBB3, DYNC1H1, TUBA3E, TUBB2B
 Reactome 6 / 40 20.7× 3.82e-7 2.13e-5 ✓ sig.
Anchoring of the basal body to the plasma membrane
TUBA1A, PAFAH1B1, B9D2, TMEM216, NDE1, DYNC1H1, TUBB, TUBG1
 Reactome 8 / 98 11.3× 5.06e-7 2.71e-5 ✓ sig.

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
neuron migration
AUTS2, FGFR1, TUBA1A, TUBB2A, DCX, PAFAH1B1, NDE1, ARX, ASPM, CEP85L, RELN, TUBB2B
 GO:0001764 14 / 132 22.8× 1.33e-15 1.01e-12 ✓ sig.
microtubule cytoskeleton organization
TUBA1A, TUBB2A, PAFAH1B1, TOGARAM1, TUBB3, APC2, TUBA3E, TUBB, TUBB2B, TUBG1, CDK5, TUBGCP2
 GO:0000226 12 / 149 17.3× 4.48e-12 1.77e-9 ✓ sig.
microtubule-based process
TUBA1A, TUBB2A, PAFAH1B1, TUBB3, TUBA3E, TUBB, TUBB2B, TUBG1
 GO:0007017 8 / 46 37.4× 3.59e-11 1.14e-8 ✓ sig.
cerebral cortex development
TUBA1A, TUBB2A, PAFAH1B1, NDE1, ASPM, FOXG1, RELN, TUBB2B, CDK5
 GO:0021987 9 / 88 22.0× 2.85e-10 7.30e-8 ✓ sig.
forebrain development
FOXP1, PAFAH1B1, NDE1, ARX, FOXG1, RELN, CDK5
 GO:0030900 7 / 76 19.8× 6.25e-8 8.17e-6 ✓ sig.
cilium assembly
KIAA0586, ARL3, B9D2, FAM149B1, IFT74, INPP5E, KIAA0753, TMEM216, TMEM237, TOGARAM1
 GO:0060271 10 / 237 9.1× 1.52e-7 1.72e-5 ✓ sig.
nervous system development
ARID1A, ARID1B, FZD3, L1CAM, OPHN1, SEMA6B, VLDLR, DCX, PAFAH1B1, NDE1, ARX, APC2
 GO:0007399 15 / 631 5.1× 1.99e-7 2.16e-5 ✓ sig.
mitotic cell cycle
TUBA1A, TUBB2A, TUBB3, TUBA3E, TUBB, TUBB2B, TUBG1, TUBGCP2
 GO:0000278 8 / 142 12.1× 3.21e-7 3.22e-5 ✓ sig.
layer formation in cerebral cortex
PAFAH1B1, RELN, CDK5, ADGRG1
 GO:0021819 4 / 18 47.7× 1.28e-6 1.01e-4 ✓ sig.
protein O-linked glycosylation via mannose
POMGNT1, POMT1, POMT2, TMTC3
 GO:0035269 4 / 18 47.7× 1.28e-6 1.01e-4 ✓ sig.
cell migration
FGFR1, L1CAM, LAMB1, PAFAH1B1, NDE1, APC2, CTNNA2, RELN, CDK5, ADGRG1
 GO:0016477 10 / 303 7.1× 1.44e-6 1.11e-4 ✓ sig.
cell division
TUBA1A, PAFAH1B1, ARL3, CHMP1A, NDE1, CEP55, ASPM, DYNC1H1, TUBB, KATNB1, CDK5
 GO:0051301 11 / 406 5.8× 2.83e-6 1.90e-4 ✓ sig.
neuroblast proliferation
PAFAH1B1, NDE1, ASPM, FOXG1, NBN
 GO:0007405 5 / 48 22.4× 2.85e-6 1.91e-4 ✓ sig.
interneuron migration
PAFAH1B1, ARX, RELN
 GO:1904936 3 / 11 58.6× 1.57e-5 7.44e-4 ✓ sig.
hippocampus development
SEMA6B, TUBA1A, PAFAH1B1, RELN, CDK5
 GO:0021766 5 / 74 14.5× 2.44e-5 1.04e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Lissencephaly Macrogyria 0.509 27 4.23e-69 3.16e-67 ✓ sig.
Congenital brain malformation Congenital hypoplasia of part of brain 0.944 17 2.33e-57 1.44e-55 ✓ sig.
Congenital brain malformation Microgyria 0.944 17 2.33e-57 1.44e-55 ✓ sig.
Congenital hypoplasia of part of brain Microgyria 0.944 17 2.33e-57 1.44e-55 ✓ sig.
Hydranencephaly Microgyria 0.739 17 6.15e-53 3.55e-51 ✓ sig.
Congenital brain malformation Hydranencephaly 0.739 17 6.15e-53 3.55e-51 ✓ sig.
Congenital hypoplasia of part of brain Hydranencephaly 0.739 17 6.15e-53 3.55e-51 ✓ sig.
Macrogyria Microgyria 0.567 17 1.21e-49 6.66e-48 ✓ sig.
Congenital hypoplasia of part of brain Macrogyria 0.567 17 1.21e-49 6.66e-48 ✓ sig.
Congenital brain malformation Macrogyria 0.567 17 1.21e-49 6.66e-48 ✓ sig.
Hydranencephaly Macrogyria 0.529 18 6.89e-49 3.71e-47 ✓ sig.
Congenital hypoplasia of part of brain Lissencephaly 0.333 17 2.30e-44 1.13e-42 ✓ sig.
Lissencephaly Microgyria 0.333 17 2.30e-44 1.13e-42 ✓ sig.
Congenital brain malformation Lissencephaly 0.333 17 2.30e-44 1.13e-42 ✓ sig.
Hydranencephaly Lissencephaly 0.327 18 3.58e-43 1.68e-41 ✓ sig.
Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay Lissencephaly 0.061 5 1.03e-7 7.59e-7 ✓ sig.
Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay Macrogyria 0.065 4 5.73e-7 3.70e-6 ✓ sig.
Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay Congenital brain malformation 0.059 3 7.80e-6 4.15e-5 ✓ sig.
Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay Congenital hypoplasia of part of brain 0.059 3 7.80e-6 4.15e-5 ✓ sig.
ciliopathy-IFT74 Microgyria 0.056 1 1.10e-3 1.81e-3 ✓ sig.
joubert syndrome 36 Microgyria 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Congenital hypoplasia of part of brain joubert syndrome 36 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Congenital brain malformation joubert syndrome 36 0.056 1 1.10e-3 1.81e-3 ✓ sig.
joubert syndrome 14 Microgyria 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Congenital hypoplasia of part of brain joubert syndrome 14 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Congenital brain malformation joubert syndrome 14 0.056 1 1.10e-3 1.81e-3 ✓ sig.
ciliopathy-IFT74 Congenital brain malformation 0.056 1 1.10e-3 1.81e-3 ✓ sig.
ciliopathy-IFT74 Congenital hypoplasia of part of brain 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Hydranencephaly joubert syndrome 14 0.043 1 1.43e-3 2.21e-3 ✓ sig.
Hydranencephaly joubert syndrome 36 0.043 1 1.43e-3 2.21e-3 ✓ sig.
joubert syndrome 36 Macrogyria 0.033 1 1.88e-3 2.75e-3 ✓ sig.