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 137

10 diseases · 15 shared-gene connections
10 Diseases
138 Unique genes
0.076 Avg. similarity score
Seckel syndrome Most-connected disease (7 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 ⇵
Seckel syndrome 7 7 18
Congenital microcephaly 5 5 31
Microcephaly 5 5 106
Primary microcephaly 4 4 35
microcephaly with or without short stature 4 4 1
Cerebellar-facial-dental syndrome 1 1 1
Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome 1 1 2
microcephalic osteodysplastic primordial dwarfism type II 1 1 1
primordial dwarfism-immunodeficiency-lipodystrophy syndrome 1 1 1
seckel syndrome 10 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CEP152 5 / 10 Congenital microcephaly, Microcephaly, microcephaly with or without short stature, Primary microcephaly and 1 more
CDK5RAP2 4 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly, Seckel syndrome
CPAP 4 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly, Seckel syndrome
ASPM 3 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly
CENPE 3 / 10 Microcephaly, Primary microcephaly, Seckel syndrome
CEP63 3 / 10 Microcephaly, Primary microcephaly, Seckel syndrome
CIT 3 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly
KNL1 3 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly
MCPH1 3 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly
PHC1 3 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly
RNF17 3 / 10 Congenital microcephaly, Microcephaly, Seckel syndrome
STIL 3 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly
WDR62 3 / 10 Congenital microcephaly, Microcephaly, Primary microcephaly
ANGPT2 2 / 10 Microcephaly, Primary microcephaly
ANKLE2 2 / 10 Microcephaly, Primary microcephaly
BRF1 2 / 10 Cerebellar-facial-dental syndrome, Congenital microcephaly
CASK 2 / 10 Congenital microcephaly, Microcephaly
CDK6 2 / 10 Microcephaly, Primary microcephaly
CEP135 2 / 10 Microcephaly, Primary microcephaly
COPB2 2 / 10 Microcephaly, Primary microcephaly
DPP6 2 / 10 Microcephaly, Primary microcephaly
FOXG1 2 / 10 Congenital microcephaly, Microcephaly
KIF14 2 / 10 Microcephaly, Primary microcephaly
LMNB1 2 / 10 Microcephaly, Primary microcephaly
MFSD2A 2 / 10 Microcephaly, Primary microcephaly
NCAPD3 2 / 10 Microcephaly, Primary microcephaly
NSMCE2 2 / 10 Seckel syndrome, seckel syndrome 10
NUP37 2 / 10 Microcephaly, Primary microcephaly
PCNT 2 / 10 microcephalic osteodysplastic primordial dwarfism type II, Seckel syndrome
PDCD6IP 2 / 10 Microcephaly, Primary microcephaly
PLK4 2 / 10 Microcephaly, Seckel syndrome
PNKP 2 / 10 Congenital microcephaly, Microcephaly
PPP1R15B 2 / 10 Microcephaly, Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome
PRIM1 2 / 10 primordial dwarfism-immunodeficiency-lipodystrophy syndrome, Seckel syndrome
RBBP8 2 / 10 Microcephaly, Seckel syndrome
RTTN 2 / 10 Congenital microcephaly, Microcephaly
SASS6 2 / 10 Microcephaly, Primary microcephaly
TEDC1 2 / 10 Microcephaly, Primary microcephaly
TRAIP 2 / 10 Microcephaly, Seckel syndrome
TRAPPC14 2 / 10 Microcephaly, Primary microcephaly
TRMT10A 2 / 10 Microcephaly, Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome
ZNF335 2 / 10 Microcephaly, Primary microcephaly
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
CDK5RAP2, CEP135, CEP152, CEP63, MZT2B, TUBA3E, DYNC1H1, PLK4, TUBA1A, TUBG1, CENPJ, TUBGCP4
 Reactome 16 / 94 14.8× 8.17e-15 2.61e-12 ✓ sig.
Recruitment of mitotic centrosome proteins and complexes
CDK5RAP2, CEP135, CEP152, CEP63, MZT2B, DYNC1H1, PLK4, TUBA1A, TUBG1, CENPJ, TUBGCP4, TUBGCP6
 Reactome 15 / 82 15.9× 1.92e-14 5.63e-12 ✓ sig.
Loss of Nlp from mitotic centrosomes
CDK5RAP2, CEP135, CEP152, CEP63, DYNC1H1, PLK4, TUBA1A, TUBG1, CENPJ, NDE1, PPP2R1A, PCNT
 Reactome 12 / 70 14.9× 1.97e-11 3.30e-9 ✓ sig.
Loss of proteins required for interphase microtubule organization from the centrosome
CDK5RAP2, CEP135, CEP152, CEP63, DYNC1H1, PLK4, TUBA1A, TUBG1, CENPJ, NDE1, PPP2R1A, PCNT
 Reactome 12 / 70 14.9× 1.97e-11 3.30e-9 ✓ sig.
AURKA Activation by TPX2
CDK5RAP2, CEP135, CEP152, CEP63, DYNC1H1, PLK4, TUBA1A, TUBG1, CENPJ, NDE1, PPP2R1A, PCNT
 Reactome 12 / 73 14.3× 3.30e-11 5.31e-9 ✓ sig.
Anchoring of the basal body to the plasma membrane
CDK5RAP2, CEP135, CEP152, CEP63, RAB11A, DYNC1H1, PLK4, TUBA1A, TUBG1, CENPJ, NDE1, PPP2R1A
 Reactome 13 / 98 11.5× 8.03e-11 1.18e-8 ✓ sig.
Regulation of PLK1 Activity at G2/M Transition
CDK5RAP2, CEP135, CEP152, CEP63, DYNC1H1, PLK4, TUBA1A, TUBG1, CENPJ, NDE1, PPP2R1A, PCNT
 Reactome 12 / 88 11.9× 3.19e-10 4.10e-8 ✓ sig.
Mitotic Prometaphase
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 13 / 113 10.0× 4.96e-10 6.06e-8 ✓ sig.
RHO GTPases Activate Formins
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 14 / 140 8.7× 6.82e-10 7.97e-8 ✓ sig.
EML4 and NUDC in mitotic spindle formation
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 13 / 117 9.7× 7.69e-10 8.86e-8 ✓ sig.
Resolution of Sister Chromatid Cohesion
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 13 / 126 9.0× 1.94e-9 2.01e-7 ✓ sig.
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
CENPE, KNL1, NUP37, BUB1B, DYNC1H1, KIF2A, SPDL1, BUB1, NDE1, PPP2R1A, NUP85
 Reactome 11 / 96 10.0× 1.18e-8 1.01e-6 ✓ sig.
Separation of Sister Chromatids
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 13 / 190 6.0× 2.71e-7 1.56e-5 ✓ sig.
HDR through Single Strand Annealing (SSA)
RBBP8, TOP3A, NBN, ATR, ATRIP, DNA2
 Reactome 6 / 37 14.1× 3.58e-6 1.44e-4 ✓ sig.
Presynaptic phase of homologous DNA pairing and strand exchange
RBBP8, TOP3A, NBN, ATR, ATRIP, DNA2
 Reactome 6 / 39 13.4× 4.93e-6 1.88e-4 ✓ 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 ⇵
cell division
ANKLE2, ASPM, CDK6, CENPE, CEP63, CIT, KIF14, KNL1, NCAPD3, NUP37, PDCD6IP, INO80
 GO:0051301 27 / 406 9.0× 2.11e-18 2.67e-15 ✓ sig.
centriole replication
CDK5RAP2, CEP135, CEP152, CEP63, SASS6, WDR62, RTTN, PLK4, CENPJ, CEP295
 GO:0007099 10 / 24 56.4× 6.22e-16 5.07e-13 ✓ sig.
microtubule cytoskeleton organization
CDK5RAP2, TUBA3E, KIF2A, KIFBP, TBCD, TUBA1A, TUBG1, RHO, GAPDH, TUBGCP4, TUBGCP6, NUSAP1
 GO:0000226 13 / 149 11.8× 7.79e-11 2.28e-8 ✓ sig.
cerebral cortex development
ASPM, KIF14, MCPH1, WDR62, FOXG1, NR2E1, SLC2A1, TUBA1A, NDE1, EOMES
 GO:0021987 10 / 88 15.4× 9.60e-10 2.16e-7 ✓ sig.
mitotic cell cycle
CENPE, CIT, MCPH1, TUBA3E, TBCD, TUBA1A, TUBG1, NCAPD2, TUBGCP4, TUBGCP6, KIF11
 GO:0000278 11 / 142 10.5× 8.34e-9 1.47e-6 ✓ sig.
mitotic spindle organization
CENPE, STIL, WDR62, DYNC1H1, KIF2A, TUBG1, KIF11, PCNT
 GO:0007052 8 / 58 18.7× 1.01e-8 1.73e-6 ✓ sig.
positive regulation of centriole replication
SASS6, STIL, PLK4, CENPJ
 GO:0046601 4 / 5 108× 1.42e-8 2.31e-6 ✓ sig.
microtubule nucleation
TUBG1, CENPJ, TUBGCP4, TUBGCP6, NDE1, PCNT
 GO:0007020 6 / 26 31.2× 2.96e-8 4.35e-6 ✓ sig.
DNA damage checkpoint signaling
CEP63, DONSON, ERCC6, TP53BP1, NBN, ATR, ATRIP
 GO:0000077 7 / 47 20.2× 5.05e-8 6.83e-6 ✓ sig.
positive regulation of spindle assembly
SASS6, STIL, DYNC1H1, CENPJ
 GO:1905832 4 / 8 67.7× 1.95e-7 2.12e-5 ✓ sig.
centrosome duplication
CEP152, SASS6, STIL, CENPJ, NDE1
 GO:0051298 5 / 19 35.6× 2.19e-7 2.34e-5 ✓ sig.
microtubule-based movement
CENPE, KIF14, DNAH2, RAB11A, DYNC1H1, KIF2A, KIF5C, KIF11
 GO:0007018 8 / 87 12.5× 2.58e-7 2.69e-5 ✓ sig.
DNA damage response
CDK6, CEP63, MCM7, INO80, PNKP, SMARCAL1, CTLA4, ERCC6, TRAIP, TP53BP1, RBBP8, WDR4
 GO:0006974 18 / 577 4.2× 2.59e-7 2.69e-5 ✓ sig.
tRNA-type intron splice site recognition and cleavage
TSEN2, TSEN34, TSEN54
 GO:0000379 3 / 3 135× 3.94e-7 3.83e-5 ✓ sig.
spindle assembly
CEP63, INO80, TUBGCP4, TUBGCP6, KIF11, PPP2R1A
 GO:0051225 6 / 40 20.3× 4.54e-7 4.31e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Microcephaly Primary microcephaly 0.246 28 3.80e-56 2.31e-54 ✓ sig.
Congenital microcephaly Microcephaly 0.122 15 3.62e-25 9.40e-24 ✓ sig.
Congenital microcephaly Primary microcephaly 0.175 10 3.83e-20 7.80e-19 ✓ sig.
Microcephaly Seckel syndrome 0.078 9 1.13e-15 1.79e-14 ✓ sig.
Primary microcephaly Seckel syndrome 0.102 5 3.78e-10 3.78e-9 ✓ sig.
Congenital microcephaly Seckel syndrome 0.087 4 4.03e-8 3.19e-7 ✓ sig.
Microcephaly Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome 0.019 2 4.69e-5 2.25e-4 ✓ sig.
microcephalic osteodysplastic primordial dwarfism type II Seckel syndrome 0.053 1 1.17e-3 1.88e-3 ✓ sig.
microcephaly with or without short stature Seckel syndrome 0.053 1 1.17e-3 1.88e-3 ✓ sig.
primordial dwarfism-immunodeficiency-lipodystrophy syndrome Seckel syndrome 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Seckel syndrome seckel syndrome 10 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Cerebellar-facial-dental syndrome Congenital microcephaly 0.031 1 2.01e-3 2.89e-3 ✓ sig.
Congenital microcephaly microcephaly with or without short stature 0.031 1 2.01e-3 2.89e-3 ✓ sig.
microcephaly with or without short stature Primary microcephaly 0.028 1 2.27e-3 3.18e-3 ✓ sig.
Microcephaly microcephaly with or without short stature 0.009 1 6.88e-3 8.16e-3 ✓ sig.