Disease Clusters | GeDiPNet

← Back to all clusters

Cluster 513

5 diseases · 7 shared-gene connections

5 Diseases

2 Unique genes

0.405 Avg. similarity score

17q24.2 microdeletion 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.

17q24.2 microdeletion syndrome Developmental and speech delay, postnatal microcephaly, and dysmorphic features Intellectual disability facial dysmorphism skeletal anomalies syndrome Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies Stankiewicz-isidor syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
17q24.2 microdeletion syndrome	4	4	2
Developmental and speech delay, postnatal microcephaly, and dysmorphic features	3	3	1
Intellectual disability facial dysmorphism skeletal anomalies syndrome	3	3	1
Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies	3	3	1
Stankiewicz-isidor syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
BPTF	4 / 5	17q24.2 microdeletion syndrome, Developmental and speech delay, postnatal microcephaly, and dysmorphic features, Intellectual disability facial dysmorphism skeletal anomalies syndrome, Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
PSMD12	2 / 5	17q24.2 microdeletion syndrome, Stankiewicz-isidor 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 ⇵
Proteasome PSMD12	KEGG	1 / 46	131×	7.65e-3	4.81e-2 ✓ sig.
Cross-presentation of soluble exogenous antigens (endosomes) PSMD12	Reactome	1 / 50	120×	8.31e-3	5.07e-2
Ubiquitin-dependent degradation of Cyclin D PSMD12	Reactome	1 / 51	118×	8.48e-3	5.13e-2
Regulation of ornithine decarboxylase (ODC) PSMD12	Reactome	1 / 51	118×	8.48e-3	5.13e-2
G2/M Checkpoints PSMD12	Reactome	1 / 51	118×	8.48e-3	5.13e-2
Vpu mediated degradation of CD4 PSMD12	Reactome	1 / 52	115×	8.64e-3	5.20e-2
Autodegradation of the E3 ubiquitin ligase COP1 PSMD12	Reactome	1 / 52	115×	8.64e-3	5.20e-2
Ubiquitin Mediated Degradation of Phosphorylated Cdc25A PSMD12	Reactome	1 / 52	115×	8.64e-3	5.20e-2
Vif-mediated degradation of APOBEC3G PSMD12	Reactome	1 / 54	111×	8.97e-3	5.31e-2
FBXL7 down-regulates AURKA during mitotic entry and in early mitosis PSMD12	Reactome	1 / 54	111×	8.97e-3	5.31e-2
SCF-beta-TrCP mediated degradation of Emi1 PSMD12	Reactome	1 / 55	109×	9.14e-3	5.37e-2
Degradation of AXIN PSMD12	Reactome	1 / 55	109×	9.14e-3	5.37e-2
Regulation of RUNX3 expression and activity PSMD12	Reactome	1 / 55	109×	9.14e-3	5.37e-2
AUF1 (hnRNP D0) binds and destabilizes mRNA PSMD12	Reactome	1 / 56	107×	9.30e-3	5.43e-2
Hh mutants that don't undergo autocatalytic processing are degraded by ERAD PSMD12	Reactome	1 / 56	107×	9.30e-3	5.43e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
embryonic placenta development BPTF	GO:0001892	1 / 26	359×	2.78e-3	2.51e-2 ✓ sig.
endoderm development BPTF	GO:0007492	1 / 34	275×	3.64e-3	2.86e-2 ✓ sig.
cellular response to nerve growth factor stimulus BPTF	GO:1990090	1 / 35	267×	3.74e-3	2.90e-2 ✓ sig.
anterior/posterior pattern specification BPTF	GO:0009952	1 / 112	83.4×	1.20e-2	5.06e-2
brain development BPTF	GO:0007420	1 / 244	38.3×	2.59e-2	7.51e-2
chromatin remodeling BPTF	GO:0006338	1 / 320	29.2×	3.40e-2	8.61e-2
proteasome-mediated ubiquitin-dependent protein catabolic process PSMD12	GO:0043161	1 / 343	27.2×	3.64e-2	8.92e-2
chromatin organization BPTF	GO:0006325	1 / 449	20.8×	4.75e-2	1.04e-1
negative regulation of DNA-templated transcription BPTF	GO:0045892	1 / 631	14.8×	6.64e-2	1.27e-1
negative regulation of transcription by RNA polymerase II BPTF	GO:0000122	1 / 1,002	9.3×	1.04e-1	1.70e-1
positive regulation of transcription by RNA polymerase II BPTF	GO:0045944	1 / 1,208	7.7×	1.25e-1	1.92e-1
regulation of DNA-templated transcription BPTF	GO:0006355	1 / 1,454	6.4×	1.50e-1	2.16e-1
regulation of transcription by RNA polymerase II BPTF	GO:0006357	1 / 1,602	5.8×	1.64e-1	2.31e-1

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Developmental and speech delay, postnatal microcephaly, and dysmorphic features	Intellectual disability facial dysmorphism skeletal anomalies syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Developmental and speech delay, postnatal microcephaly, and dysmorphic features	Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual disability facial dysmorphism skeletal anomalies syndrome	Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies	0.500	1	6.46e-5	1.98e-4 ✓ sig.
17q24.2 microdeletion syndrome	Intellectual disability facial dysmorphism skeletal anomalies syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
17q24.2 microdeletion syndrome	Developmental and speech delay, postnatal microcephaly, and dysmorphic features	0.333	1	1.29e-4	3.27e-4 ✓ sig.
17q24.2 microdeletion syndrome	Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies	0.333	1	1.29e-4	3.27e-4 ✓ sig.
17q24.2 microdeletion syndrome	Stankiewicz-isidor syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.

Disease Clusters?