Disease Clusters | GeDiPNet

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Cluster 197

8 diseases · 18 shared-gene connections

8 Diseases

33 Unique genes

0.177 Avg. similarity score

Clinodactyly Most-connected disease (7 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.

Clinodactyly Micrognathism Chromosome 2q32-q33 deletion syndrome Glass syndrome SATB2 associated disorder Satb2 associated syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Clinodactyly	7	7	18
Micrognathism	6	6	17
Chromosome 2q32-q33 deletion syndrome	5	5	2
Glass syndrome	5	5	1
SATB2 associated disorder	5	5	1
Satb2 associated syndrome	5	5	1
coffin-lowry syndrome	2	2	1
thrombocytopenia-absent radius syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SATB2	6 / 8	Chromosome 2q32-q33 deletion syndrome, Clinodactyly, Glass syndrome, Micrognathism and 2 more
RPS6KA3	3 / 8	Clinodactyly, coffin-lowry syndrome, Micrognathism
DYNC2H1	2 / 8	Clinodactyly, Micrognathism
RBM8A	2 / 8	Clinodactyly, thrombocytopenia-absent radius 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 ⇵
WNT mediated activation of DVL DVL3, CSNK2B	Reactome	2 / 9	80.9×	2.60e-4	4.80e-3 ✓ sig.
Synthesis of PIPs at the Golgi membrane ARF3, INPP5E	Reactome	2 / 18	40.4×	1.09e-3	1.45e-2 ✓ sig.
Loss of MECP2 binding ability to 5hmC-DNA MECP2	Reactome	1 / 1	364×	2.75e-3	2.89e-2 ✓ sig.
Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) SLC12A6	Reactome	1 / 1	364×	2.75e-3	2.89e-2 ✓ sig.
Defective ABCC9 causes dilated cardiomyopathy 10, familial atrial fibrillation 12 and hypertrichotic osteochondrodysplasia ABCC9	Reactome	1 / 2	182×	5.49e-3	4.65e-2 ✓ sig.
ARL13B-mediated ciliary trafficking of INPP5E INPP5E	Reactome	1 / 3	121×	8.22e-3	6.07e-2
Loss of MECP2 binding ability to 5mC-DNA MECP2	Reactome	1 / 3	121×	8.22e-3	6.07e-2
ATP sensitive Potassium channels ABCC9	Reactome	1 / 4	91.0×	1.09e-2	7.25e-2
RSK activation RPS6KA3	Reactome	1 / 4	91.0×	1.09e-2	7.25e-2
MECP2 regulates neuronal receptors and channels MECP2	Reactome	1 / 4	91.0×	1.09e-2	7.25e-2
Telomere C-strand (Lagging Strand) Synthesis POLD1	Reactome	1 / 5	72.8×	1.37e-2	8.23e-2
CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling RPS6KA3	Reactome	1 / 5	72.8×	1.37e-2	8.23e-2
Regulation of MECP2 expression and activity MECP2	Reactome	1 / 6	60.7×	1.64e-2	9.17e-2
ChREBP activates metabolic gene expression FASN	Reactome	1 / 7	52.0×	1.91e-2	1.00e-1
Cation-coupled Chloride cotransporters SLC12A6	Reactome	1 / 7	52.0×	1.91e-2	1.00e-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 ⇵
hindlimb morphogenesis TFAP2B, PITX1	GO:0035137	2 / 9	126×	1.08e-4	3.20e-3 ✓ sig.
negative regulation of smooth muscle cell differentiation FOXO4, MECP2	GO:0051151	2 / 10	113×	1.35e-4	3.78e-3 ✓ sig.
neuromuscular process controlling posture SCN1A, MECP2	GO:0050884	2 / 15	75.5×	3.13e-4	6.93e-3 ✓ sig.
cartilage development SATB2, COL2A1, PITX1	GO:0051216	3 / 89	19.1×	5.14e-4	9.73e-3 ✓ sig.
coronary vasculature development DYNC2H1, ABCC9	GO:0060976	2 / 27	41.9×	1.03e-3	1.54e-2 ✓ sig.
vascular process in circulatory system ABCC9	GO:0003018	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
response to hydrogen sulfide ABCC9	GO:1904880	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
trans-synaptic signaling by BDNF MECP2	GO:0099191	1 / 1	566×	1.77e-3	2.11e-2 ✓ sig.
kidney development DYNC2H1, TFAP2B, CEP290	GO:0001822	3 / 146	11.6×	2.15e-3	2.35e-2 ✓ sig.
skeletal system development RPS6KA3, COL2A1, PITX1	GO:0001501	3 / 151	11.3×	2.36e-3	2.49e-2 ✓ sig.
negative regulation of blood vessel endothelial cell migration CSNK2B, MECP2	GO:0043537	2 / 43	26.3×	2.61e-3	2.62e-2 ✓ sig.
skeletal system morphogenesis ANKRD11, COL2A1	GO:0048705	2 / 45	25.2×	2.86e-3	2.76e-2 ✓ sig.
potassium ion import across plasma membrane SLC12A6, ABCC9	GO:1990573	2 / 46	24.6×	2.98e-3	2.82e-2 ✓ sig.
regulation of system process DMD	GO:0044057	1 / 2	283×	3.53e-3	3.08e-2 ✓ sig.
regulation of muscle system process DMD	GO:0090257	1 / 2	283×	3.53e-3	3.08e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Clinodactyly	Micrognathism	0.091	3	9.03e-7	5.64e-6 ✓ sig.
SATB2 associated disorder	Satb2 associated syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Glass syndrome	SATB2 associated disorder	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Glass syndrome	Satb2 associated syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Chromosome 2q32-q33 deletion syndrome	Satb2 associated syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Chromosome 2q32-q33 deletion syndrome	SATB2 associated disorder	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Chromosome 2q32-q33 deletion syndrome	Glass syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
coffin-lowry syndrome	Micrognathism	0.056	1	1.10e-3	1.81e-3 ✓ sig.
Glass syndrome	Micrognathism	0.056	1	1.10e-3	1.81e-3 ✓ sig.
Micrognathism	SATB2 associated disorder	0.056	1	1.10e-3	1.81e-3 ✓ sig.
Micrognathism	Satb2 associated syndrome	0.056	1	1.10e-3	1.81e-3 ✓ sig.
Clinodactyly	coffin-lowry syndrome	0.053	1	1.17e-3	1.88e-3 ✓ sig.
Clinodactyly	Glass syndrome	0.053	1	1.17e-3	1.88e-3 ✓ sig.
Clinodactyly	SATB2 associated disorder	0.053	1	1.17e-3	1.88e-3 ✓ sig.
Clinodactyly	Satb2 associated syndrome	0.053	1	1.17e-3	1.88e-3 ✓ sig.
Clinodactyly	thrombocytopenia-absent radius syndrome	0.053	1	1.17e-3	1.88e-3 ✓ sig.
Chromosome 2q32-q33 deletion syndrome	Micrognathism	0.053	1	2.21e-3	3.10e-3 ✓ sig.
Chromosome 2q32-q33 deletion syndrome	Clinodactyly	0.050	1	2.34e-3	3.23e-3 ✓ sig.

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