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Cluster 621

5 diseases · 7 shared-gene connections

5 Diseases

4 Unique genes

0.329 Avg. similarity score

Intellectual developmental disorder dysmorphic facial 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.

Intellectual developmental disorder dysmorphic facial Intellectual developmental disorder, autosomal dominant 23 Intellectual disability-facial dysmorphism syndrome due to setd5 haploinsufficiency Mental retardation, autosomal dominant 23 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 ⇵
Intellectual developmental disorder dysmorphic facial	4	4	4
Intellectual developmental disorder, autosomal dominant 23	3	3	1
Intellectual disability-facial dysmorphism syndrome due to setd5 haploinsufficiency	3	3	1
Mental retardation, autosomal dominant 23	3	3	1
Congenital heart defect, intellectual disability, facial dysmorphism syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SETD5	4 / 5	Intellectual developmental disorder dysmorphic facial, Intellectual developmental disorder, autosomal dominant 23, Intellectual disability-facial dysmorphism syndrome due to setd5 haploinsufficiency, Mental retardation, autosomal dominant 23
CDK13	2 / 5	Congenital heart defect, intellectual disability, facial dysmorphism syndrome, Intellectual developmental disorder dysmorphic facial

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 ⇵
TP53 Regulates Transcription of DNA Repair Genes CDK13, CCNK	Reactome	2 / 65	92.4×	1.72e-4	2.92e-3 ✓ sig.
SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription CCNK	Reactome	1 / 32	93.8×	1.06e-2	5.90e-2
RNA Polymerase II Transcription Elongation CCNK	Reactome	1 / 59	50.9×	1.95e-2	8.46e-2
Formation of RNA Pol II elongation complex CCNK	Reactome	1 / 61	49.2×	2.02e-2	8.61e-2
RNA polymerase II transcribes snRNA genes CCNK	Reactome	1 / 74	40.6×	2.44e-2	9.62e-2
RNA Polymerase II Pre-transcription Events CCNK	Reactome	1 / 84	35.7×	2.77e-2	1.03e-1
Neutrophil degranulation CDK13	Reactome	1 / 480	6.3×	1.51e-1	2.76e-1

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 transcription elongation by RNA polymerase II CDK13, CCNK	GO:0032968	2 / 57	164×	5.46e-5	1.97e-3 ✓ sig.
regulation of signal transduction CDK13, CCNK	GO:0009966	2 / 101	92.5×	1.72e-4	4.56e-3 ✓ sig.
negative regulation of transcription by RNA polymerase III SETD5	GO:0016480	1 / 4	1,168×	8.56e-4	1.33e-2 ✓ sig.
regulation of cell cycle CDK13, CCNK	GO:0051726	2 / 262	35.7×	1.15e-3	1.58e-2 ✓ sig.
regulation of DNA-templated transcription elongation SETD5	GO:0032784	1 / 7	667×	1.50e-3	1.82e-2 ✓ sig.
radial glial cell differentiation CCDC85C	GO:0060019	1 / 8	584×	1.71e-3	1.96e-2 ✓ sig.
regulation of chromatin organization SETD5	GO:1902275	1 / 11	425×	2.35e-3	2.30e-2 ✓ sig.
positive regulation of DNA-templated transcription, elongation CCNK	GO:0032786	1 / 13	359×	2.78e-3	2.51e-2 ✓ sig.
host-mediated suppression of viral genome replication CCNK	GO:0044828	1 / 13	359×	2.78e-3	2.51e-2 ✓ sig.
negative regulation of stem cell differentiation CDK13	GO:2000737	1 / 18	260×	3.85e-3	2.94e-2 ✓ sig.
regulation of cyclin-dependent protein serine/threonine kinase activity CCNK	GO:0000079	1 / 22	212×	4.70e-3	3.25e-2 ✓ sig.
alternative mRNA splicing, via spliceosome CDK13	GO:0000380	1 / 25	187×	5.34e-3	3.43e-2 ✓ sig.
regulation of synapse assembly SETD5	GO:0051963	1 / 29	161×	6.19e-3	3.70e-2 ✓ sig.
establishment of cell polarity CCDC85C	GO:0030010	1 / 46	102×	9.81e-3	4.61e-2 ✓ sig.
establishment of protein localization CCDC85C	GO:0045184	1 / 51	91.6×	1.09e-2	4.83e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Intellectual developmental disorder, autosomal dominant 23	Mental retardation, autosomal dominant 23	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual developmental disorder, autosomal dominant 23	Intellectual disability-facial dysmorphism syndrome due to setd5 haploinsufficiency	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual disability-facial dysmorphism syndrome due to setd5 haploinsufficiency	Mental retardation, autosomal dominant 23	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Congenital heart defect, intellectual disability, facial dysmorphism syndrome	Intellectual developmental disorder dysmorphic facial	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Intellectual developmental disorder dysmorphic facial	Mental retardation, autosomal dominant 23	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Intellectual developmental disorder dysmorphic facial	Intellectual developmental disorder, autosomal dominant 23	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Intellectual developmental disorder dysmorphic facial	Intellectual disability-facial dysmorphism syndrome due to setd5 haploinsufficiency	0.200	1	2.58e-4	5.38e-4 ✓ sig.

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