Disease Clusters | GeDiPNet

← Back to all clusters

Cluster 368

5 diseases · 6 shared-gene connections

5 Diseases

12 Unique genes

0.196 Avg. similarity score

BAP1-related tumor predisposition 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.

BAP1-related tumor predisposition syndrome Mucoepidermoid carcinoma Tumor predisposition syndrome Testicular neoplasms tumor predisposition syndrome 2

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
BAP1-related tumor predisposition syndrome	3	3	1
Mucoepidermoid carcinoma	3	3	1
Tumor predisposition syndrome	3	3	6
Testicular neoplasms	2	2	7
tumor predisposition syndrome 2	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
BAP1	4 / 5	BAP1-related tumor predisposition syndrome, Mucoepidermoid carcinoma, Testicular neoplasms, Tumor predisposition syndrome
MBD4	2 / 5	Tumor predisposition syndrome, tumor predisposition syndrome 2

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 ⇵
Fanconi anemia pathway ERCC1, ERCC4, BRCA2	KEGG	3 / 54	55.6×	1.84e-5	5.59e-4 ✓ sig.
HDR through Single Strand Annealing (SSA) ERCC1, ERCC4	Reactome	2 / 37	54.1×	5.98e-4	9.16e-3 ✓ sig.
Fanconi Anemia Pathway ERCC1, ERCC4	Reactome	2 / 40	50.0×	6.99e-4	1.04e-2 ✓ sig.
Dual Incision in GG-NER ERCC1, ERCC4	Reactome	2 / 41	48.8×	7.34e-4	1.08e-2 ✓ sig.
Formation of Incision Complex in GG-NER ERCC1, ERCC4	Reactome	2 / 43	46.6×	8.08e-4	1.16e-2 ✓ sig.
Nucleotide excision repair ERCC1, ERCC4	KEGG	2 / 63	31.8×	1.73e-3	2.05e-2 ✓ sig.
Dual incision in TC-NER ERCC1, ERCC4	Reactome	2 / 66	30.3×	1.89e-3	2.19e-2 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer FGF9, KITLG	Reactome	2 / 75	26.7×	2.44e-3	2.64e-2 ✓ sig.
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks BAP1, CHEK2	Reactome	2 / 76	26.3×	2.50e-3	2.69e-2 ✓ sig.
PIP3 activates AKT signaling FGF9, KITLG	Reactome	2 / 93	21.5×	3.72e-3	3.59e-2 ✓ sig.
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling FGF9, KITLG	Reactome	2 / 103	19.4×	4.55e-3	4.12e-2 ✓ sig.
RAF/MAP kinase cascade FGF9, KITLG	Reactome	2 / 124	16.1×	6.52e-3	5.22e-2
FGFR3b ligand binding and activation FGF9	Reactome	1 / 7	143×	6.97e-3	5.45e-2
Recognition and association of DNA glycosylase with site containing an affected pyrimidine MBD4	Reactome	1 / 8	125×	7.97e-3	5.96e-2
Cleavage of the damaged pyrimidine MBD4	Reactome	1 / 8	125×	7.97e-3	5.96e-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 ⇵
cell population proliferation BAP1, ERCC1, FGF9, KITLG, BRCA2	GO:0008283	5 / 263	29.6×	3.88e-7	3.78e-5 ✓ sig.
male gonad development DMRT1, ERCC1, FGF9, KITLG	GO:0008584	4 / 117	53.2×	6.95e-7	6.18e-5 ✓ sig.
telomeric DNA-containing double minutes formation ERCC1, ERCC4	GO:0061819	2 / 3	1,038×	1.13e-6	9.16e-5 ✓ sig.
negative regulation of protection from non-homologous end joining at telomere ERCC1, ERCC4	GO:1905765	2 / 3	1,038×	1.13e-6	9.16e-5 ✓ sig.
nucleotide-excision repair ERCC1, ERCC4, BRCA2	GO:0006289	3 / 42	111×	2.29e-6	1.60e-4 ✓ sig.
negative regulation of telomere maintenance ERCC1, ERCC4	GO:0032205	2 / 5	623×	3.78e-6	2.40e-4 ✓ sig.
DNA repair ERCC1, ERCC4, BRCA2, MBD4, CHEK2	GO:0006281	5 / 420	18.5×	3.89e-6	2.46e-4 ✓ sig.
establishment of protein localization to telomere BRCA2, POT1	GO:0070200	2 / 7	445×	7.92e-6	4.34e-4 ✓ sig.
telomere maintenance ERCC1, ERCC4, POT1	GO:0000723	3 / 66	70.8×	9.05e-6	4.83e-4 ✓ sig.
developmental process involved in reproduction DMRT1, KITLG	GO:0003006	2 / 10	311×	1.70e-5	7.89e-4 ✓ sig.
DNA damage response ERCC1, ERCC4, BRCA2, MBD4, CHEK2	GO:0006974	5 / 577	13.5×	1.82e-5	8.34e-4 ✓ sig.
double-strand break repair ERCC1, BRCA2, CHEK2	GO:0006302	3 / 87	53.7×	2.08e-5	9.26e-4 ✓ sig.
UV protection ERCC1, ERCC4	GO:0009650	2 / 12	260×	2.49e-5	1.06e-3 ✓ sig.
male sex determination DMRT1, FGF9	GO:0030238	2 / 12	260×	2.49e-5	1.06e-3 ✓ sig.
replicative senescence ERCC1, CHEK2	GO:0090399	2 / 16	195×	4.51e-5	1.67e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
BAP1-related tumor predisposition syndrome	Mucoepidermoid carcinoma	0.500	1	6.49e-5	2.34e-4 ✓ sig.
BAP1-related tumor predisposition syndrome	Tumor predisposition syndrome	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Mucoepidermoid carcinoma	Tumor predisposition syndrome	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Tumor predisposition syndrome	tumor predisposition syndrome 2	0.143	1	3.90e-4	8.52e-4 ✓ sig.
BAP1-related tumor predisposition syndrome	Testicular neoplasms	0.125	1	4.55e-4	9.55e-4 ✓ sig.
Mucoepidermoid carcinoma	Testicular neoplasms	0.125	1	4.55e-4	9.55e-4 ✓ sig.

Disease Clusters?