Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

← Back to all clusters

Cluster 301

6 diseases · 9 shared-gene connections
6 Diseases
13 Unique genes
0.186 Avg. similarity score
Cornelia de lange syndrome Most-connected disease (5 links)
Log in to save this analysis

Save This Analysis

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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Cornelia de lange syndrome 5 5 10
De lange syndrome 4 4 6
Congenital muscular hypertrophy-cerebral syndrome 3 3 1
Wiedemann-steiner syndrome 3 3 5
Wilson-turner syndrome 2 2 2
Alazami-yuan syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SMC1A 4 / 6 Congenital muscular hypertrophy-cerebral syndrome, Cornelia de lange syndrome, De lange syndrome, Wiedemann-steiner syndrome
HDAC8 3 / 6 Cornelia de lange syndrome, De lange syndrome, Wilson-turner syndrome
SMC3 3 / 6 Cornelia de lange syndrome, De lange syndrome, Wiedemann-steiner syndrome
BRD4 2 / 6 Cornelia de lange syndrome, De lange syndrome
KMT2A 2 / 6 Cornelia de lange syndrome, Wiedemann-steiner syndrome
NIPBL 2 / 6 Cornelia de lange syndrome, De lange syndrome
RAD21 2 / 6 Cornelia de lange syndrome, De lange syndrome
TAF6 2 / 6 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
SMC1A, NIPBL, RAD21, SMC3
 Reactome 4 / 10 370× 1.73e-10 2.38e-8 ✓ sig.
Establishment of Sister Chromatid Cohesion
SMC1A, RAD21, SMC3
 Reactome 3 / 11 252× 1.63e-7 9.98e-6 ✓ sig.
Cell cycle
SMC1A, HDAC8, NIPBL, RAD21, SMC3
 KEGG 5 / 158 29.2× 4.37e-7 2.38e-5 ✓ sig.
Resolution of Sister Chromatid Cohesion
SMC1A, HDAC8, RAD21, SMC3
 Reactome 4 / 126 29.3× 7.68e-6 2.68e-4 ✓ sig.
Separation of Sister Chromatids
SMC1A, HDAC8, RAD21, SMC3
 Reactome 4 / 190 19.4× 3.88e-5 1.04e-3 ✓ sig.
SUMOylation of DNA damage response and repair proteins
SMC1A, RAD21, SMC3
 Reactome 3 / 77 36.0× 6.92e-5 1.66e-3 ✓ sig.
Estrogen-dependent gene expression
SMC1A, RAD21, SMC3
 Reactome 3 / 150 18.5× 4.98e-4 7.95e-3 ✓ sig.
RNA Polymerase II Pre-transcription Events
TAF6, AFF4
 Reactome 2 / 84 22.0× 3.59e-3 3.49e-2 ✓ sig.
Oocyte meiosis
SMC1A, SMC3
 KEGG 2 / 138 13.4× 9.41e-3 6.62e-2
tRNA modification in the nucleus and cytosol
TRMT61A
 Reactome 1 / 19 48.6× 2.04e-2 1.04e-1
Notch-HLH transcription pathway
HDAC8
 Reactome 1 / 28 33.0× 2.99e-2 1.29e-1
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
ARID1B
 Reactome 1 / 38 24.3× 4.04e-2 1.53e-1
Basal transcription factors
TAF6
 KEGG 1 / 44 21.0× 4.66e-2 1.65e-1
RNA Polymerase II Promoter Escape
TAF6
 Reactome 1 / 47 19.7× 4.97e-2 1.71e-1
RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
TAF6
 Reactome 1 / 47 19.7× 4.97e-2 1.71e-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
SMC1A, NIPBL, RAD21, SMC3
 GO:0034087 4 / 7 821× 4.92e-12 1.93e-9 ✓ sig.
mitotic sister chromatid cohesion
SMC1A, HDAC8, NIPBL, SMC3
 GO:0007064 4 / 16 359× 2.55e-10 6.63e-8 ✓ sig.
establishment of meiotic sister chromatid cohesion
SMC1A, RAD21, SMC3
 GO:0034089 3 / 4 1,078× 1.05e-9 2.34e-7 ✓ sig.
sister chromatid cohesion
SMC1A, RAD21, SMC3
 GO:0007062 3 / 20 216× 2.98e-7 3.03e-5 ✓ sig.
ear morphogenesis
NIPBL, CHD7
 GO:0042471 2 / 5 575× 4.46e-6 2.74e-4 ✓ sig.
replication-born double-strand break repair via sister chromatid exchange
NIPBL, RAD21
 GO:1990414 2 / 6 479× 6.69e-6 3.78e-4 ✓ sig.
chromatin organization
BRD4, HDAC8, KMT2A, ARID1B, CHD7
 GO:0006325 5 / 449 16.0× 8.60e-6 4.63e-4 ✓ sig.
cognition
NIPBL, KMT2A, CHD7
 GO:0050890 3 / 64 67.4× 1.07e-5 5.49e-4 ✓ sig.
DNA damage response
SMC1A, BRD4, NIPBL, RAD21, SMC3
 GO:0006974 5 / 577 12.5× 2.89e-5 1.19e-3 ✓ sig.
chromatin looping
NIPBL, RAD21
 GO:0140588 2 / 14 205× 4.05e-5 1.54e-3 ✓ sig.
chromatin remodeling
BRD4, NIPBL, ARID1B, CHD7
 GO:0006338 4 / 320 18.0× 5.34e-5 1.89e-3 ✓ sig.
regulation of gene expression
NIPBL, KMT2A, AFF4, CHD7
 GO:0010468 4 / 402 14.3× 1.29e-4 3.67e-3 ✓ sig.
positive regulation of multicellular organism growth
NIPBL, CHD7
 GO:0040018 2 / 34 84.6× 2.48e-4 5.88e-3 ✓ sig.
mitotic sister chromatid segregation
SMC1A, NIPBL
 GO:0000070 2 / 38 75.7× 3.10e-4 6.87e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
KMT2A, ARID1B
 GO:0045815 2 / 41 70.1× 3.61e-4 7.60e-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 1.14e-20 2.37e-19 ✓ sig.
Cornelia de lange syndrome Wiedemann-steiner syndrome 0.231 3 1.97e-9 1.83e-8 ✓ sig.
De lange syndrome Wiedemann-steiner syndrome 0.200 2 1.26e-6 7.70e-6 ✓ sig.
Congenital muscular hypertrophy-cerebral syndrome Wiedemann-steiner syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital muscular hypertrophy-cerebral syndrome De lange syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Alazami-yuan syndrome Cornelia de lange syndrome 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Congenital muscular hypertrophy-cerebral syndrome Cornelia de lange syndrome 0.091 1 6.49e-4 1.22e-3 ✓ sig.
De lange syndrome Wilson-turner syndrome 0.125 1 7.79e-4 1.39e-3 ✓ sig.
Cornelia de lange syndrome Wilson-turner syndrome 0.083 1 1.30e-3 2.04e-3 ✓ sig.