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Cluster 224

7 diseases · 11 shared-gene connections

7 Diseases

44 Unique genes

0.176 Avg. similarity score

syndromic intellectual disability Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: syndromic intellectual disability 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.

syndromic intellectual disability 8q24.3 microdeletion syndrome Intellectual developmental disorder dysmorphic cardiac short stature Verheij syndrome Charge syndrome Congenital heart defect, intellectual disability, facial dysmorphism syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
syndromic intellectual disability	5	5	36
8q24.3 microdeletion syndrome	4	4	1
Intellectual developmental disorder dysmorphic cardiac short stature	4	4	1
Verheij syndrome	4	4	1
Charge syndrome	3	3	9
Congenital heart defect, intellectual disability, facial dysmorphism syndrome	1	1	1
Diets-jongmans syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
PUF60	5 / 7	8q24.3 microdeletion syndrome, Charge syndrome, Intellectual developmental disorder dysmorphic cardiac short stature, syndromic intellectual disability and 1 more
CDK13	2 / 7	Congenital heart defect, intellectual disability, facial dysmorphism syndrome, syndromic intellectual disability
KDM3B	2 / 7	Diets-jongmans syndrome, syndromic intellectual disability

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 ⇵
Regulation of TP53 Activity through Acetylation EP300, KAT6A, CHD4	Reactome	3 / 23	35.6×	7.72e-5	1.89e-3 ✓ sig.
Polycomb repressive complex EP300, AUTS2, ASXL2, ASXL3	KEGG	4 / 83	13.2×	2.33e-4	4.52e-3 ✓ sig.
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known EP300, AUTS2, CSNK2A1	Reactome	3 / 38	21.5×	3.54e-4	6.31e-3 ✓ sig.
DCC mediated attractive signaling RAC1, TRIO	Reactome	2 / 11	49.6×	7.07e-4	1.08e-2 ✓ sig.
HDMs demethylate histones KDM6A, KDM3B, KDM6B	Reactome	3 / 50	16.4×	7.97e-4	1.19e-2 ✓ sig.
Lysine degradation KMT2D, KMT2C, NSD2	KEGG	3 / 63	13.0×	1.56e-3	1.98e-2 ✓ sig.
Transcriptional regulation of white adipocyte differentiation EP300, MED13L, MED23	Reactome	3 / 67	12.2×	1.87e-3	2.26e-2 ✓ sig.
PKMTs methylate histone lysines KMT2D, KMT2C, NSD2	Reactome	3 / 71	11.5×	2.20e-3	2.54e-2 ✓ sig.
Signal transduction by L1 CSNK2A1, RAC1	Reactome	2 / 21	26.0×	2.64e-3	2.89e-2 ✓ sig.
Adherens junction EP300, CSNK2A1, RAC1	KEGG	3 / 93	8.8×	4.73e-3	4.37e-2 ✓ sig.
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function EP300, KMT2D, KMT2C	Reactome	3 / 97	8.4×	5.32e-3	4.72e-2 ✓ sig.
NGF-stimulated transcription EP300, CHD4	Reactome	2 / 35	15.6×	7.23e-3	5.77e-2
Processing of Capped Intron-Containing Pre-mRNA HNRNPR, HNRNPH1	Reactome	2 / 37	14.8×	8.05e-3	6.17e-2
PPARA activates gene expression EP300, MED13L, MED23	Reactome	3 / 115	7.1×	8.52e-3	6.39e-2
NRAGE signals death through JNK RAC1, TRIO	Reactome	2 / 55	9.9×	1.72e-2	9.85e-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 ⇵
chromatin organization CHD7, KDM6A, KMT2D, KDM3B, BPTF, CTCF, H1-4, KAT6A, KDM6B, KMT2C, CHD4, BRD4	GO:0006325	13 / 449	12.3×	1.97e-11	6.84e-9 ✓ sig.
chromatin remodeling CHD7, EP300, KDM6A, RERE, KDM3B, BPTF, KDM6B, KMT2C, CHD4, BRD4, NSD2	GO:0006338	11 / 320	14.6×	1.45e-10	4.07e-8 ✓ sig.
positive regulation of transcription by RNA polymerase II CHD7, EP300, KMT2D, TNFRSF1A, CDK13, AUTS2, ASXL2, ASXL3, BPTF, CTCF, KDM6B, KMT2C	GO:0045944	16 / 1,208	5.6×	6.25e-9	1.13e-6 ✓ sig.
regulation of DNA-templated transcription CHD7, EP300, KMT2D, RERE, ASXL2, ASXL3, BPTF, CTCF, KAT6A, KMT2C, HOXA1, MEIS2	GO:0006355	15 / 1,454	4.4×	5.72e-7	5.36e-5 ✓ sig.
positive regulation of T-helper 17 cell lineage commitment EP300, BRD4	GO:2000330	2 / 8	106×	1.50e-4	4.24e-3 ✓ sig.
N-terminal protein amino acid acetylation NAA15, NAA20	GO:0006474	2 / 8	106×	1.50e-4	4.24e-3 ✓ sig.
animal organ morphogenesis EP300, ASXL2, ASXL3, MEIS2	GO:0009887	4 / 130	13.1×	2.45e-4	6.02e-3 ✓ sig.
positive regulation of transcription elongation by RNA polymerase II CDK13, BRD4, MED23	GO:0032968	3 / 57	22.4×	3.26e-4	7.35e-3 ✓ sig.
protein acetylation EP300, KAT6A	GO:0006473	2 / 13	65.3×	4.16e-4	8.73e-3 ✓ sig.
heart development EP300, KDM6A, WDR11, CTCF, KDM6B	GO:0007507	5 / 273	7.8×	4.37e-4	9.01e-3 ✓ sig.
cognition CHD7, SOBP, HOXA1	GO:0050890	3 / 64	19.9×	4.59e-4	9.34e-3 ✓ sig.
aggrephagy CSNK2A1, WDFY3	GO:0035973	2 / 15	56.6×	5.58e-4	1.06e-2 ✓ sig.
regulation of transcription by RNA polymerase II EP300, KDM3B, BPTF, CSNK2A1, CTCF, H1-4, KAT6A, HOXA1, MED13L, BRD4, MED23	GO:0006357	11 / 1,602	2.9×	9.60e-4	1.52e-2 ✓ sig.
methylation KMT2D, KMT2C, NSUN2, NSD2	GO:0032259	4 / 191	8.9×	1.04e-3	1.61e-2 ✓ sig.
head development CHD7, WDR11	GO:0060322	2 / 21	40.4×	1.11e-3	1.67e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
8q24.3 microdeletion syndrome	Intellectual developmental disorder dysmorphic cardiac short stature	0.500	1	6.49e-5	2.33e-4 ✓ sig.
8q24.3 microdeletion syndrome	Verheij syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Intellectual developmental disorder dysmorphic cardiac short stature	Verheij syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
8q24.3 microdeletion syndrome	Charge syndrome	0.100	1	5.84e-4	1.16e-3 ✓ sig.
Charge syndrome	Intellectual developmental disorder dysmorphic cardiac short stature	0.100	1	5.84e-4	1.16e-3 ✓ sig.
Charge syndrome	Verheij syndrome	0.100	1	5.84e-4	1.16e-3 ✓ sig.
8q24.3 microdeletion syndrome	syndromic intellectual disability	0.027	1	2.34e-3	3.24e-3 ✓ sig.
Congenital heart defect, intellectual disability, facial dysmorphism syndrome	syndromic intellectual disability	0.027	1	2.34e-3	3.24e-3 ✓ sig.
Diets-jongmans syndrome	syndromic intellectual disability	0.027	1	2.34e-3	3.24e-3 ✓ sig.
Intellectual developmental disorder dysmorphic cardiac short stature	syndromic intellectual disability	0.027	1	2.34e-3	3.24e-3 ✓ sig.
syndromic intellectual disability	Verheij syndrome	0.027	1	2.34e-3	3.24e-3 ✓ sig.

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