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Cluster 240

8 diseases · 15 shared-gene connections

8 Diseases

8 Unique genes

0.315 Avg. similarity score

Buschke-ollendorff syndrome Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Qualitative platelet defect 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.

Qualitative platelet defect Buschke-ollendorff syndrome Dermatofibrosis lenticularis disseminata Melorheostosis Osteopoikilosis 12q14 microdeletion syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Buschke-ollendorff syndrome	5	5	1
Dermatofibrosis lenticularis disseminata	5	5	1
Melorheostosis	5	5	2
Osteopoikilosis	5	5	1
12q14 microdeletion syndrome	4	4	2
Tietz syndrome	4	4	5
Cardiofaciocutaneous syndrome 3	1	1	1
Qualitative platelet defect	1	1	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
LEMD3	6 / 8	12q14 microdeletion syndrome, Buschke-ollendorff syndrome, Dermatofibrosis lenticularis disseminata, Melorheostosis and 2 more
ABCC4	2 / 8	Qualitative platelet defect, Tietz syndrome
MAP2K1	2 / 8	Cardiofaciocutaneous syndrome 3, Melorheostosis

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 ⇵
Melanoma MITF, MAP2K1	KEGG	2 / 73	41.1×	9.97e-4	1.13e-2 ✓ sig.
Melanogenesis MITF, MAP2K1	KEGG	2 / 101	29.7×	1.90e-3	1.83e-2 ✓ sig.
Osteoclast differentiation MITF, MAP2K1	KEGG	2 / 142	21.1×	3.71e-3	2.96e-2 ✓ sig.
Conjugation of benzoate with glycine GLYATL1	Reactome	1 / 6	250×	3.99e-3	3.12e-2 ✓ sig.
Negative feedback regulation of MAPK pathway MAP2K1	Reactome	1 / 6	250×	3.99e-3	3.12e-2 ✓ sig.
Conjugation of salicylate with glycine GLYATL1	Reactome	1 / 8	188×	5.32e-3	3.80e-2 ✓ sig.
Prostanoid ligand receptors TBXA2R	Reactome	1 / 9	167×	5.98e-3	4.10e-2 ✓ sig.
Nuclear Envelope Breakdown LEMD3	Reactome	1 / 9	167×	5.98e-3	4.10e-2 ✓ sig.
MAPK3 (ERK1) activation MAP2K1	Reactome	1 / 10	150×	6.64e-3	4.39e-2 ✓ sig.
Transcriptional misregulation in cancer HMGA2, MITF	KEGG	2 / 198	15.2×	7.09e-3	4.58e-2 ✓ sig.
Frs2-mediated activation MAP2K1	Reactome	1 / 12	125×	7.97e-3	4.94e-2 ✓ sig.
Uptake and function of anthrax toxins MAP2K1	Reactome	1 / 13	115×	8.63e-3	5.19e-2
cAMP signaling pathway ABCC4, MAP2K1	KEGG	2 / 226	13.3×	9.16e-3	5.38e-2
Depolymerisation of the Nuclear Lamina LEMD3	Reactome	1 / 15	100×	9.95e-3	5.67e-2
Formation of Senescence-Associated Heterochromatin Foci (SAHF) HMGA2	Reactome	1 / 16	93.8×	1.06e-2	5.90e-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 ⇵
positive regulation of protein serine/threonine kinase activity HMGA2, MAP2K1	GO:0071902	2 / 15	311×	1.68e-5	8.10e-4 ✓ sig.
endodermal cell differentiation HMGA2, MAP2K1	GO:0035987	2 / 36	130×	1.00e-4	3.10e-3 ✓ sig.
mesodermal-endodermal cell signaling HMGA2	GO:0003131	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
thromboxane A2 signaling pathway TBXA2R	GO:0038193	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
cAMP transport ABCC4	GO:0070730	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
guanine nucleotide transmembrane transport ABCC4	GO:1903790	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
melanocyte apoptotic process MITF	GO:1902362	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
negative regulation of homotypic cell-cell adhesion MAP2K1	GO:0034111	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
Golgi inheritance MAP2K1	GO:0048313	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
positive regulation of gene expression HMGA2, MITF, MAP2K1	GO:0010628	3 / 504	13.9×	9.87e-4	1.45e-2 ✓ sig.
regulation of growth hormone secretion HMGA2	GO:0060123	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
regulation of peptide hormone secretion HMGA2	GO:0090276	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
cerebellar cortex formation MAP2K1	GO:0021697	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
regulation of RNA biosynthetic process MITF	GO:2001141	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
positive regulation of endodermal cell differentiation MAP2K1	GO:1903226	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Buschke-ollendorff syndrome	Dermatofibrosis lenticularis disseminata	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Buschke-ollendorff syndrome	Osteopoikilosis	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Dermatofibrosis lenticularis disseminata	Osteopoikilosis	0.500	1	6.46e-5	1.98e-4 ✓ sig.
12q14 microdeletion syndrome	Buschke-ollendorff syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
12q14 microdeletion syndrome	Dermatofibrosis lenticularis disseminata	0.333	1	1.29e-4	3.27e-4 ✓ sig.
12q14 microdeletion syndrome	Osteopoikilosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Buschke-ollendorff syndrome	Melorheostosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cardiofaciocutaneous syndrome 3	Melorheostosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Dermatofibrosis lenticularis disseminata	Melorheostosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Melorheostosis	Osteopoikilosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
12q14 microdeletion syndrome	Melorheostosis	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Buschke-ollendorff syndrome	Tietz syndrome	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Dermatofibrosis lenticularis disseminata	Tietz syndrome	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Osteopoikilosis	Tietz syndrome	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Qualitative platelet defect	Tietz syndrome	0.143	1	6.46e-4	1.09e-3 ✓ sig.

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