Disease Clusters | GeDiPNet

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Cluster 283

6 diseases · 10 shared-gene connections

6 Diseases

33 Unique genes

0.087 Avg. similarity score

Adrenal gland neoplasms Most-connected disease (4 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.

Adrenal gland neoplasms Corneal disease Corneal edema pitt-hopkins syndrome Paranoia White spongue nevus

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Adrenal gland neoplasms	4	4	7
Corneal disease	4	4	12
Corneal edema	4	4	4
pitt-hopkins syndrome	4	4	1
Paranoia	3	3	12
White spongue nevus	1	1	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
TCF4	5 / 6	Adrenal gland neoplasms, Corneal disease, Corneal edema, Paranoia and 1 more
KRT4	2 / 6	Corneal disease, White spongue nevus

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 ⇵
MET activates PTK2 signaling COL24A1, COL5A1, LAMB1	Reactome	3 / 30	36.4×	7.30e-5	1.73e-3 ✓ sig.
Synthesis of bile acids and bile salts via 27-hydroxycholesterol RXRA, AKR1C4	Reactome	2 / 15	48.5×	7.52e-4	1.10e-2 ✓ sig.
IL-6-type cytokine receptor ligand interactions TYK2, LIFR	Reactome	2 / 17	42.8×	9.70e-4	1.33e-2 ✓ sig.
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol RXRA, AKR1C4	Reactome	2 / 24	30.3×	1.95e-3	2.23e-2 ✓ sig.
Dopamine clearance from the synaptic cleft SLC6A3	Reactome	1 / 1	364×	2.75e-3	2.89e-2 ✓ sig.
Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) SLC6A3	Reactome	1 / 1	364×	2.75e-3	2.89e-2 ✓ sig.
Th17 cell differentiation RXRA, HLA-DRB4, TYK2	KEGG	3 / 109	10.0×	3.25e-3	3.26e-2 ✓ sig.
Toxoplasmosis LAMB1, HLA-DRB4, TYK2	KEGG	3 / 112	9.7×	3.51e-3	3.43e-2 ✓ sig.
Allograft rejection HLA-A, HLA-DRB4	KEGG	2 / 39	18.7×	5.09e-3	4.43e-2 ✓ sig.
Formation of the cornified envelope KRT3, KRT4, KRT13	Reactome	3 / 130	8.4×	5.33e-3	4.57e-2 ✓ sig.
N-glycan trimming and elongation in the cis-Golgi MANEA	Reactome	1 / 2	182×	5.49e-3	4.65e-2 ✓ sig.
Type I diabetes mellitus HLA-A, HLA-DRB4	KEGG	2 / 44	16.5×	6.44e-3	5.18e-2
Collagen chain trimerization COL24A1, COL5A1	Reactome	2 / 44	16.5×	6.44e-3	5.18e-2
Graft-versus-host disease HLA-A, HLA-DRB4	KEGG	2 / 45	16.2×	6.73e-3	5.32e-2
Keratinization KRT3, KRT4, KRT13	Reactome	3 / 152	7.2×	8.21e-3	6.07e-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 ⇵
dopamine catabolic process DBH, SLC6A3	GO:0042420	2 / 11	103×	1.65e-4	4.39e-3 ✓ sig.
intermediate filament organization KRT3, KRT4, KRT13	GO:0045109	3 / 70	24.3×	2.53e-4	5.98e-3 ✓ sig.
maternal behavior MBD2, DBH	GO:0042711	2 / 14	80.9×	2.72e-4	6.26e-3 ✓ sig.
response to pain TAC1, DBH	GO:0048265	2 / 19	59.6×	5.08e-4	9.66e-3 ✓ sig.
epithelial cell differentiation KRT3, KRT4, KRT13	GO:0030855	3 / 110	15.4×	9.52e-4	1.47e-2 ✓ sig.
integrin biosynthetic process COL5A1	GO:0045112	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
glycolate metabolic process IGF1	GO:0009441	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
muscle hypertrophy IGF1	GO:0014896	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
negative regulation of oocyte development IGF1	GO:0060283	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
regulation of vascular associated smooth muscle cell proliferation DBH	GO:1904705	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
neuronal-glial interaction involved in cerebral cortex radial glia guided migration LAMB1	GO:0021812	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
associative learning TAC1, DBH	GO:0008306	2 / 40	28.3×	2.26e-3	2.42e-2 ✓ sig.
blood vessel remodeling IGF1, DBH	GO:0001974	2 / 42	27.0×	2.49e-3	2.56e-2 ✓ sig.
antigen processing and presentation HLA-A, HLA-DRB4	GO:0019882	2 / 48	23.6×	3.24e-3	2.94e-2 ✓ sig.
negative regulation of endodermal cell differentiation COL5A1	GO:1903225	1 / 2	283×	3.53e-3	3.08e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Corneal edema	pitt-hopkins syndrome	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Adrenal gland neoplasms	pitt-hopkins syndrome	0.125	1	4.55e-4	9.55e-4 ✓ sig.
Corneal disease	pitt-hopkins syndrome	0.077	1	7.79e-4	1.39e-3 ✓ sig.
Paranoia	pitt-hopkins syndrome	0.077	1	7.79e-4	1.39e-3 ✓ sig.
Corneal disease	White spongue nevus	0.071	1	1.56e-3	2.36e-3 ✓ sig.
Adrenal gland neoplasms	Corneal edema	0.091	1	1.82e-3	2.66e-3 ✓ sig.
Corneal disease	Corneal edema	0.063	1	3.11e-3	4.09e-3 ✓ sig.
Corneal edema	Paranoia	0.063	1	3.11e-3	4.09e-3 ✓ sig.
Adrenal gland neoplasms	Corneal disease	0.053	1	5.44e-3	6.63e-3 ✓ sig.
Adrenal gland neoplasms	Paranoia	0.053	1	5.44e-3	6.63e-3 ✓ sig.

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