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 166

10 diseases · 19 shared-gene connections
10 Diseases
11 Unique genes
0.320 Avg. similarity score
Micropenis Most-connected disease (7 links)
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Disease Searched: Pseudovaginal perineoscrotal hypospadias 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 ⇵
Micropenis 7 7 4
Amyotrophic lateral sclerosis type 11 5 5 1
Bilateral parasagittal parieto-occipital polymicrogyria 5 5 1
Cleidocranial dysplasia with micrognathia, absent thumbs, and distal aphalangia (yunis-varon syndrome) 5 5 1
Polymicrogyria, bilateral temporooccipital 5 5 1
Yunis-varon syndrome 5 5 2
Prostatic hyperplasia 2 2 7
Pseudovaginal perineoscrotal hypospadias 2 2 1
Childhood-onset basal ganglia degeneration syndrome 1 1 1
Hypogonadotropic hypogonadism 1 with or without anosmia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FIG4 6 / 10 Amyotrophic lateral sclerosis type 11, Bilateral parasagittal parieto-occipital polymicrogyria, Cleidocranial dysplasia with micrognathia, absent thumbs, and distal aphalangia (yunis-varon syndrome), Micropenis and 2 more
SRD5A2 3 / 10 Micropenis, Prostatic hyperplasia, Pseudovaginal perineoscrotal hypospadias
ANOS1 2 / 10 Hypogonadotropic hypogonadism 1 with or without anosmia, Micropenis
VAC14 2 / 10 Childhood-onset basal ganglia degeneration syndrome, Yunis-varon syndrome
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 ⇵
Prostate cancer
SRD5A2, KLK3, PDGFB, PDGFD
 KEGG 4 / 98 44.6× 1.32e-6 5.29e-5 ✓ sig.
Synthesis of PIPs at the late endosome membrane
FIG4, VAC14
 Reactome 2 / 10 218× 3.42e-5 8.08e-4 ✓ sig.
Melanoma
FGF7, PDGFB, PDGFD
 KEGG 3 / 73 44.9× 3.43e-5 8.10e-4 ✓ sig.
Androgen biosynthesis
SRD5A2, SRD5A1
 Reactome 2 / 11 199× 4.18e-5 9.47e-4 ✓ sig.
Synthesis of PIPs at the early endosome membrane
FIG4, VAC14
 Reactome 2 / 15 146× 7.96e-5 1.58e-3 ✓ sig.
Synthesis of PIPs at the Golgi membrane
FIG4, VAC14
 Reactome 2 / 18 121× 1.16e-4 2.13e-3 ✓ sig.
PI3K-Akt signaling pathway
FGF7, PRL, PDGFB, PDGFD
 KEGG 4 / 361 12.1× 2.24e-4 3.59e-3 ✓ sig.
Signaling by PDGF
PDGFB, PDGFD
 Reactome 2 / 33 66.2× 3.97e-4 5.59e-3 ✓ sig.
Rap1 signaling pathway
FGF7, PDGFB, PDGFD
 KEGG 3 / 211 15.5× 7.95e-4 9.51e-3 ✓ sig.
Regulation of actin cytoskeleton
FGF7, PDGFB, PDGFD
 KEGG 3 / 232 14.1× 1.05e-3 1.17e-2 ✓ sig.
Ras signaling pathway
FGF7, PDGFB, PDGFD
 KEGG 3 / 237 13.8× 1.11e-3 1.23e-2 ✓ sig.
Calcium signaling pathway
FGF7, PDGFB, PDGFD
 KEGG 3 / 254 12.9× 1.36e-3 1.43e-2 ✓ sig.
Steroid hormone biosynthesis
SRD5A2, SRD5A1
 KEGG 2 / 63 34.7× 1.44e-3 1.50e-2 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
FGF7, PDGFB
 Reactome 2 / 75 29.1× 2.04e-3 1.93e-2 ✓ sig.
MAPK signaling pathway
FGF7, PDGFB, PDGFD
 KEGG 3 / 299 11.0× 2.17e-3 2.02e-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 ⇵
response to follicle-stimulating hormone
SRD5A2, SRD5A1
 GO:0032354 2 / 4 849× 1.89e-6 1.45e-4 ✓ sig.
positive regulation of cell division
FGF7, PDGFB, PDGFD
 GO:0051781 3 / 48 106× 2.59e-6 1.86e-4 ✓ sig.
positive regulation of glomerular mesangial cell proliferation
PDGFB, PDGFD
 GO:0072126 2 / 6 566× 4.72e-6 3.03e-4 ✓ sig.
female genitalia development
SRD5A2, SRD5A1
 GO:0030540 2 / 7 485× 6.60e-6 3.94e-4 ✓ sig.
androgen biosynthetic process
SRD5A2, SRD5A1
 GO:0006702 2 / 9 378× 1.13e-5 5.99e-4 ✓ sig.
hypothalamus development
SRD5A2, SRD5A1
 GO:0021854 2 / 15 227× 3.29e-5 1.35e-3 ✓ sig.
male genitalia development
SRD5A2, SRD5A1
 GO:0030539 2 / 19 179× 5.36e-5 1.94e-3 ✓ sig.
androgen metabolic process
SRD5A2, SRD5A1
 GO:0008209 2 / 20 170× 5.95e-5 2.10e-3 ✓ sig.
sex differentiation
SRD5A2, SRD5A1
 GO:0007548 2 / 26 131× 1.02e-4 3.13e-3 ✓ sig.
cellular response to platelet-derived growth factor stimulus
PDGFB, PDGFD
 GO:0036120 2 / 26 131× 1.02e-4 3.13e-3 ✓ sig.
platelet-derived growth factor receptor signaling pathway
PDGFB, PDGFD
 GO:0048008 2 / 33 103× 1.65e-4 4.42e-3 ✓ sig.
response to testosterone
SRD5A2, SRD5A1
 GO:0033574 2 / 36 94.4× 1.96e-4 5.02e-3 ✓ sig.
phosphatidylinositol biosynthetic process
FIG4, VAC14
 GO:0006661 2 / 44 77.2× 2.94e-4 6.68e-3 ✓ sig.
positive chemotaxis
FGF7, PDGFB
 GO:0050918 2 / 51 66.6× 3.95e-4 8.12e-3 ✓ sig.
positive regulation of smooth muscle cell proliferation
PDGFB, PDGFD
 GO:0048661 2 / 52 65.3× 4.11e-4 8.34e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Amyotrophic lateral sclerosis type 11 Cleidocranial dysplasia with micrognathia, absent thumbs, and distal aphalangia (yunis-varon syndrome) 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Amyotrophic lateral sclerosis type 11 Polymicrogyria, bilateral temporooccipital 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Bilateral parasagittal parieto-occipital polymicrogyria Cleidocranial dysplasia with micrognathia, absent thumbs, and distal aphalangia (yunis-varon syndrome) 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Bilateral parasagittal parieto-occipital polymicrogyria Polymicrogyria, bilateral temporooccipital 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cleidocranial dysplasia with micrognathia, absent thumbs, and distal aphalangia (yunis-varon syndrome) Polymicrogyria, bilateral temporooccipital 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Amyotrophic lateral sclerosis type 11 Bilateral parasagittal parieto-occipital polymicrogyria 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Childhood-onset basal ganglia degeneration syndrome Yunis-varon syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Polymicrogyria, bilateral temporooccipital Yunis-varon syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cleidocranial dysplasia with micrognathia, absent thumbs, and distal aphalangia (yunis-varon syndrome) Yunis-varon syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Bilateral parasagittal parieto-occipital polymicrogyria Yunis-varon syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Amyotrophic lateral sclerosis type 11 Yunis-varon syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Bilateral parasagittal parieto-occipital polymicrogyria Micropenis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Amyotrophic lateral sclerosis type 11 Micropenis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cleidocranial dysplasia with micrognathia, absent thumbs, and distal aphalangia (yunis-varon syndrome) Micropenis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Hypogonadotropic hypogonadism 1 with or without anosmia Micropenis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Micropenis Pseudovaginal perineoscrotal hypospadias 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Micropenis Polymicrogyria, bilateral temporooccipital 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Prostatic hyperplasia Pseudovaginal perineoscrotal hypospadias 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Micropenis Prostatic hyperplasia 0.091 1 1.81e-3 2.49e-3 ✓ sig.