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Cluster 583

5 diseases · 7 shared-gene connections

5 Diseases

36 Unique genes

0.446 Avg. similarity score

Pfeiffer syndrome 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.

Pfeiffer syndrome Beare-stevenson cutis gyrata syndrome Crouzon syndrome Jackson-weiss syndrome Triple negative breast cancer

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Pfeiffer syndrome	4	4	3
Beare-stevenson cutis gyrata syndrome	3	3	2
Crouzon syndrome	3	3	3
Jackson-weiss syndrome	3	3	2
Triple negative breast cancer	1	1	34

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

Gene ⇵	Member diseases ⇵	Linked diseases
FGFR2	5 / 5	Beare-stevenson cutis gyrata syndrome, Crouzon syndrome, Jackson-weiss syndrome, Pfeiffer syndrome and 1 more
FGFR1	4 / 5	Beare-stevenson cutis gyrata syndrome, Crouzon syndrome, Jackson-weiss syndrome, Pfeiffer syndrome
MDM4	2 / 5	Pfeiffer syndrome, Triple negative breast cancer

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 ⇵
Oncogene Induced Senescence ERF, MDM4, TP53	Reactome	3 / 33	30.3×	1.27e-4	2.29e-3 ✓ sig.
Stabilization of p53 MDM4, TP53	Reactome	2 / 11	60.7×	4.72e-4	6.40e-3 ✓ sig.
Central carbon metabolism in cancer FGFR2, FGFR1, TP53	KEGG	3 / 71	14.1×	1.23e-3	1.33e-2 ✓ sig.
Regulation of TP53 Activity through Methylation MDM4, TP53	Reactome	2 / 19	35.1×	1.45e-3	1.50e-2 ✓ sig.
Signaling by FGFR1 amplification mutants FGFR1	Reactome	1 / 1	334×	3.00e-3	2.54e-2 ✓ sig.
Signaling by FGFR2 amplification mutants FGFR2	Reactome	1 / 1	334×	3.00e-3	2.54e-2 ✓ sig.
Signaling by FGFR2 fusions FGFR2	Reactome	1 / 1	334×	3.00e-3	2.54e-2 ✓ sig.
Defective SLC6A18 may confer susceptibility to iminoglycinuria and/or hyperglycinuria SLC6A18	Reactome	1 / 1	334×	3.00e-3	2.54e-2 ✓ sig.
Prostate cancer FGFR2, FGFR1, TP53	KEGG	3 / 98	10.2×	3.09e-3	2.60e-2 ✓ sig.
Regulation of TP53 Degradation MDM4, TP53	Reactome	2 / 36	18.5×	5.16e-3	3.73e-2 ✓ sig.
Regulation of TP53 Expression TP53	Reactome	1 / 2	167×	5.99e-3	4.10e-2 ✓ sig.
PI3K Cascade FGFR2, FGFR1	Reactome	2 / 39	17.1×	6.04e-3	4.12e-2 ✓ sig.
Signaling by plasma membrane FGFR1 fusions FGFR1	Reactome	1 / 3	111×	8.97e-3	5.31e-2
FGFR1c and Klotho ligand binding and activation FGFR1	Reactome	1 / 3	111×	8.97e-3	5.31e-2
Gastric cancer FGFR2, TERT, TP53	KEGG	3 / 150	6.7×	1.01e-2	5.71e-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 ⇵
fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development FGFR2, FGFR1	GO:0035607	2 / 2	519×	3.61e-6	2.44e-4 ✓ sig.
orbitofrontal cortex development FGFR2, FGFR1	GO:0021769	2 / 3	346×	1.08e-5	5.78e-4 ✓ sig.
ventricular zone neuroblast division FGFR2, FGFR1	GO:0021847	2 / 3	346×	1.08e-5	5.78e-4 ✓ sig.
positive regulation of phospholipase activity FGFR2, FGFR1	GO:0010518	2 / 4	260×	2.16e-5	9.80e-4 ✓ sig.
cementum mineralization FGFR1, HACD1	GO:0071529	2 / 6	173×	5.39e-5	1.95e-3 ✓ sig.
positive regulation of Wnt signaling pathway FGFR2, LGR6, TERT	GO:0030177	3 / 48	32.4×	1.07e-4	3.25e-3 ✓ sig.
lung-associated mesenchyme development FGFR2, FGFR1	GO:0060484	2 / 9	115×	1.29e-4	3.71e-3 ✓ sig.
cellular response to hypoxia FGFR2, MDM4, TERT, TP53	GO:0071456	4 / 139	14.9×	1.44e-4	4.00e-3 ✓ sig.
chordate embryonic development FGFR2, FGFR1	GO:0043009	2 / 11	94.4×	1.96e-4	5.02e-3 ✓ sig.
epithelial to mesenchymal transition FGFR2, FGFR1, CUL5	GO:0001837	3 / 61	25.5×	2.19e-4	5.40e-3 ✓ sig.
branching involved in salivary gland morphogenesis FGFR2, FGFR1	GO:0060445	2 / 12	86.5×	2.35e-4	5.69e-3 ✓ sig.
inner ear morphogenesis FGFR2, FGFR1, FOXI1	GO:0042472	3 / 65	24.0×	2.64e-4	6.20e-3 ✓ sig.
mesenchymal cell differentiation FGFR2, FGFR1	GO:0048762	2 / 13	79.9×	2.78e-4	6.42e-3 ✓ sig.
replicative senescence TERT, TP53	GO:0090399	2 / 16	64.9×	4.26e-4	8.53e-3 ✓ sig.
entrainment of circadian clock by photoperiod NR2F6, TP53	GO:0043153	2 / 24	43.3×	9.70e-4	1.43e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Beare-stevenson cutis gyrata syndrome	Jackson-weiss syndrome	0.667	2	8.34e-9	6.60e-8 ✓ sig.
Beare-stevenson cutis gyrata syndrome	Crouzon syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Beare-stevenson cutis gyrata syndrome	Pfeiffer syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Crouzon syndrome	Jackson-weiss syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Jackson-weiss syndrome	Pfeiffer syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Crouzon syndrome	Pfeiffer syndrome	0.400	2	7.50e-8	5.34e-7 ✓ sig.
Pfeiffer syndrome	Triple negative breast cancer	0.057	2	1.32e-5	7.04e-5 ✓ sig.

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