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Cluster 225

7 diseases · 11 shared-gene connections

7 Diseases

13 Unique genes

0.184 Avg. similarity score

17p13.3 microduplication 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.

17p13.3 microduplication syndrome Chromosome 17p13.3 microdeletion syndrome Clear cell sarcoma of kidney Endometrial stromal sarcoma Miller-dieker syndrome Postaxial acrofacial dysostosis

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
17p13.3 microduplication syndrome	4	4	2
Chromosome 17p13.3 microdeletion syndrome	4	4	1
Clear cell sarcoma of kidney	4	4	6
Endometrial stromal sarcoma	4	4	5
Miller-dieker syndrome	4	4	5
Postaxial acrofacial dysostosis	1	1	1
microphthalmia, syndromic 2	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
YWHAE	5 / 7	17p13.3 microduplication syndrome, Chromosome 17p13.3 microdeletion syndrome, Clear cell sarcoma of kidney, Endometrial stromal sarcoma and 1 more
BCOR	2 / 7	Clear cell sarcoma of kidney, microphthalmia, syndromic 2
DHODH	2 / 7	Miller-dieker syndrome, Postaxial acrofacial dysostosis
NUTM2B	2 / 7	Clear cell sarcoma of kidney, Endometrial stromal sarcoma
PAFAH1B1	2 / 7	17p13.3 microduplication syndrome, Miller-dieker 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 ⇵
Loss of Nlp from mitotic centrosomes PAFAH1B1, YWHAE	Reactome	2 / 70	26.4×	2.51e-3	2.69e-2 ✓ sig.
Loss of proteins required for interphase microtubule organization from the centrosome PAFAH1B1, YWHAE	Reactome	2 / 70	26.4×	2.51e-3	2.69e-2 ✓ sig.
AURKA Activation by TPX2 PAFAH1B1, YWHAE	Reactome	2 / 73	25.3×	2.72e-3	2.87e-2 ✓ sig.
Pyrimidine biosynthesis DHODH	Reactome	1 / 3	308×	3.24e-3	3.26e-2 ✓ sig.
Recruitment of mitotic centrosome proteins and complexes PAFAH1B1, YWHAE	Reactome	2 / 82	22.5×	3.42e-3	3.38e-2 ✓ sig.
Polycomb repressive complex BCOR, SUZ12	KEGG	2 / 83	22.3×	3.50e-3	3.43e-2 ✓ sig.
Regulation of PLK1 Activity at G2/M Transition PAFAH1B1, YWHAE	Reactome	2 / 88	21.0×	3.93e-3	3.73e-2 ✓ sig.
Recruitment of NuMA to mitotic centrosomes PAFAH1B1, YWHAE	Reactome	2 / 94	19.7×	4.47e-3	4.08e-2 ✓ sig.
Anchoring of the basal body to the plasma membrane PAFAH1B1, YWHAE	Reactome	2 / 98	18.9×	4.85e-3	4.30e-2 ✓ sig.
NADE modulates death signalling YWHAE	Reactome	1 / 6	154×	6.48e-3	5.19e-2
HSF1 activation YWHAE	Reactome	1 / 12	77.0×	1.29e-2	7.95e-2
Activation of BAD and translocation to mitochondria YWHAE	Reactome	1 / 12	77.0×	1.29e-2	7.95e-2
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex YWHAE	Reactome	1 / 12	77.0×	1.29e-2	7.95e-2
Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models YWHAE	Reactome	1 / 16	57.7×	1.72e-2	9.47e-2
Telomere Extension By Telomerase TERT	Reactome	1 / 16	57.7×	1.72e-2	9.47e-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 ⇵
negative regulation of transcription by RNA polymerase II BCOR, IRX2, JAZF1, SUZ12, HIC1	GO:0000122	5 / 1,002	7.2×	3.93e-4	8.11e-3 ✓ sig.
DNA strand elongation TERT	GO:0022616	1 / 1	1,437×	6.96e-4	1.19e-2 ✓ sig.
siRNA transcription TERT	GO:0140745	1 / 1	1,437×	6.96e-4	1.19e-2 ✓ sig.
positive regulation of transdifferentiation TERT	GO:1903620	1 / 1	1,437×	6.96e-4	1.19e-2 ✓ sig.
hippocampus development PAFAH1B1, YWHAE	GO:0021766	2 / 74	38.9×	1.17e-3	1.66e-2 ✓ sig.
positive regulation of cellular response to insulin stimulus MYO1C	GO:1900078	1 / 2	719×	1.39e-3	1.84e-2 ✓ sig.
proximal/distal pattern formation involved in metanephric nephron development IRX2	GO:0072272	1 / 2	719×	1.39e-3	1.84e-2 ✓ sig.
positive regulation of hair cycle TERT	GO:0042635	1 / 2	719×	1.39e-3	1.84e-2 ✓ sig.
negative regulation of tooth mineralization BCOR	GO:0070171	1 / 2	719×	1.39e-3	1.84e-2 ✓ sig.
specification of axis polarity BCOR	GO:0065001	1 / 2	719×	1.39e-3	1.84e-2 ✓ sig.
cerebral cortex development PAFAH1B1, YWHAE	GO:0021987	2 / 88	32.7×	1.65e-3	2.03e-2 ✓ sig.
establishment of planar polarity of embryonic epithelium PAFAH1B1	GO:0042249	1 / 3	479×	2.09e-3	2.31e-2 ✓ sig.
radial glia-guided pyramidal neuron migration PAFAH1B1	GO:0140650	1 / 3	479×	2.09e-3	2.31e-2 ✓ sig.
microtubule sliding PAFAH1B1	GO:0051012	1 / 3	479×	2.09e-3	2.31e-2 ✓ sig.
platelet activating factor metabolic process PAFAH1B1	GO:0046469	1 / 3	479×	2.09e-3	2.31e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
17p13.3 microduplication syndrome	Miller-dieker syndrome	0.333	2	8.44e-8	6.27e-7 ✓ sig.
Clear cell sarcoma of kidney	Endometrial stromal sarcoma	0.200	2	1.26e-6	7.70e-6 ✓ sig.
17p13.3 microduplication syndrome	Chromosome 17p13.3 microdeletion syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Chromosome 17p13.3 microdeletion syndrome	Endometrial stromal sarcoma	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Chromosome 17p13.3 microdeletion syndrome	Miller-dieker syndrome	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Miller-dieker syndrome	Postaxial acrofacial dysostosis	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Chromosome 17p13.3 microdeletion syndrome	Clear cell sarcoma of kidney	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Clear cell sarcoma of kidney	microphthalmia, syndromic 2	0.143	1	3.90e-4	8.52e-4 ✓ sig.
17p13.3 microduplication syndrome	Endometrial stromal sarcoma	0.143	1	6.49e-4	1.22e-3 ✓ sig.
17p13.3 microduplication syndrome	Clear cell sarcoma of kidney	0.125	1	7.79e-4	1.39e-3 ✓ sig.
Endometrial stromal sarcoma	Miller-dieker syndrome	0.100	1	1.62e-3	2.44e-3 ✓ sig.

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