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Cluster 419

5 diseases · 6 shared-gene connections

5 Diseases

530 Unique genes

0.270 Avg. similarity score

Coloboma, cleft lip-palate and mental retardation syndrome Most-connected disease (3 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.

Coloboma, cleft lip-palate and mental retardation syndrome Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or impaired intellectual development Uveal coloboma-cleft lip and palate-intellectual disability Breast neoplasms Zunich neuroectodermal syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Coloboma, cleft lip-palate and mental retardation syndrome	3	3	1
Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or impaired intellectual development	3	3	2
Uveal coloboma-cleft lip and palate-intellectual disability	3	3	1
Breast neoplasms	2	2	0
Zunich neuroectodermal syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
YAP1	4 / 5	Breast neoplasms, Coloboma, cleft lip-palate and mental retardation syndrome, Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or impaired intellectual development, Uveal coloboma-cleft lip and palate-intellectual disability
PIGL	2 / 5	Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or impaired intellectual development, Zunich neuroectodermal 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 ⇵
Cellular senescence CDK2, CDK4, CDK6, CXCL8, KRAS	KEGG	5 / 157	22.5×	1.95e-6	8.60e-5 ✓ sig.
Pancreatic cancer CDK4, CDK6, KRAS, RAD51	KEGG	4 / 77	36.7×	3.49e-6	1.41e-4 ✓ sig.
Pathways in cancer CDK2, CDK4, CDK6, CXCL8, KRAS, LRP6, RAD51	KEGG	7 / 533	9.3×	4.30e-6	1.68e-4 ✓ sig.
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 CDK4, CDK6	Reactome	2 / 3	471×	5.65e-6	2.10e-4 ✓ sig.
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 CDK4, CDK6	Reactome	2 / 3	471×	5.65e-6	2.10e-4 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications CCL2, CDK4, CXCL8, KRAS	KEGG	4 / 101	28.0×	1.03e-5	3.44e-4 ✓ sig.
Human cytomegalovirus infection CCL2, CDK4, CDK6, CXCL8, KRAS	KEGG	5 / 226	15.6×	1.16e-5	3.80e-4 ✓ sig.
Senescence-Associated Secretory Phenotype (SASP) CDK2, CDK4, CDK6, CXCL8	Reactome	4 / 111	25.5×	1.50e-5	4.71e-4 ✓ sig.
Bladder cancer CDK4, CXCL8, KRAS	KEGG	3 / 41	51.7×	2.43e-5	7.00e-4 ✓ sig.
PTK6 Regulates Cell Cycle CDK2, CDK4	Reactome	2 / 6	235×	2.82e-5	7.91e-4 ✓ sig.
Measles CDK2, CDK4, CDK6, TLR9	KEGG	4 / 139	20.3×	3.64e-5	9.81e-4 ✓ sig.
Malaria CCL2, CXCL8, TLR9	KEGG	3 / 50	42.4×	4.43e-5	1.16e-3 ✓ sig.
Breast cancer CDK4, CDK6, KRAS, LRP6	KEGG	4 / 148	19.1×	4.65e-5	1.20e-3 ✓ sig.
Cell cycle CDK2, CDK4, CDK6, CDT1	KEGG	4 / 158	17.9×	6.01e-5	1.48e-3 ✓ sig.
Hepatitis C CDK2, CDK4, CDK6, KRAS	KEGG	4 / 159	17.8×	6.15e-5	1.51e-3 ✓ 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 ⇵
regulation of G2/M transition of mitotic cell cycle CDK2, CDK4, CDK6	GO:0010389	3 / 15	220×	2.83e-7	2.90e-5 ✓ sig.
positive regulation of gene expression YAP1, CCL2, CDK6, CXCL8, KRAS, TLR9	GO:0010628	6 / 504	13.1×	3.59e-6	2.30e-4 ✓ sig.
cellular response to lipopolysaccharide CCL2, CDK4, CXCL8, TLR9	GO:0071222	4 / 187	23.5×	2.09e-5	9.29e-4 ✓ sig.
regulation of gene expression YAP1, CDK2, CDK4, CDK6, PRMT5	GO:0010468	5 / 402	13.7×	2.25e-5	9.83e-4 ✓ sig.
cell division CDK2, CDK4, CDK6, CDT1, KIFC1	GO:0051301	5 / 406	13.5×	2.36e-5	1.02e-3 ✓ sig.
G1/S transition of mitotic cell cycle CDK2, CDK4, CDK6	GO:0000082	3 / 85	38.8×	5.90e-5	2.03e-3 ✓ sig.
negative regulation of epithelial cell differentiation YAP1, KRAS	GO:0030857	2 / 17	129×	1.05e-4	3.14e-3 ✓ sig.
signal transduction CCL2, CDK2, CDK4, CDK6, CXCL8, KRAS, ROR2, TLR9	GO:0007165	8 / 2,125	4.1×	2.60e-4	6.08e-3 ✓ sig.
cellular response to gamma radiation YAP1, RAD51	GO:0071480	2 / 28	78.5×	2.90e-4	6.56e-3 ✓ sig.
positive regulation of DNA replication CDK2, CDT1	GO:0045740	2 / 29	75.8×	3.12e-4	6.91e-3 ✓ sig.
cellular response to fibroblast growth factor stimulus CCL2, CXCL8	GO:0044344	2 / 33	66.6×	4.05e-4	8.28e-3 ✓ sig.
helper T cell extravasation CCL2	GO:0035684	1 / 1	1,099×	9.10e-4	1.42e-2 ✓ sig.
chemokine (C-C motif) ligand 2 signaling pathway CCL2	GO:0038148	1 / 1	1,099×	9.10e-4	1.42e-2 ✓ sig.
regulation of single stranded viral RNA replication via double stranded DNA intermediate CXCL8	GO:0045091	1 / 1	1,099×	9.10e-4	1.42e-2 ✓ sig.
response to mineralocorticoid KRAS	GO:0051385	1 / 1	1,099×	9.10e-4	1.42e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Coloboma, cleft lip-palate and mental retardation syndrome	Uveal coloboma-cleft lip and palate-intellectual disability	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Coloboma, cleft lip-palate and mental retardation syndrome	Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or impaired intellectual development	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or impaired intellectual development	Uveal coloboma-cleft lip and palate-intellectual disability	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or impaired intellectual development	Zunich neuroectodermal syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Breast neoplasms	Coloboma, cleft lip-palate and mental retardation syndrome	0.059	1	1.04e-3	1.72e-3 ✓ sig.
Breast neoplasms	Uveal coloboma-cleft lip and palate-intellectual disability	0.059	1	1.04e-3	1.72e-3 ✓ sig.

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