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Cluster 536

5 diseases · 7 shared-gene connections

5 Diseases

3 Unique genes

0.345 Avg. similarity score

Benign familial pemphigus Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

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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.

Benign familial pemphigus Alport syndrome 2, autosomal recessive Diffuse mesangial sclerosis Hematuria, benign familial, 1 Hailey-hailey disease

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Benign familial pemphigus	4	4	2
Alport syndrome 2, autosomal recessive	3	3	1
Diffuse mesangial sclerosis	3	3	2
Hematuria, benign familial, 1	3	3	1
Hailey-hailey disease	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
COL4A4	4 / 5	Alport syndrome 2, autosomal recessive, Benign familial pemphigus, Diffuse mesangial sclerosis, Hematuria, benign familial, 1
ATP2C1	2 / 5	Benign familial pemphigus, Hailey-hailey disease

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 ⇵
Laminin interactions COL4A4, LAMB2	Reactome	2 / 28	286×	1.57e-5	4.26e-4 ✓ sig.
ECM-receptor interaction COL4A4, LAMB2	KEGG	2 / 89	90.0×	1.62e-4	2.78e-3 ✓ sig.
Small cell lung cancer COL4A4, LAMB2	KEGG	2 / 93	86.1×	1.77e-4	2.98e-3 ✓ sig.
Amoebiasis COL4A4, LAMB2	KEGG	2 / 103	77.7×	2.17e-4	3.50e-3 ✓ sig.
Focal adhesion COL4A4, LAMB2	KEGG	2 / 203	39.4×	8.43e-4	9.95e-3 ✓ sig.
Human papillomavirus infection COL4A4, LAMB2	KEGG	2 / 333	24.0×	2.26e-3	2.08e-2 ✓ sig.
PI3K-Akt signaling pathway COL4A4, LAMB2	KEGG	2 / 361	22.2×	2.65e-3	2.34e-2 ✓ sig.
Extracellular matrix organization COL4A4	Reactome	1 / 15	267×	3.74e-3	2.98e-2 ✓ sig.
Anchoring fibril formation COL4A4	Reactome	1 / 15	267×	3.74e-3	2.98e-2 ✓ sig.
Crosslinking of collagen fibrils COL4A4	Reactome	1 / 18	222×	4.49e-3	3.39e-2 ✓ sig.
NCAM1 interactions COL4A4	Reactome	1 / 21	191×	5.24e-3	3.76e-2 ✓ sig.
Pathways in cancer COL4A4, LAMB2	KEGG	2 / 533	15.0×	5.72e-3	4.00e-2 ✓ sig.
Non-integrin membrane-ECM interactions COL4A4	Reactome	1 / 24	167×	5.98e-3	4.10e-2 ✓ sig.
MET activates PTK2 signaling LAMB2	Reactome	1 / 30	133×	7.48e-3	4.73e-2 ✓ sig.
Signaling by PDGF COL4A4	Reactome	1 / 33	121×	8.22e-3	5.04e-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 ⇵
metanephric glomerular basement membrane development LAMB2	GO:0072274	1 / 1	6,229×	1.61e-4	4.34e-3 ✓ sig.
Golgi calcium ion homeostasis ATP2C1	GO:0032468	1 / 2	3,115×	3.21e-4	7.04e-3 ✓ sig.
Golgi calcium ion transport ATP2C1	GO:0032472	1 / 2	3,115×	3.21e-4	7.04e-3 ✓ sig.
trans-Golgi network membrane organization ATP2C1	GO:0098629	1 / 2	3,115×	3.21e-4	7.04e-3 ✓ sig.
metanephric podocyte development LAMB2	GO:0072249	1 / 2	3,115×	3.21e-4	7.04e-3 ✓ sig.
axon extension involved in regeneration LAMB2	GO:0048677	1 / 3	2,076×	4.82e-4	9.24e-3 ✓ sig.
intracellular manganese ion homeostasis ATP2C1	GO:0030026	1 / 5	1,246×	8.03e-4	1.28e-2 ✓ sig.
positive regulation of Golgi to plasma membrane protein transport ATP2C1	GO:0042998	1 / 6	1,038×	9.63e-4	1.42e-2 ✓ sig.
regulation of basement membrane organization LAMB2	GO:0110011	1 / 6	1,038×	9.63e-4	1.42e-2 ✓ sig.
manganese ion transport ATP2C1	GO:0006828	1 / 9	692×	1.44e-3	1.79e-2 ✓ sig.
manganese ion transmembrane transport ATP2C1	GO:0071421	1 / 9	692×	1.44e-3	1.79e-2 ✓ sig.
glomerular basement membrane development COL4A4	GO:0032836	1 / 10	623×	1.60e-3	1.88e-2 ✓ sig.
positive regulation of integrin-mediated signaling pathway LAMB2	GO:2001046	1 / 13	479×	2.09e-3	2.17e-2 ✓ sig.
astrocyte development LAMB2	GO:0014002	1 / 15	415×	2.41e-3	2.32e-2 ✓ sig.
positive regulation of muscle cell differentiation LAMB2	GO:0051149	1 / 16	389×	2.57e-3	2.40e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Alport syndrome 2, autosomal recessive	Hematuria, benign familial, 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Alport syndrome 2, autosomal recessive	Diffuse mesangial sclerosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Alport syndrome 2, autosomal recessive	Benign familial pemphigus	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Benign familial pemphigus	Hematuria, benign familial, 1	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Benign familial pemphigus	Hailey-hailey disease	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Diffuse mesangial sclerosis	Hematuria, benign familial, 1	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Benign familial pemphigus	Diffuse mesangial sclerosis	0.250	1	2.58e-4	5.38e-4 ✓ sig.

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