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 250

8 diseases · 19 shared-gene connections
8 Diseases
6 Unique genes
0.374 Avg. similarity score
Chromosome xq25 duplication syndrome Most-connected disease (6 links)
Log in to save this analysis

Save This Analysis

Disease Searched: Mullegama-klein-martinez syndrome 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 ⇵
Chromosome xq25 duplication syndrome 6 6 1
Developmental delay with microcephaly and congenital anomalies 6 6 1
Growth delay 6 6 3
Xq25 microduplication syndrome 6 6 1
Holoprosencephaly 13, x-linked 5 5 1
Mullegama-klein-martinez syndrome 5 5 1
Abnormality of head or neck 3 3 4
Clinodactyly of the 5th finger 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
STAG2 7 / 8 Abnormality of head or neck, Chromosome xq25 duplication syndrome, Developmental delay with microcephaly and congenital anomalies, Growth delay and 3 more
SOX4 2 / 8 Clinodactyly of the 5th finger, Growth delay
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 ⇵
Hypusine synthesis from eIF5A-lysine
DHPS
 Reactome 1 / 4 500× 2.00e-3 1.90e-2 ✓ sig.
Cohesin Loading onto Chromatin
STAG2
 Reactome 1 / 10 200× 4.99e-3 3.64e-2 ✓ sig.
Establishment of Sister Chromatid Cohesion
STAG2
 Reactome 1 / 11 182× 5.48e-3 3.87e-2 ✓ sig.
MicroRNA (miRNA) biogenesis
DROSHA
 Reactome 1 / 24 83.4× 1.19e-2 6.32e-2
Deactivation of the beta-catenin transactivating complex
SOX4
 Reactome 1 / 42 47.7× 2.08e-2 8.77e-2
SUMOylation of DNA damage response and repair proteins
STAG2
 Reactome 1 / 77 26.0× 3.79e-2 1.23e-1
Ribosome biogenesis in eukaryotes
DROSHA
 KEGG 1 / 125 16.0× 6.09e-2 1.62e-1
Resolution of Sister Chromatid Cohesion
STAG2
 Reactome 1 / 126 15.9× 6.13e-2 1.63e-1
Estrogen-dependent gene expression
STAG2
 Reactome 1 / 150 13.3× 7.27e-2 1.79e-1
Cell cycle
STAG2
 KEGG 1 / 158 12.7× 7.64e-2 1.85e-1
Separation of Sister Chromatids
STAG2
 Reactome 1 / 190 10.5× 9.13e-2 2.05e-1
Proteoglycans in cancer
DROSHA
 KEGG 1 / 204 9.8× 9.77e-2 2.13e-1
MicroRNAs in cancer
SOX4
 KEGG 1 / 311 6.4× 1.46e-1 2.71e-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 ⇵
spermidine metabolic process
DHPS
 GO:0008216 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
ribosome biogenesis
HEATR3, DROSHA
 GO:0042254 2 / 122 51.1× 6.23e-4 1.11e-2 ✓ sig.
spermidine catabolic process
DHPS
 GO:0046203 1 / 2 1,557× 6.42e-4 1.11e-2 ✓ sig.
glucose homeostasis
SOX4, DHPS
 GO:0042593 2 / 134 46.5× 7.51e-4 1.23e-2 ✓ sig.
pyramidal neuron migration to cerebral cortex
ZMIZ1
 GO:0021852 1 / 3 1,038× 9.63e-4 1.42e-2 ✓ sig.
regulation of miRNA metabolic process
DROSHA
 GO:2000628 1 / 3 1,038× 9.63e-4 1.42e-2 ✓ sig.
vitellogenesis
ZMIZ1
 GO:0007296 1 / 4 779× 1.28e-3 1.67e-2 ✓ sig.
pro-B cell differentiation
SOX4
 GO:0002328 1 / 4 779× 1.28e-3 1.67e-2 ✓ sig.
ascending aorta morphogenesis
SOX4
 GO:0035910 1 / 4 779× 1.28e-3 1.67e-2 ✓ sig.
atrial septum primum morphogenesis
SOX4
 GO:0003289 1 / 5 623× 1.60e-3 1.88e-2 ✓ sig.
glial cell development
SOX4
 GO:0021782 1 / 5 623× 1.60e-3 1.88e-2 ✓ sig.
regulation of DNA damage response, signal transduction by p53 class mediator
SOX4
 GO:0043516 1 / 7 445× 2.25e-3 2.24e-2 ✓ sig.
establishment of mitotic sister chromatid cohesion
STAG2
 GO:0034087 1 / 7 445× 2.25e-3 2.24e-2 ✓ sig.
noradrenergic neuron differentiation
SOX4
 GO:0003357 1 / 7 445× 2.25e-3 2.24e-2 ✓ sig.
regulation of regulatory T cell differentiation
DROSHA
 GO:0045589 1 / 8 389× 2.57e-3 2.40e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Mullegama-klein-martinez syndrome Xq25 microduplication syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome xq25 duplication syndrome Xq25 microduplication syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome xq25 duplication syndrome Developmental delay with microcephaly and congenital anomalies 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome xq25 duplication syndrome Holoprosencephaly 13, x-linked 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome xq25 duplication syndrome Mullegama-klein-martinez syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Holoprosencephaly 13, x-linked Mullegama-klein-martinez syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Holoprosencephaly 13, x-linked Xq25 microduplication syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Developmental delay with microcephaly and congenital anomalies Xq25 microduplication syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Developmental delay with microcephaly and congenital anomalies Holoprosencephaly 13, x-linked 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Developmental delay with microcephaly and congenital anomalies Mullegama-klein-martinez syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Growth delay Mullegama-klein-martinez syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Growth delay Holoprosencephaly 13, x-linked 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Growth delay Xq25 microduplication syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Developmental delay with microcephaly and congenital anomalies Growth delay 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Clinodactyly of the 5th finger Growth delay 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Chromosome xq25 duplication syndrome Growth delay 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Abnormality of head or neck Developmental delay with microcephaly and congenital anomalies 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Abnormality of head or neck Xq25 microduplication syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Abnormality of head or neck Chromosome xq25 duplication syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.