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 208

9 diseases · 21 shared-gene connections
9 Diseases
15 Unique genes
0.287 Avg. similarity score
Adrenocorticotropic hormone-producing pituitary gland carcinoma Most-connected disease (7 links)
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Disease Searched: Sinoatrial node dysfunction and deafness 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 ⇵
Adrenocorticotropic hormone-producing pituitary gland carcinoma 7 7 4
Breast cyst 6 6 1
Primary hyperaldosteronism-seizures-neurological abnormalities syndrome 6 6 1
Severe hypotonia 6 6 1
Sinoatrial node dysfunction and deafness 6 6 1
Brain compression 5 5 2
Large cell medulloblastoma 4 4 11
Pituitary adenoma 4, adrenocorticotropic hormone-secreting 1 1 1
X-linked female restricted facial dysmorphism, short stature, choanal atresia, intellectual disability 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CACNA1D 7 / 9 Adrenocorticotropic hormone-producing pituitary gland carcinoma, Brain compression, Breast cyst, Large cell medulloblastoma and 3 more
USP8 2 / 9 Adrenocorticotropic hormone-producing pituitary gland carcinoma, Pituitary adenoma 4, adrenocorticotropic hormone-secreting
USP9X 2 / 9 Adrenocorticotropic hormone-producing pituitary gland carcinoma, X-linked female restricted facial dysmorphism, short stature, choanal atresia, intellectual disability
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 ⇵
Downregulation of SMAD2/3:SMAD4 transcriptional activity
USP9X, NCOR1
 Reactome 2 / 22 72.8× 3.32e-4 4.86e-3 ✓ sig.
Cushing syndrome
CACNA1D, MEN1, USP8
 KEGG 3 / 155 15.5× 8.56e-4 1.01e-2 ✓ sig.
Endometrial cancer
CTNNA3, HRAS
 KEGG 2 / 59 27.1× 2.39e-3 2.17e-2 ✓ sig.
GnRH secretion
CACNA1D, HRAS
 KEGG 2 / 65 24.6× 2.89e-3 2.49e-2 ✓ sig.
RAS GTPase cycle mutants
HRAS
 Reactome 1 / 3 267× 3.74e-3 2.98e-2 ✓ sig.
Neurofascin interactions
ANK1
 Reactome 1 / 4 200× 4.99e-3 3.64e-2 ✓ sig.
Arrhythmogenic right ventricular cardiomyopathy
CACNA1D, CTNNA3
 KEGG 2 / 86 18.6× 5.01e-3 3.64e-2 ✓ sig.
Formation of the beta-catenin:TCF transactivating complex
MEN1, SMARCA4
 Reactome 2 / 88 18.2× 5.24e-3 3.76e-2 ✓ sig.
GnRH signaling pathway
CACNA1D, HRAS
 KEGG 2 / 93 17.2× 5.83e-3 4.04e-2 ✓ sig.
Activation of RAS in B cells
HRAS
 Reactome 1 / 5 160× 6.23e-3 4.21e-2 ✓ sig.
Endocrine resistance
HRAS, NCOR1
 KEGG 2 / 99 16.2× 6.59e-3 4.37e-2 ✓ sig.
Mitophagy - animal
HRAS, USP8
 KEGG 2 / 105 15.3× 7.38e-3 4.70e-2 ✓ sig.
Estrogen-stimulated signaling through PRKCZ
HRAS
 Reactome 1 / 6 133× 7.47e-3 4.73e-2 ✓ sig.
RAS signaling downstream of NF1 loss-of-function variants
HRAS
 Reactome 1 / 7 114× 8.71e-3 5.22e-2
FLT3 Signaling
HRAS
 Reactome 1 / 7 114× 8.71e-3 5.22e-2

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
negative regulation of transcription by RNA polymerase II
USP9X, CIC, MEN1, SUFU, SMARCA4, NCOR1
 GO:0000122 6 / 1,002 7.5× 7.71e-5 2.55e-3 ✓ sig.
negative regulation of androgen receptor signaling pathway
SMARCA4, NCOR1
 GO:0060766 2 / 17 147× 8.12e-5 2.65e-3 ✓ sig.
negative regulation of DNA-templated transcription
CIC, MEN1, BCLAF1, SMARCA4, NCOR1
 GO:0045892 5 / 631 9.9× 9.79e-5 3.04e-3 ✓ sig.
protein K63-linked deubiquitination
USP9X, USP8
 GO:0070536 2 / 26 95.8× 1.93e-4 4.97e-3 ✓ sig.
negative regulation of JNK cascade
MEN1, NCOR1
 GO:0046329 2 / 32 77.9× 2.94e-4 6.68e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
MEN1, SMARCA4
 GO:0045815 2 / 41 60.8× 4.84e-4 9.28e-3 ✓ sig.
regulation of heart rate by cardiac conduction
CACNA1D, CTNNA3
 GO:0086091 2 / 43 57.9× 5.33e-4 9.88e-3 ✓ sig.
intrinsic apoptotic signaling pathway
HRAS, DDX3X
 GO:0097193 2 / 45 55.4× 5.84e-4 1.06e-2 ✓ sig.
positive regulation of cellular response to drug
SUFU
 GO:2001040 1 / 1 1,246× 8.03e-4 1.28e-2 ✓ sig.
negative regulation of osteoblast differentiation
MEN1, SUFU
 GO:0045668 2 / 71 35.1× 1.45e-3 1.79e-2 ✓ sig.
smoothened signaling pathway involved in spinal cord motor neuron cell fate specification
SUFU
 GO:0021776 1 / 2 623× 1.60e-3 1.88e-2 ✓ sig.
response to DNA damage checkpoint signaling
SMC1A
 GO:0072423 1 / 2 623× 1.60e-3 1.88e-2 ✓ sig.
Ras protein signal transduction
HRAS, USP8
 GO:0007265 2 / 79 31.5× 1.79e-3 2.01e-2 ✓ sig.
positive regulation of transcription by RNA polymerase II
MEN1, BCLAF1, HRAS, SMARCA4, DDX3X
 GO:0045944 5 / 1,208 5.2× 1.95e-3 2.09e-2 ✓ sig.
smoothened signaling pathway involved in ventral spinal cord interneuron specification
SUFU
 GO:0021775 1 / 3 415× 2.41e-3 2.32e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Severe hypotonia Sinoatrial node dysfunction and deafness 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Primary hyperaldosteronism-seizures-neurological abnormalities syndrome Severe hypotonia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Primary hyperaldosteronism-seizures-neurological abnormalities syndrome Sinoatrial node dysfunction and deafness 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Breast cyst Severe hypotonia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Breast cyst Primary hyperaldosteronism-seizures-neurological abnormalities syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Breast cyst Sinoatrial node dysfunction and deafness 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain compression Breast cyst 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Brain compression Primary hyperaldosteronism-seizures-neurological abnormalities syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Brain compression Sinoatrial node dysfunction and deafness 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Brain compression Severe hypotonia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Adrenocorticotropic hormone-producing pituitary gland carcinoma X-linked female restricted facial dysmorphism, short stature, choanal atresia, intellectual disability 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Adrenocorticotropic hormone-producing pituitary gland carcinoma Breast cyst 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Adrenocorticotropic hormone-producing pituitary gland carcinoma Pituitary adenoma 4, adrenocorticotropic hormone-secreting 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Adrenocorticotropic hormone-producing pituitary gland carcinoma Severe hypotonia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Adrenocorticotropic hormone-producing pituitary gland carcinoma Sinoatrial node dysfunction and deafness 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Adrenocorticotropic hormone-producing pituitary gland carcinoma Primary hyperaldosteronism-seizures-neurological abnormalities syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Adrenocorticotropic hormone-producing pituitary gland carcinoma Brain compression 0.167 1 5.16e-4 9.13e-4 ✓ sig.
Breast cyst Large cell medulloblastoma 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Large cell medulloblastoma Primary hyperaldosteronism-seizures-neurological abnormalities syndrome 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Large cell medulloblastoma Sinoatrial node dysfunction and deafness 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Large cell medulloblastoma Severe hypotonia 0.083 1 7.10e-4 1.17e-3 ✓ sig.