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 51

15 diseases · 27 shared-gene connections
15 Diseases
71 Unique genes
0.183 Avg. similarity score
Congenital nemaline myopathy Most-connected disease (8 links)
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Disease Searched: Neuronal ceroid lipofuscinosis 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 nemaline myopathy 8 8 5
Nemaline myopathy 7 7 18
Congenital neck anomaly 6 6 2
Deglutition disorder 5 5 11
Distal nebulin myopathy 5 5 1
Nebulin-related myopathy 5 5 1
nemaline myopathy 2 5 5 1
Neuronal ceroid lipofuscinosis 2 2 31
Visual disorder 2 2 20
nemaline myopathy 10 2 2 1
nemaline myopathy 8 2 2 1
nemaline myopathy 9 2 2 1
adult neuronal ceroid lipofuscinosis 1 1 2
nemaline myopathy 6 1 1 1
nemaline myopathy 7 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
NEB 7 / 15 Congenital neck anomaly, Congenital nemaline myopathy, Deglutition disorder, Distal nebulin myopathy and 3 more
KLHL40 3 / 15 Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 8
KLHL41 3 / 15 Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 9
LMOD3 3 / 15 Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 10
RIF1 3 / 15 Congenital neck anomaly, Deglutition disorder, Nemaline myopathy
ACTA1 2 / 15 Congenital nemaline myopathy, Nemaline myopathy
CFL2 2 / 15 Nemaline myopathy, nemaline myopathy 7
CLN3 2 / 15 Neuronal ceroid lipofuscinosis, Visual disorder
CLN5 2 / 15 Neuronal ceroid lipofuscinosis, Visual disorder
CLN6 2 / 15 Neuronal ceroid lipofuscinosis, Visual disorder
CTSF 2 / 15 adult neuronal ceroid lipofuscinosis, Neuronal ceroid lipofuscinosis
DNAJC5 2 / 15 adult neuronal ceroid lipofuscinosis, Neuronal ceroid lipofuscinosis
KBTBD13 2 / 15 Nemaline myopathy, nemaline myopathy 6
PPT1 2 / 15 Neuronal ceroid lipofuscinosis, Visual disorder
TSEN2 2 / 15 Deglutition disorder, Visual disorder
TSEN34 2 / 15 Deglutition disorder, Visual disorder
TSEN54 2 / 15 Deglutition disorder, Visual disorder
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 ⇵
Striated Muscle Contraction
NEB, ACTA1, TPM2, TPM3, TNNT1, TNNT3, TNNI1
 Reactome 7 / 36 32.9× 1.36e-9 1.53e-7 ✓ sig.
Cytoskeleton in muscle cells
NEB, ACTA1, MYPN, TPM2, TPM3, ANKRD1, FLNC, TNNT1, TNNT3, LMOD3, MYH10, TNNI1
 KEGG 12 / 232 8.7× 9.51e-9 8.74e-7 ✓ sig.
Lysosome
CTSF, PPT1, CLN5, CTSD, TPP1, CLN3, SMPD1, MFSD8
 KEGG 8 / 133 10.2× 1.08e-6 5.60e-5 ✓ sig.
Motor proteins
ACTA1, TPM2, TPM3, MYO18B, TNNT1, TNNT3, MYH10, TNNI1
 KEGG 8 / 194 7.0× 1.79e-5 5.73e-4 ✓ sig.
Negative feedback regulation of MAPK pathway
MAPK1, MAPK3
 Reactome 2 / 6 56.4× 5.09e-4 8.38e-3 ✓ sig.
Suppression of apoptosis
MAPK1, MAPK3
 Reactome 2 / 7 48.3× 7.10e-4 1.08e-2 ✓ sig.
Regulation of HSF1-mediated heat shock response
SIRT1, GSK3B, MAPK1, MAPK3
 Reactome 4 / 69 9.8× 7.26e-4 1.10e-2 ✓ sig.
Gastrin-CREB signalling pathway via PKC and MAPK
MAPK1, MAPK3
 Reactome 2 / 9 37.6× 1.21e-3 1.62e-2 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
RPS6KB1, GSK3B, MAPK1, MAPK3
 KEGG 4 / 80 8.5× 1.26e-3 1.68e-2 ✓ sig.
Apoptosis
CTSF, PARP1, CTSD, MAPK1, MAPK3
 KEGG 5 / 137 6.2× 1.28e-3 1.70e-2 ✓ sig.
Insulin signaling pathway
PPARGC1A, RPS6KB1, GSK3B, MAPK1, MAPK3
 KEGG 5 / 138 6.1× 1.32e-3 1.74e-2 ✓ sig.
Thyroid cancer
MAPK1, MAPK3, TPM3
 KEGG 3 / 37 13.7× 1.33e-3 1.75e-2 ✓ sig.
Apelin signaling pathway
PPARGC1A, RPS6KB1, TFAM, MAPK1, MAPK3
 KEGG 5 / 140 6.0× 1.41e-3 1.83e-2 ✓ sig.
Activation of the AP-1 family of transcription factors
MAPK1, MAPK3
 Reactome 2 / 10 33.8× 1.50e-3 1.92e-2 ✓ sig.
Regulation of the apoptosome activity
MAPK1, MAPK3
 Reactome 2 / 10 33.8× 1.50e-3 1.92e-2 ✓ 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 ⇵
lysosome organization
PPT1, CLN5, CLN8, GRN, TPP1, CLN3, CLN6, MFSD8
 GO:0007040 8 / 65 32.4× 1.23e-10 3.52e-8 ✓ sig.
negative regulation of neuron apoptotic process
DNAJC5, PPARGC1A, PPT1, SIRT1, CLN8, GRN, CLN3, MFSD8, SOD2
 GO:0043524 9 / 160 14.8× 9.33e-9 1.60e-6 ✓ sig.
sarcomere organization
MYPN, ANKRD1, CFL2, FLNC, TNNT1, TNNT3
 GO:0045214 6 / 43 36.7× 1.32e-8 2.18e-6 ✓ sig.
lysosomal lumen acidification
PPT1, CLN5, GRN, CLN3, CLN6
 GO:0007042 5 / 25 52.6× 3.44e-8 4.93e-6 ✓ sig.
tRNA-type intron splice site recognition and cleavage
TSEN2, TSEN34, TSEN54
 GO:0000379 3 / 3 263× 5.26e-8 7.12e-6 ✓ sig.
macromolecule catabolic process
PPT1, CLN8, CLN6
 GO:0009057 3 / 3 263× 5.26e-8 7.12e-6 ✓ sig.
lysosomal protein catabolic process
GRN, TPP1, CLN3, MFSD8
 GO:1905146 4 / 16 65.8× 3.36e-7 3.45e-5 ✓ sig.
mitochondrion organization
FIS1, MFN1, PARP1, PPARGC1A, GSK3B, MFSD8, SOD2
 GO:0007005 7 / 130 14.2× 6.16e-7 5.70e-5 ✓ sig.
Bergmann glial cell differentiation
GFAP, MAPK1, MAPK3
 GO:0060020 3 / 11 71.8× 8.48e-6 4.76e-4 ✓ sig.
regulation of ATP-dependent activity
TPM2, TNNT3
 GO:0043462 2 / 2 263× 1.42e-5 7.13e-4 ✓ sig.
tRNA splicing, via endonucleolytic cleavage and ligation
TSEN2, TSEN34, TSEN54
 GO:0006388 3 / 13 60.7× 1.46e-5 7.28e-4 ✓ sig.
myofibril assembly
KLHL41, LMOD3, MYH10
 GO:0030239 3 / 15 52.6× 2.31e-5 1.04e-3 ✓ sig.
protein catabolic process
PPT1, CLN5, CLN8, TPP1, CLN6
 GO:0030163 5 / 97 13.6× 3.37e-5 1.38e-3 ✓ sig.
interleukin-34-mediated signaling pathway
MAPK1, MAPK3
 GO:0061514 2 / 3 175× 4.26e-5 1.65e-3 ✓ sig.
cardiac neural crest cell development involved in heart development
MAPK1, MAPK3
 GO:0061308 2 / 3 175× 4.26e-5 1.65e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital nemaline myopathy Nemaline myopathy 0.263 5 1.19e-15 1.77e-14 ✓ sig.
Neuronal ceroid lipofuscinosis Visual disorder 0.083 4 6.37e-8 4.62e-7 ✓ sig.
Deglutition disorder Visual disorder 0.103 3 3.07e-7 1.97e-6 ✓ sig.
Congenital neck anomaly Deglutition disorder 0.167 2 4.64e-7 2.90e-6 ✓ sig.
Congenital neck anomaly Nemaline myopathy 0.105 2 1.29e-6 7.42e-6 ✓ sig.
adult neuronal ceroid lipofuscinosis Neuronal ceroid lipofuscinosis 0.063 2 3.92e-6 2.07e-5 ✓ sig.
Nebulin-related myopathy nemaline myopathy 2 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Distal nebulin myopathy nemaline myopathy 2 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Distal nebulin myopathy Nebulin-related myopathy 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital neck anomaly Nebulin-related myopathy 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital neck anomaly Distal nebulin myopathy 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital neck anomaly nemaline myopathy 2 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital nemaline myopathy nemaline myopathy 2 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital nemaline myopathy nemaline myopathy 9 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital nemaline myopathy nemaline myopathy 8 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital nemaline myopathy Nebulin-related myopathy 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital nemaline myopathy Distal nebulin myopathy 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital nemaline myopathy nemaline myopathy 10 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital neck anomaly Congenital nemaline myopathy 0.143 1 6.49e-4 1.24e-3 ✓ sig.
Deglutition disorder Nebulin-related myopathy 0.083 1 7.14e-4 1.34e-3 ✓ sig.
Deglutition disorder nemaline myopathy 2 0.083 1 7.14e-4 1.34e-3 ✓ sig.
Deglutition disorder Distal nebulin myopathy 0.083 1 7.14e-4 1.34e-3 ✓ sig.
Nemaline myopathy nemaline myopathy 10 0.053 1 1.17e-3 1.90e-3 ✓ sig.
Nemaline myopathy nemaline myopathy 6 0.053 1 1.17e-3 1.90e-3 ✓ sig.
Nemaline myopathy nemaline myopathy 7 0.053 1 1.17e-3 1.90e-3 ✓ sig.
Nemaline myopathy nemaline myopathy 8 0.053 1 1.17e-3 1.90e-3 ✓ sig.
Nemaline myopathy nemaline myopathy 9 0.053 1 1.17e-3 1.90e-3 ✓ sig.