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 130

11 diseases · 22 shared-gene connections
11 Diseases
23 Unique genes
0.286 Avg. similarity score
Bladder inflammatory myofibroblastic tumor Most-connected disease (7 links)
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Disease Searched: Nemaline myopathy 1, autosomal dominant or recessive 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 ⇵
Bladder inflammatory myofibroblastic tumor 7 7 5
Congenital generalized hypercontractile muscle stiffness syndrome 5 5 1
Congenital myopathy 4a, autosomal dominant 5 5 1
Congenital myopathy 4b, autosomal recessive 5 5 1
Liver inflammatory myofibroblastic tumor 5 5 9
Nemaline myopathy 1, autosomal dominant or recessive 5 5 1
Cap myopathy 4 4 3
Inflammatory myofibroblastic tumor 3 3 19
Aica-ribosiduria 2 2 1
Microcephaly, developmental delay, and brittle hair and nails 2 2 1
Spastic paraplegia 57, autosomal recessive 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TPM3 8 / 11 Bladder inflammatory myofibroblastic tumor, Cap myopathy, Congenital generalized hypercontractile muscle stiffness syndrome, Congenital myopathy 4a, autosomal dominant and 4 more
ALK 3 / 11 Bladder inflammatory myofibroblastic tumor, Inflammatory myofibroblastic tumor, Liver inflammatory myofibroblastic tumor
ATIC 3 / 11 Aica-ribosiduria, Bladder inflammatory myofibroblastic tumor, Liver inflammatory myofibroblastic tumor
CARS1 3 / 11 Inflammatory myofibroblastic tumor, Liver inflammatory myofibroblastic tumor, Microcephaly, developmental delay, and brittle hair and nails
CLTC 3 / 11 Bladder inflammatory myofibroblastic tumor, Inflammatory myofibroblastic tumor, Liver inflammatory myofibroblastic tumor
TPM4 3 / 11 Bladder inflammatory myofibroblastic tumor, Inflammatory myofibroblastic tumor, Liver inflammatory myofibroblastic tumor
NPM1 2 / 11 Inflammatory myofibroblastic tumor, Liver inflammatory myofibroblastic tumor
RANBP2 2 / 11 Inflammatory myofibroblastic tumor, Liver inflammatory myofibroblastic tumor
TFG 2 / 11 Liver inflammatory myofibroblastic tumor, Spastic paraplegia 57, autosomal recessive
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 ⇵
Longevity regulating pathway
CREB3L1, TP53, FOXO1, KRAS, CREB3L2, PIK3CA
 KEGG 6 / 90 34.8× 1.36e-8 9.77e-7 ✓ sig.
Prostate cancer
CREB3L1, TP53, FOXO1, KRAS, CREB3L2, PIK3CA
 KEGG 6 / 98 32.0× 2.28e-8 1.54e-6 ✓ sig.
Pathways in cancer
TPM3, ALK, TP53, FOXO1, FLT4, TFG, KRAS, PIK3CA, KIT
 KEGG 9 / 533 8.8× 2.92e-7 1.43e-5 ✓ sig.
Thyroid cancer
TPM3, TP53, TFG, KRAS
 KEGG 4 / 37 56.5× 6.47e-7 2.86e-5 ✓ sig.
PI3K-Akt signaling pathway
CREB3L1, TP53, FLT4, KRAS, CREB3L2, PIK3CA, KIT
 KEGG 7 / 361 10.1× 3.38e-6 1.18e-4 ✓ sig.
Breast cancer
TP53, FLT4, KRAS, PIK3CA, KIT
 KEGG 5 / 148 17.6× 7.47e-6 2.29e-4 ✓ sig.
Adrenergic signaling in cardiomyocytes
TPM2, TPM3, CREB3L1, TPM4, CREB3L2
 KEGG 5 / 154 17.0× 9.07e-6 2.69e-4 ✓ sig.
Central carbon metabolism in cancer
TP53, KRAS, PIK3CA, KIT
 KEGG 4 / 71 29.4× 9.12e-6 2.70e-4 ✓ sig.
Non-small cell lung cancer
ALK, TP53, KRAS, PIK3CA
 KEGG 4 / 73 28.6× 1.02e-5 2.96e-4 ✓ sig.
Hepatitis B
CREB3L1, TP53, KRAS, CREB3L2, PIK3CA
 KEGG 5 / 163 16.0× 1.20e-5 3.38e-4 ✓ sig.
Human papillomavirus infection
CREB3L1, TP53, FOXO1, KRAS, CREB3L2, PIK3CA
 KEGG 6 / 333 9.4× 2.94e-5 7.13e-4 ✓ sig.
Transcriptional misregulation in cancer
PAX3, TP53, FOXO1, FUS, PAX7
 KEGG 5 / 198 13.2× 3.06e-5 7.36e-4 ✓ sig.
Smooth Muscle Contraction
TPM2, TPM3, TPM4
 Reactome 3 / 34 46.1× 3.53e-5 8.29e-4 ✓ sig.
Viral carcinogenesis
CREB3L1, TP53, KRAS, CREB3L2, PIK3CA
 KEGG 5 / 205 12.7× 3.61e-5 8.43e-4 ✓ sig.
Melanogenesis
CREB3L1, KRAS, CREB3L2, KIT
 KEGG 4 / 101 20.7× 3.69e-5 8.57e-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 ⇵
regulation of cell population proliferation
ALK, TP53, FOXO1, NPM1, KIT
 GO:0042127 5 / 201 20.2× 3.94e-6 2.61e-4 ✓ sig.
regulation of DNA damage response, signal transduction by p53 class mediator
TP53, NPM1
 GO:0043516 2 / 7 232× 3.03e-5 1.26e-3 ✓ sig.
energy homeostasis
ALK, FOXO1, PIK3CA
 GO:0097009 3 / 64 38.1× 6.46e-5 2.24e-3 ✓ sig.
muscle contraction
TPM2, TPM3, TPM4
 GO:0006936 3 / 85 28.7× 1.51e-4 4.16e-3 ✓ sig.
glial cell proliferation
TP53, KRAS
 GO:0014009 2 / 18 90.3× 2.19e-4 5.40e-3 ✓ sig.
regulation of gluconeogenesis
RANBP2, FOXO1
 GO:0006111 2 / 19 85.5× 2.45e-4 5.86e-3 ✓ sig.
vascular endothelial growth factor signaling pathway
FLT4, PIK3CA
 GO:0038084 2 / 19 85.5× 2.45e-4 5.86e-3 ✓ sig.
positive regulation of cellular senescence
TP53, KRAS
 GO:2000774 2 / 20 81.2× 2.72e-4 6.31e-3 ✓ sig.
regulation of mitotic spindle organization
CLTC, DCTN1
 GO:0060236 2 / 20 81.2× 2.72e-4 6.31e-3 ✓ sig.
positive regulation of DNA-templated transcription
PAX3, TP53, FOXO1, NPM1, FUS, CREB3L2
 GO:0045893 6 / 778 6.3× 2.81e-4 6.46e-3 ✓ sig.
protein autophosphorylation
ALK, FLT4, KIT
 GO:0046777 3 / 113 21.6× 3.49e-4 7.48e-3 ✓ sig.
negative regulation of apoptotic process
TP53, FOXO1, FLT4, NPM1, PAX7
 GO:0043066 5 / 524 7.8× 3.77e-4 7.84e-3 ✓ sig.
cell surface receptor protein tyrosine kinase signaling pathway
ALK, FLT4, KIT
 GO:0007169 3 / 120 20.3× 4.16e-4 8.43e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
CREB3L1, PAX3, TP53, FOXO1, NPM1, PAX7, CREB3L2
 GO:0045944 7 / 1,208 4.7× 4.54e-4 8.90e-3 ✓ sig.
osteoblast differentiation
CREB3L1, TPM4, CLTC
 GO:0001649 3 / 137 17.8× 6.13e-4 1.09e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Inflammatory myofibroblastic tumor Liver inflammatory myofibroblastic tumor 0.368 7 9.71e-21 1.46e-19 ✓ sig.
Bladder inflammatory myofibroblastic tumor Liver inflammatory myofibroblastic tumor 0.500 5 1.70e-17 2.27e-16 ✓ sig.
Bladder inflammatory myofibroblastic tumor Inflammatory myofibroblastic tumor 0.222 4 3.79e-12 3.93e-11 ✓ sig.
Congenital myopathy 4b, autosomal recessive Nemaline myopathy 1, autosomal dominant or recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital generalized hypercontractile muscle stiffness syndrome Nemaline myopathy 1, autosomal dominant or recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital generalized hypercontractile muscle stiffness syndrome Congenital myopathy 4a, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital generalized hypercontractile muscle stiffness syndrome Congenital myopathy 4b, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 4a, autosomal dominant Nemaline myopathy 1, autosomal dominant or recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 4a, autosomal dominant Congenital myopathy 4b, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cap myopathy Nemaline myopathy 1, autosomal dominant or recessive 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cap myopathy Congenital myopathy 4b, autosomal recessive 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cap myopathy Congenital myopathy 4a, autosomal dominant 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cap myopathy Congenital generalized hypercontractile muscle stiffness syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bladder inflammatory myofibroblastic tumor Congenital myopathy 4a, autosomal dominant 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Bladder inflammatory myofibroblastic tumor Nemaline myopathy 1, autosomal dominant or recessive 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Bladder inflammatory myofibroblastic tumor Congenital generalized hypercontractile muscle stiffness syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Bladder inflammatory myofibroblastic tumor Congenital myopathy 4b, autosomal recessive 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Aica-ribosiduria Bladder inflammatory myofibroblastic tumor 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Liver inflammatory myofibroblastic tumor Spastic paraplegia 57, autosomal recessive 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Liver inflammatory myofibroblastic tumor Microcephaly, developmental delay, and brittle hair and nails 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Aica-ribosiduria Liver inflammatory myofibroblastic tumor 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Inflammatory myofibroblastic tumor Microcephaly, developmental delay, and brittle hair and nails 0.059 1 1.03e-3 1.57e-3 ✓ sig.