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Cluster 533

5 diseases · 6 shared-gene connections

5 Diseases

14 Unique genes

0.209 Avg. similarity score

Cornelia de lange 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.

Cornelia de lange syndrome De lange syndrome Nut midline carcinoma Wiedemann-steiner syndrome Alazami-yuan syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cornelia de lange syndrome	4	4	10
De lange syndrome	3	3	6
Nut midline carcinoma	2	2	3
Wiedemann-steiner syndrome	2	2	5
Alazami-yuan syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
BRD4	3 / 5	Cornelia de lange syndrome, De lange syndrome, Nut midline carcinoma
SMC1A	3 / 5	Cornelia de lange syndrome, De lange syndrome, Wiedemann-steiner syndrome
SMC3	3 / 5	Cornelia de lange syndrome, De lange syndrome, Wiedemann-steiner syndrome
HDAC8	2 / 5	Cornelia de lange syndrome, De lange syndrome
KMT2A	2 / 5	Cornelia de lange syndrome, Wiedemann-steiner syndrome
NIPBL	2 / 5	Cornelia de lange syndrome, De lange syndrome
RAD21	2 / 5	Cornelia de lange syndrome, De lange syndrome
TAF6	2 / 5	Alazami-yuan syndrome, Cornelia de lange 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 ⇵
Cohesin Loading onto Chromatin NIPBL, RAD21, SMC1A, SMC3	Reactome	4 / 10	343×	2.42e-10	2.59e-8 ✓ sig.
Establishment of Sister Chromatid Cohesion RAD21, SMC1A, SMC3	Reactome	3 / 11	234×	2.07e-7	1.06e-5 ✓ sig.
Cell cycle HDAC8, NIPBL, RAD21, SMC1A, SMC3	KEGG	5 / 158	27.1×	6.73e-7	2.96e-5 ✓ sig.
Resolution of Sister Chromatid Cohesion HDAC8, RAD21, SMC1A, SMC3	Reactome	4 / 126	27.2×	1.07e-5	3.07e-4 ✓ sig.
Separation of Sister Chromatids HDAC8, RAD21, SMC1A, SMC3	Reactome	4 / 190	18.1×	5.37e-5	1.15e-3 ✓ sig.
SUMOylation of DNA damage response and repair proteins RAD21, SMC1A, SMC3	Reactome	3 / 77	33.4×	8.77e-5	1.71e-3 ✓ sig.
Estrogen-dependent gene expression RAD21, SMC1A, SMC3	Reactome	3 / 150	17.2×	6.28e-4	7.98e-3 ✓ sig.
RNA Polymerase II Pre-transcription Events TAF6, AFF4	Reactome	2 / 84	20.4×	4.17e-3	3.21e-2 ✓ sig.
Oocyte meiosis SMC1A, SMC3	KEGG	2 / 138	12.4×	1.09e-2	6.01e-2
tRNA modification in the nucleus and cytosol TRMT61A	Reactome	1 / 19	45.2×	2.19e-2	9.03e-2
Notch-HLH transcription pathway HDAC8	Reactome	1 / 28	30.6×	3.22e-2	1.13e-1
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ARID1B	Reactome	1 / 38	22.6×	4.34e-2	1.33e-1
Basal transcription factors TAF6	KEGG	1 / 44	19.5×	5.01e-2	1.45e-1
RNA Polymerase II Promoter Escape TAF6	Reactome	1 / 47	18.3×	5.34e-2	1.50e-1
RNA Polymerase II Transcription Pre-Initiation And Promoter Opening TAF6	Reactome	1 / 47	18.3×	5.34e-2	1.50e-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 ⇵
establishment of mitotic sister chromatid cohesion NIPBL, RAD21, SMC1A, SMC3	GO:0034087	4 / 7	763×	6.89e-12	2.71e-9 ✓ sig.
mitotic sister chromatid cohesion HDAC8, NIPBL, SMC1A, SMC3	GO:0007064	4 / 16	334×	3.57e-10	9.51e-8 ✓ sig.
establishment of meiotic sister chromatid cohesion RAD21, SMC1A, SMC3	GO:0034089	3 / 4	1,001×	1.34e-9	3.00e-7 ✓ sig.
sister chromatid cohesion RAD21, SMC1A, SMC3	GO:0007062	3 / 20	200×	3.79e-7	3.85e-5 ✓ sig.
chromatin organization BRD4, HDAC8, KMT2A, ARID1B, CHD7, BRD3	GO:0006325	6 / 449	17.8×	4.75e-7	4.67e-5 ✓ sig.
chromatin remodeling BRD4, NIPBL, ARID1B, CHD7, BRD3	GO:0006338	5 / 320	20.9×	2.52e-6	1.83e-4 ✓ sig.
ear morphogenesis NIPBL, CHD7	GO:0042471	2 / 5	534×	5.21e-6	3.27e-4 ✓ sig.
replication-born double-strand break repair via sister chromatid exchange NIPBL, RAD21	GO:1990414	2 / 6	445×	7.80e-6	4.51e-4 ✓ sig.
cognition NIPBL, KMT2A, CHD7	GO:0050890	3 / 64	62.6×	1.36e-5	6.89e-4 ✓ sig.
DNA damage response BRD4, NIPBL, RAD21, SMC1A, SMC3	GO:0006974	5 / 577	11.6×	4.38e-5	1.67e-3 ✓ sig.
chromatin looping NIPBL, RAD21	GO:0140588	2 / 14	191×	4.72e-5	1.77e-3 ✓ sig.
regulation of gene expression NIPBL, KMT2A, AFF4, CHD7	GO:0010468	4 / 402	13.3×	1.78e-4	4.68e-3 ✓ sig.
protein localization to chromatin RAD21, BRD3	GO:0071168	2 / 31	86.1×	2.39e-4	5.76e-3 ✓ sig.
positive regulation of multicellular organism growth NIPBL, CHD7	GO:0040018	2 / 34	78.5×	2.88e-4	6.59e-3 ✓ sig.
mitotic sister chromatid segregation NIPBL, SMC1A	GO:0000070	2 / 38	70.3×	3.61e-4	7.64e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Cornelia de lange syndrome	De lange syndrome	0.545	6	1.10e-20	1.64e-19 ✓ sig.
Cornelia de lange syndrome	Wiedemann-steiner syndrome	0.231	3	1.94e-9	1.63e-8 ✓ sig.
De lange syndrome	Wiedemann-steiner syndrome	0.200	2	1.25e-6	7.51e-6 ✓ sig.
Alazami-yuan syndrome	Cornelia de lange syndrome	0.091	1	6.46e-4	1.09e-3 ✓ sig.
De lange syndrome	Nut midline carcinoma	0.111	1	1.16e-3	1.73e-3 ✓ sig.
Cornelia de lange syndrome	Nut midline carcinoma	0.077	1	1.94e-3	2.65e-3 ✓ sig.

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