Disease Clusters | GeDiPNet

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Cluster 140

11 diseases · 25 shared-gene connections

11 Diseases

11 Unique genes

0.318 Avg. similarity score

Genitopatellar syndrome Most-connected disease (7 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Sbbyss 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.

Sbbyss syndrome Genitopatellar syndrome Simpson syndrome Blepharophimosis-intellectual disability syndrome KAT6B-related disorders Blepharophimosis syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Genitopatellar syndrome	7	7	1
Sbbyss syndrome	7	7	1
Simpson syndrome	7	7	1
Blepharophimosis-intellectual disability syndrome	6	6	4
KAT6B-related disorders	6	6	1
Blepharophimosis syndrome	5	5	3
Multiple congenital anomalies	5	5	7
Ohdo syndrome, sbbys variant	4	4	1
Neurofacioskeletal syndrome with or without renal agenesis	1	1	1
Nicolaides-baraitser syndrome	1	1	1
Oculocerebrofacial syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
KAT6B	8 / 11	Blepharophimosis syndrome, Blepharophimosis-intellectual disability syndrome, Genitopatellar syndrome, KAT6B-related disorders and 4 more
HS2ST1	2 / 11	Multiple congenital anomalies, Neurofacioskeletal syndrome with or without renal agenesis
MED12	2 / 11	Blepharophimosis syndrome, Blepharophimosis-intellectual disability syndrome
SMARCA2	2 / 11	Blepharophimosis-intellectual disability syndrome, Nicolaides-baraitser syndrome
UBE3B	2 / 11	Blepharophimosis-intellectual disability syndrome, Oculocerebrofacial 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 ⇵
ATP-dependent chromatin remodeling SMARCA2, TRRAP	KEGG	2 / 117	18.7×	4.89e-3	3.60e-2 ✓ sig.
Cation-coupled Chloride cotransporters SLC12A2	Reactome	1 / 7	156×	6.40e-3	4.28e-2 ✓ sig.
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) CDX2	Reactome	1 / 14	78.0×	1.28e-2	6.57e-2
Virion - Lassa virus and SFTS virus MYH10	KEGG	1 / 17	64.2×	1.55e-2	7.39e-2
SUMOylation of transcription factors FOXL2	Reactome	1 / 18	60.7×	1.64e-2	7.63e-2
RHO GTPases activate PAKs MYH10	Reactome	1 / 23	47.5×	2.09e-2	8.78e-2
Glycosaminoglycan biosynthesis - heparan sulfate / heparin HS2ST1	KEGG	1 / 24	45.5×	2.18e-2	9.00e-2
HS-GAG biosynthesis HS2ST1	Reactome	1 / 30	36.4×	2.71e-2	1.02e-1
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known SMARCA2	Reactome	1 / 38	28.7×	3.43e-2	1.17e-1
Vibrio cholerae infection SLC12A2	KEGG	1 / 51	21.4×	4.58e-2	1.37e-1
Transcriptional regulation of white adipocyte differentiation MED12	Reactome	1 / 67	16.3×	5.97e-2	1.60e-1
RMTs methylate histone arginines SMARCA2	Reactome	1 / 79	13.8×	7.01e-2	1.76e-1
Formation of the beta-catenin:TCF transactivating complex TRRAP	Reactome	1 / 88	12.4×	7.77e-2	1.87e-1
Salivary secretion SLC12A2	KEGG	1 / 93	11.7×	8.20e-2	1.92e-1
HATs acetylate histones KAT6B	Reactome	1 / 93	11.7×	8.20e-2	1.92e-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 ⇵
positive regulation of DNA-templated transcription MED12, KAT6B, FOXL2, SMARCA2, CDX2, TRRAP	GO:0045893	6 / 778	13.1×	1.97e-6	1.50e-4 ✓ sig.
regulation of transcription by RNA polymerase II MED12, KAT6B, FOXL2, SMARCA2, CDX2, TRRAP	GO:0006357	6 / 1,602	6.4×	1.24e-4	3.62e-3 ✓ sig.
establishment or maintenance of epithelial cell apical/basal polarity CDX2, FAT1	GO:0045197	2 / 29	117×	1.27e-4	3.66e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II MED12, KAT6B, FOXL2, SMARCA2, CDX2	GO:0045944	5 / 1,208	7.0×	3.72e-4	7.81e-3 ✓ sig.
establishment of epithelial cell apical/basal polarity involved in camera-type eye morphogenesis FAT1	GO:0003412	1 / 1	1,699×	5.89e-4	1.06e-2 ✓ sig.
female somatic sex determination FOXL2	GO:0019101	1 / 1	1,699×	5.89e-4	1.06e-2 ✓ sig.
granulosa cell differentiation FOXL2	GO:0060014	1 / 1	1,699×	5.89e-4	1.06e-2 ✓ sig.
positive regulation of cell volume SLC12A2	GO:0045795	1 / 1	1,699×	5.89e-4	1.06e-2 ✓ sig.
somatic stem cell population maintenance MED12, CDX2	GO:0035019	2 / 64	53.1×	6.23e-4	1.10e-2 ✓ sig.
regulation of DNA-templated transcription KAT6B, FOXL2, SMARCA2, CDX2, TRRAP	GO:0006355	5 / 1,454	5.8×	8.79e-4	1.36e-2 ✓ sig.
positive regulation of cell differentiation SMARCA2, CDX2	GO:0045597	2 / 83	40.9×	1.04e-3	1.51e-2 ✓ sig.
positive regulation of aspartate secretion SLC12A2	GO:1904450	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.
inorganic cation import across plasma membrane SLC12A2	GO:0098659	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.
inorganic anion import across plasma membrane SLC12A2	GO:0098658	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.
fourth ventricle development MYH10	GO:0021592	1 / 2	849×	1.18e-3	1.59e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Blepharophimosis syndrome	Blepharophimosis-intellectual disability syndrome	0.333	2	1.50e-7	1.02e-6 ✓ sig.
Genitopatellar syndrome	Ohdo syndrome, sbbys variant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Sbbyss syndrome	Simpson syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Ohdo syndrome, sbbys variant	Sbbyss syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Ohdo syndrome, sbbys variant	Simpson syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
KAT6B-related disorders	Ohdo syndrome, sbbys variant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
KAT6B-related disorders	Sbbyss syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
KAT6B-related disorders	Simpson syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Genitopatellar syndrome	KAT6B-related disorders	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Genitopatellar syndrome	Sbbyss syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Genitopatellar syndrome	Simpson syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Blepharophimosis syndrome	KAT6B-related disorders	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Blepharophimosis syndrome	Sbbyss syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Blepharophimosis syndrome	Genitopatellar syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Blepharophimosis syndrome	Simpson syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome	Sbbyss syndrome	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome	Genitopatellar syndrome	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome	Simpson syndrome	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome	Nicolaides-baraitser syndrome	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome	Oculocerebrofacial syndrome	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Multiple congenital anomalies	Simpson syndrome	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Genitopatellar syndrome	Multiple congenital anomalies	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Multiple congenital anomalies	Sbbyss syndrome	0.125	1	4.52e-4	8.26e-4 ✓ sig.
KAT6B-related disorders	Multiple congenital anomalies	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Multiple congenital anomalies	Neurofacioskeletal syndrome with or without renal agenesis	0.125	1	4.52e-4	8.26e-4 ✓ sig.

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