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 102

12 diseases · 27 shared-gene connections
12 Diseases
35 Unique genes
0.258 Avg. similarity score
Congenital hypothyroidism Most-connected disease (8 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 hypothyroidism 8 8 14
Congenital hypothyroidism without goiter 7 7 6
Congenital thyroid atrophy 7 7 6
Thyroid agenesis 6 6 7
Congenital hypothyroidism due to absence of thyroid gland 5 5 4
Testicular disease 5 5 14
X-linked central congenital hypothyroidism with late-onset testicular enlargement 5 5 1
Spermatocele 3 3 8
Thyroid dyshormonogenesis 3 3 7
Genetic transient congenital hypothyroidism 2 2 1
Iodide peroxidase deficiency 2 2 1
Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PAX8 7 / 12 Congenital hypothyroidism, Congenital hypothyroidism due to absence of thyroid gland, Congenital hypothyroidism without goiter, Congenital thyroid atrophy and 3 more
IGSF1 6 / 12 Congenital hypothyroidism, Congenital hypothyroidism without goiter, Congenital thyroid atrophy, Testicular disease and 2 more
NKX2-5 5 / 12 Congenital hypothyroidism, Congenital hypothyroidism due to absence of thyroid gland, Congenital hypothyroidism without goiter, Congenital thyroid atrophy and 1 more
TSHR 5 / 12 Congenital hypothyroidism, Congenital hypothyroidism due to absence of thyroid gland, Congenital hypothyroidism without goiter, Congenital thyroid atrophy and 1 more
THRA 4 / 12 Congenital hypothyroidism, Congenital hypothyroidism without goiter, Congenital thyroid atrophy, Thyroid agenesis
TSHB 4 / 12 Congenital hypothyroidism, Congenital hypothyroidism without goiter, Congenital thyroid atrophy, Thyroid agenesis
DUOX2 3 / 12 Congenital hypothyroidism, Genetic transient congenital hypothyroidism, Thyroid dyshormonogenesis
SLC26A4 3 / 12 Congenital hypothyroidism, Congenital hypothyroidism due to absence of thyroid gland, Thyroid agenesis
TPO 3 / 12 Congenital hypothyroidism, Iodide peroxidase deficiency, Thyroid dyshormonogenesis
DUOXA2 2 / 12 Congenital hypothyroidism, Thyroid dyshormonogenesis
IYD 2 / 12 Congenital hypothyroidism, Thyroid dyshormonogenesis
PPP3CA 2 / 12 Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development, Testicular disease
SLC5A5 2 / 12 Congenital hypothyroidism, Thyroid dyshormonogenesis
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 ⇵
Thyroid hormone synthesis
PAX8, SLC26A4, TSHR, TSHB, DUOX2, DUOXA2, IYD, SLC5A5, TPO, TG
 KEGG 10 / 75 45.8× 7.85e-15 2.53e-12 ✓ sig.
Thyroxine biosynthesis
TSHB, DUOX2, IYD, SLC5A5, TPO
 Reactome 5 / 7 245× 3.26e-12 6.41e-10 ✓ sig.
Autoimmune thyroid disease
TSHR, TSHB, TPO, TG, FASLG
 KEGG 5 / 54 31.8× 4.46e-7 2.42e-5 ✓ sig.
Multifunctional anion exchangers
SLC26A4, SLC26A7
 Reactome 2 / 9 76.3× 2.93e-4 5.27e-3 ✓ sig.
Glycoprotein hormones
TSHB, INHBB
 Reactome 2 / 12 57.2× 5.35e-4 8.39e-3 ✓ sig.
Hormone ligand-binding receptors
TSHR, TSHB
 Reactome 2 / 12 57.2× 5.35e-4 8.39e-3 ✓ sig.
Defective SLC26A4 causes Pendred syndrome (PDS)
SLC26A4
 Reactome 1 / 1 343× 2.91e-3 3.01e-2 ✓ sig.
Defective SLC5A5 causes thyroid dyshormonogenesis 1 (TDH1)
SLC5A5
 Reactome 1 / 1 343× 2.91e-3 3.01e-2 ✓ sig.
G alpha (s) signalling events
TSHR, TSHB, PDE1A
 Reactome 3 / 140 7.4× 7.73e-3 5.83e-2
HSP90 chaperone cycle for steroid hormone receptors (SHR)
TUBB1, FKBP4
 Reactome 2 / 55 12.5× 1.11e-2 7.32e-2
Antagonism of Activin by Follistatin
INHBB
 Reactome 1 / 4 85.8× 1.16e-2 7.50e-2
HHAT G278V abrogates palmitoylation of Hh-Np
SHH
 Reactome 1 / 4 85.8× 1.16e-2 7.50e-2
Regulation of lipolysis in adipocytes
TSHR, TSHB
 KEGG 2 / 59 11.6× 1.27e-2 7.89e-2
FasL/ CD95L signaling
FASLG
 Reactome 1 / 5 68.6× 1.45e-2 8.53e-2
Long-term potentiation
PPP3CA, GRIN2B
 KEGG 2 / 67 10.2× 1.62e-2 9.12e-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 ⇵
thyroid gland development
NKX2-5, PAX8, THRA, TUBB1, TG, SHH
 GO:0030878 6 / 30 107× 1.58e-11 5.55e-9 ✓ sig.
thyroid hormone generation
DUOX2, SLC26A7, SLC5A5, TPO, TG
 GO:0006590 5 / 16 167× 7.36e-11 2.17e-8 ✓ sig.
iodide transport
SLC26A4, SLC26A7, SLC5A5, TG
 GO:0015705 4 / 8 267× 7.18e-10 1.67e-7 ✓ sig.
hormone biosynthetic process
DUOX2, TPO, TG
 GO:0042446 3 / 12 133× 1.31e-6 1.03e-4 ✓ sig.
thyroid-stimulating hormone signaling pathway
PAX8, TSHR
 GO:0038194 2 / 2 534× 3.41e-6 2.21e-4 ✓ sig.
apoptotic signaling pathway
INHBB, SHH, TNFSF12, FASLG
 GO:0097190 4 / 84 25.4× 1.79e-5 8.22e-4 ✓ sig.
cellular response to gonadotropin stimulus
PAX8, SLC5A5
 GO:0071371 2 / 7 153× 7.11e-5 2.35e-3 ✓ sig.
copper ion transport
FKBP4, ATP7B
 GO:0006825 2 / 11 97.1× 1.85e-4 4.79e-3 ✓ sig.
oxalate transport
SLC26A4, SLC26A7
 GO:0019532 2 / 11 97.1× 1.85e-4 4.79e-3 ✓ sig.
thyroid hormone metabolic process
IYD, TG
 GO:0042403 2 / 13 82.1× 2.62e-4 6.12e-3 ✓ sig.
sulfate transmembrane transport
SLC26A4, SLC26A7
 GO:1902358 2 / 16 66.7× 4.02e-4 8.24e-3 ✓ sig.
prostate gland development
FKBP4, SHH
 GO:0030850 2 / 16 66.7× 4.02e-4 8.24e-3 ✓ sig.
hydrogen peroxide catabolic process
DUOX2, TPO
 GO:0042744 2 / 21 50.8× 7.00e-4 1.20e-2 ✓ sig.
positive regulation of cell motility
DUOX2, DUOXA2
 GO:2000147 2 / 23 46.4× 8.41e-4 1.35e-2 ✓ sig.
cell-cell signaling
TSHR, TSHB, SHH, FASLG
 GO:0007267 4 / 234 9.1× 9.25e-4 1.44e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital hypothyroidism without goiter Congenital thyroid atrophy 0.857 6 5.41e-23 1.24e-21 ✓ sig.
Congenital hypothyroidism Thyroid agenesis 0.467 7 8.44e-23 1.92e-21 ✓ sig.
Congenital thyroid atrophy Thyroid agenesis 0.750 6 3.79e-22 8.33e-21 ✓ sig.
Congenital hypothyroidism without goiter Thyroid agenesis 0.750 6 3.79e-22 8.33e-21 ✓ sig.
Congenital hypothyroidism Congenital hypothyroidism without goiter 0.400 6 1.62e-19 3.17e-18 ✓ sig.
Congenital hypothyroidism Congenital thyroid atrophy 0.400 6 1.62e-19 3.17e-18 ✓ sig.
Congenital hypothyroidism Thyroid dyshormonogenesis 0.294 5 5.83e-15 8.78e-14 ✓ sig.
Congenital hypothyroidism due to absence of thyroid gland Thyroid agenesis 0.500 4 1.49e-14 2.18e-13 ✓ sig.
Congenital hypothyroidism Congenital hypothyroidism due to absence of thyroid gland 0.267 4 4.28e-13 5.66e-12 ✓ sig.
Congenital hypothyroidism due to absence of thyroid gland Congenital thyroid atrophy 0.375 3 1.31e-10 1.37e-9 ✓ sig.
Congenital hypothyroidism due to absence of thyroid gland Congenital hypothyroidism without goiter 0.375 3 1.31e-10 1.37e-9 ✓ sig.
Congenital hypothyroidism without goiter Testicular disease 0.105 2 1.15e-5 5.97e-5 ✓ sig.
Congenital thyroid atrophy Testicular disease 0.105 2 1.15e-5 5.97e-5 ✓ sig.
Testicular disease Thyroid agenesis 0.100 2 1.61e-5 8.16e-5 ✓ sig.
Congenital hypothyroidism without goiter X-linked central congenital hypothyroidism with late-onset testicular enlargement 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Congenital thyroid atrophy X-linked central congenital hypothyroidism with late-onset testicular enlargement 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Iodide peroxidase deficiency Thyroid dyshormonogenesis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Thyroid agenesis X-linked central congenital hypothyroidism with late-onset testicular enlargement 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Genetic transient congenital hypothyroidism Thyroid dyshormonogenesis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Congenital hypothyroidism X-linked central congenital hypothyroidism with late-onset testicular enlargement 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development Testicular disease 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Testicular disease X-linked central congenital hypothyroidism with late-onset testicular enlargement 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Congenital hypothyroidism Iodide peroxidase deficiency 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Congenital hypothyroidism Genetic transient congenital hypothyroidism 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Congenital hypothyroidism due to absence of thyroid gland Spermatocele 0.083 1 2.08e-3 2.95e-3 ✓ sig.
Congenital hypothyroidism without goiter Spermatocele 0.071 1 3.11e-3 4.09e-3 ✓ sig.
Congenital thyroid atrophy Spermatocele 0.071 1 3.11e-3 4.09e-3 ✓ sig.