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Cluster 370

5 diseases · 7 shared-gene connections

5 Diseases

9 Unique genes

0.271 Avg. similarity score

Charge 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.

Charge syndrome 8q24.3 microdeletion syndrome Intellectual developmental disorder dysmorphic cardiac short stature Verheij syndrome kabuki syndrome 2

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Charge syndrome	4	4	9
8q24.3 microdeletion syndrome	3	3	1
Intellectual developmental disorder dysmorphic cardiac short stature	3	3	1
Verheij syndrome	3	3	1
kabuki syndrome 2	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
PUF60	4 / 5	8q24.3 microdeletion syndrome, Charge syndrome, Intellectual developmental disorder dysmorphic cardiac short stature, Verheij syndrome
KDM6A	2 / 5	Charge syndrome, kabuki 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 ⇵
Formation of the beta-catenin:TCF transactivating complex EP300, KMT2D	Reactome	2 / 88	30.3×	1.85e-3	2.15e-2 ✓ sig.
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function EP300, KMT2D	Reactome	2 / 97	27.5×	2.24e-3	2.48e-2 ✓ sig.
LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production EP300	Reactome	1 / 5	267×	3.74e-3	3.59e-2 ✓ sig.
TNFR1-mediated ceramide production TNFRSF1A	Reactome	1 / 6	222×	4.49e-3	4.08e-2 ✓ sig.
Regulation of FOXO transcriptional activity by acetylation EP300	Reactome	1 / 7	191×	5.24e-3	4.50e-2 ✓ sig.
TNF signaling TNFRSF1A	Reactome	1 / 7	191×	5.24e-3	4.50e-2 ✓ sig.
PI5P Regulates TP53 Acetylation EP300	Reactome	1 / 9	148×	6.73e-3	5.32e-2
RUNX3 regulates p14-ARF EP300	Reactome	1 / 9	148×	6.73e-3	5.32e-2
Influenza A EP300, TNFRSF1A	KEGG	2 / 173	15.4×	6.95e-3	5.45e-2
Tuberculosis EP300, TNFRSF1A	KEGG	2 / 181	14.7×	7.58e-3	5.75e-2
Regulation of gene expression by Hypoxia-inducible Factor EP300	Reactome	1 / 11	121×	8.22e-3	6.07e-2
Kaposi sarcoma-associated herpesvirus infection EP300, TNFRSF1A	KEGG	2 / 196	13.6×	8.85e-3	6.37e-2
Activation of the TFAP2 (AP-2) family of transcription factors EP300	Reactome	1 / 12	111×	8.96e-3	6.42e-2
NOTCH1 Intracellular Domain Regulates Transcription EP300	Reactome	1 / 13	103×	9.70e-3	6.74e-2
TNFR1-induced proapoptotic signaling TNFRSF1A	Reactome	1 / 13	103×	9.70e-3	6.74e-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 remodeling CHD7, EP300, KDM6A, RERE	GO:0006338	4 / 320	26.0×	9.94e-6	5.19e-4 ✓ sig.
head development CHD7, WDR11	GO:0060322	2 / 21	198×	4.31e-5	1.61e-3 ✓ sig.
transcription by RNA polymerase II CHD7, EP300, TNFRSF1A	GO:0006366	3 / 261	23.9×	2.13e-4	5.27e-3 ✓ sig.
response to estrogen EP300, KMT2D	GO:0043627	2 / 49	84.7×	2.40e-4	5.74e-3 ✓ sig.
heart development EP300, KDM6A, WDR11	GO:0007507	3 / 273	22.8×	2.43e-4	5.79e-3 ✓ sig.
cell surface receptor signaling pathway via JAK-STAT EP300, TNFRSF1A	GO:0007259	2 / 67	62.0×	4.49e-4	8.89e-3 ✓ sig.
beta-catenin-TCF complex assembly KMT2D	GO:1904837	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
right ventricular compact myocardium morphogenesis CHD7	GO:0003226	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
behavioral defense response EP300	GO:0002209	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
negative regulation of protein oligomerization EP300	GO:0032460	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
swimming EP300	GO:0036268	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
peptidyl-lysine propionylation EP300	GO:0061921	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
regulation of tubulin deacetylation EP300	GO:0090043	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
peptidyl-lysine crotonylation EP300	GO:0140066	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
peptidyl-lysine butyrylation EP300	GO:0140067	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ 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	2.34e-4 ✓ sig.
8q24.3 microdeletion syndrome	Verheij syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Intellectual developmental disorder dysmorphic cardiac short stature	Verheij syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
8q24.3 microdeletion syndrome	Charge syndrome	0.100	1	5.84e-4	1.14e-3 ✓ sig.
Charge syndrome	Intellectual developmental disorder dysmorphic cardiac short stature	0.100	1	5.84e-4	1.14e-3 ✓ sig.
Charge syndrome	kabuki syndrome 2	0.100	1	5.84e-4	1.14e-3 ✓ sig.
Charge syndrome	Verheij syndrome	0.100	1	5.84e-4	1.14e-3 ✓ sig.

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