Disease Clusters | GeDiPNet

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Cluster 164

9 diseases · 18 shared-gene connections

9 Diseases

9 Unique genes

0.310 Avg. similarity score

Anonychia Most-connected disease (6 links)

Significant edges only (q < 0.05) Spacing Colour by

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.

Anonychia Bent bone dysplasia Campomelic dysplasia Camptomelic dysplasia Cooks syndrome isolated Pierre-Robin syndrome

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Anonychia	6	6	4
Bent bone dysplasia	5	5	3
Campomelic dysplasia	5	5	1
Camptomelic dysplasia	5	5	1
Cooks syndrome	5	5	1
isolated Pierre-Robin syndrome	5	5	1
Pachyonychia congenita	2	2	4
Sebocystomatosis	2	2	1
LAMA5-related multisystemic syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SOX9	6 / 9	Anonychia, Bent bone dysplasia, Campomelic dysplasia, Camptomelic dysplasia and 2 more
KRT17	3 / 9	Anonychia, Pachyonychia congenita, Sebocystomatosis
LAMA5	2 / 9	Bent bone dysplasia, LAMA5-related multisystemic 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 ⇵
Formation of the cornified envelope KRT17, KRT16, KRT6A, KRT6B	Reactome	4 / 130	41.1×	1.58e-6	7.23e-5 ✓ sig.
Keratinization KRT17, KRT16, KRT6A, KRT6B	Reactome	4 / 152	35.1×	2.96e-6	1.23e-4 ✓ sig.
Laminin interactions COL7A1, LAMA5	Reactome	2 / 28	95.3×	1.87e-4	3.72e-3 ✓ sig.
Signaling by FGFR2 amplification mutants FGFR2	Reactome	1 / 1	1,334×	7.49e-4	1.09e-2 ✓ sig.
Signaling by FGFR2 fusions FGFR2	Reactome	1 / 1	1,334×	7.49e-4	1.09e-2 ✓ sig.
Staphylococcus aureus infection KRT17, KRT16	KEGG	2 / 99	27.0×	2.33e-3	2.55e-2 ✓ sig.
Estrogen signaling pathway KRT17, KRT16	KEGG	2 / 139	19.2×	4.54e-3	4.11e-2 ✓ sig.
FGFR2b ligand binding and activation FGFR2	Reactome	1 / 10	133×	7.47e-3	5.69e-2
Transcriptional regulation by RUNX2 SOX9	Reactome	1 / 12	111×	8.96e-3	6.42e-2
FGFR2c ligand binding and activation FGFR2	Reactome	1 / 13	103×	9.70e-3	6.74e-2
Extracellular matrix organization COL7A1	Reactome	1 / 15	89.0×	1.12e-2	7.34e-2
Anchoring fibril formation COL7A1	Reactome	1 / 15	89.0×	1.12e-2	7.34e-2
Activated point mutants of FGFR2 FGFR2	Reactome	1 / 17	78.5×	1.27e-2	7.87e-2
Phospholipase C-mediated cascade; FGFR2 FGFR2	Reactome	1 / 18	74.1×	1.34e-2	8.14e-2
Regulation of FZD by ubiquitination RSPO4	Reactome	1 / 21	63.5×	1.56e-2	8.93e-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 ⇵
morphogenesis of an epithelium KRT17, SOX9, KRT16, KRT6A	GO:0002009	4 / 51	163×	6.14e-9	1.12e-6 ✓ sig.
intermediate filament organization KRT17, KRT16, KRT6A, KRT6B	GO:0045109	4 / 70	119×	2.24e-8	3.45e-6 ✓ sig.
keratinization KRT17, KRT16, KRT6A, KRT6B	GO:0031424	4 / 73	114×	2.66e-8	3.99e-6 ✓ sig.
prostate gland morphogenesis SOX9, FGFR2	GO:0060512	2 / 5	831×	2.06e-6	1.47e-4 ✓ sig.
otic vesicle formation SOX9, FGFR2	GO:0030916	2 / 7	593×	4.32e-6	2.67e-4 ✓ sig.
lacrimal gland development SOX9, FGFR2	GO:0032808	2 / 7	593×	4.32e-6	2.67e-4 ✓ sig.
limb bud formation SOX9, FGFR2	GO:0060174	2 / 9	461×	7.41e-6	4.11e-4 ✓ sig.
branching involved in salivary gland morphogenesis FGFR2, LAMA5	GO:0060445	2 / 12	346×	1.36e-5	6.62e-4 ✓ sig.
morphogenesis of embryonic epithelium FGFR2, LAMA5	GO:0016331	2 / 13	319×	1.60e-5	7.57e-4 ✓ sig.
positive regulation of mesenchymal cell proliferation SOX9, FGFR2	GO:0002053	2 / 26	160×	6.66e-5	2.23e-3 ✓ sig.
hair follicle morphogenesis KRT17, FGFR2	GO:0031069	2 / 34	122×	1.15e-4	3.35e-3 ✓ sig.
skeletal system morphogenesis FGFR2, LAMA5	GO:0048705	2 / 45	92.3×	2.02e-4	5.08e-3 ✓ sig.
branching involved in ureteric bud morphogenesis SOX9, LAMA5	GO:0001658	2 / 45	92.3×	2.02e-4	5.08e-3 ✓ sig.
positive regulation of Wnt signaling pathway RSPO4, FGFR2	GO:0030177	2 / 48	86.5×	2.30e-4	5.57e-3 ✓ sig.
hair follicle development SOX9, LAMA5	GO:0001942	2 / 48	86.5×	2.30e-4	5.57e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Campomelic dysplasia	Camptomelic dysplasia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Campomelic dysplasia	Cooks syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Campomelic dysplasia	isolated Pierre-Robin syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Camptomelic dysplasia	Cooks syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Camptomelic dysplasia	isolated Pierre-Robin syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Cooks syndrome	isolated Pierre-Robin syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Bent bone dysplasia	LAMA5-related multisystemic syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Bent bone dysplasia	Campomelic dysplasia	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Bent bone dysplasia	Camptomelic dysplasia	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Bent bone dysplasia	Cooks syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Bent bone dysplasia	isolated Pierre-Robin syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Anonychia	Sebocystomatosis	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Anonychia	Campomelic dysplasia	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Pachyonychia congenita	Sebocystomatosis	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Anonychia	isolated Pierre-Robin syndrome	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Anonychia	Cooks syndrome	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Anonychia	Camptomelic dysplasia	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Anonychia	Pachyonychia congenita	0.125	1	1.04e-3	1.72e-3 ✓ sig.

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