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Cluster 281

6 diseases · 14 shared-gene connections

6 Diseases

7 Unique genes

0.350 Avg. similarity score

Reynolds syndrome Most-connected disease (5 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.

Reynolds syndrome Rhizomelic skeletal dysplasia with or without pelger-huet anomaly greenberg dysplasia regressive spondylometaphyseal dysplasia Congenital retrognathism Pelger-huet anomaly

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Reynolds syndrome	5	5	1
Rhizomelic skeletal dysplasia with or without pelger-huet anomaly	5	5	1
greenberg dysplasia	5	5	1
regressive spondylometaphyseal dysplasia	5	5	1
Congenital retrognathism	4	4	6
Pelger-huet anomaly	4	4	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
LBR	6 / 6	Congenital retrognathism, greenberg dysplasia, Pelger-huet anomaly, regressive spondylometaphyseal dysplasia and 2 more

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 ⇵
Defective ABCC8 can cause hypoglycemias and hyperglycemias ABCC8	Reactome	1 / 2	858×	1.17e-3	1.52e-2 ✓ sig.
ATP sensitive Potassium channels ABCC8	Reactome	1 / 4	429×	2.33e-3	2.55e-2 ✓ sig.
Regulation of MECP2 expression and activity LBR	Reactome	1 / 6	286×	3.49e-3	3.42e-2 ✓ sig.
Transcriptional misregulation in cancer NSD2, CEBPE	KEGG	2 / 198	17.3×	5.38e-3	4.59e-2 ✓ sig.
Regulation of insulin secretion ABCC8	Reactome	1 / 16	107×	9.29e-3	6.56e-2
Initiation of Nuclear Envelope (NE) Reformation LBR	Reactome	1 / 19	90.3×	1.10e-2	7.27e-2
Steroid biosynthesis LBR	KEGG	1 / 20	85.8×	1.16e-2	7.50e-2
Cholesterol biosynthesis LBR	Reactome	1 / 21	81.7×	1.22e-2	7.72e-2
ABC transporters ABCC8	KEGG	1 / 45	38.1×	2.59e-2	1.19e-1
Type II diabetes mellitus ABCC8	KEGG	1 / 47	36.5×	2.71e-2	1.22e-1
HDMs demethylate histones ARID5B	Reactome	1 / 50	34.3×	2.88e-2	1.26e-1
Lysine degradation NSD2	KEGG	1 / 63	27.2×	3.62e-2	1.44e-1
Acute myeloid leukemia CEBPE	KEGG	1 / 68	25.2×	3.90e-2	1.49e-1
Nonhomologous End-Joining (NHEJ) NSD2	Reactome	1 / 69	24.9×	3.95e-2	1.51e-1
PKMTs methylate histone lysines NSD2	Reactome	1 / 71	24.2×	4.07e-2	1.53e-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 ⇵
face morphogenesis ANKRD11, ARID5B	GO:0060325	2 / 33	162×	6.32e-5	2.14e-3 ✓ sig.
skeletal system morphogenesis ANKRD11, ARID5B	GO:0048705	2 / 45	119×	1.18e-4	3.43e-3 ✓ sig.
negative regulation of neuroblast migration ABCC8	GO:0061855	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
positive regulation of uterine smooth muscle relaxation ABCC8	GO:1900721	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
atrial septum secundum morphogenesis NSD2	GO:0003290	1 / 2	1,335×	7.49e-4	1.25e-2 ✓ sig.
positive regulation of sodium ion transmembrane transporter activity WNK3	GO:2000651	1 / 2	1,335×	7.49e-4	1.25e-2 ✓ sig.
glutamate secretion, neurotransmission ABCC8	GO:0061535	1 / 3	890×	1.12e-3	1.62e-2 ✓ sig.
negative regulation of blood-brain barrier permeability ABCC8	GO:1905604	1 / 3	890×	1.12e-3	1.62e-2 ✓ sig.
atrial septum primum morphogenesis NSD2	GO:0003289	1 / 5	534×	1.87e-3	2.19e-2 ✓ sig.
positive regulation of tight junction disassembly ABCC8	GO:1905075	1 / 5	534×	1.87e-3	2.19e-2 ✓ sig.
negative regulation of pancreatic juice secretion WNK3	GO:0090188	1 / 5	534×	1.87e-3	2.19e-2 ✓ sig.
positive regulation of isotype switching to IgA isotypes NSD2	GO:0048298	1 / 6	445×	2.25e-3	2.41e-2 ✓ sig.
response to pH ABCC8	GO:0009268	1 / 7	381×	2.62e-3	2.62e-2 ✓ sig.
regulation of double-strand break repair via nonhomologous end joining NSD2	GO:2001032	1 / 8	334×	2.99e-3	2.82e-2 ✓ sig.
neutrophil differentiation LBR	GO:0030223	1 / 8	334×	2.99e-3	2.82e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
greenberg dysplasia	Reynolds syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
greenberg dysplasia	Rhizomelic skeletal dysplasia with or without pelger-huet anomaly	0.500	1	6.49e-5	2.34e-4 ✓ sig.
greenberg dysplasia	regressive spondylometaphyseal dysplasia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
regressive spondylometaphyseal dysplasia	Reynolds syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
regressive spondylometaphyseal dysplasia	Rhizomelic skeletal dysplasia with or without pelger-huet anomaly	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Reynolds syndrome	Rhizomelic skeletal dysplasia with or without pelger-huet anomaly	0.500	1	6.49e-5	2.34e-4 ✓ sig.
greenberg dysplasia	Pelger-huet anomaly	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Pelger-huet anomaly	Reynolds syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Pelger-huet anomaly	Rhizomelic skeletal dysplasia with or without pelger-huet anomaly	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Pelger-huet anomaly	regressive spondylometaphyseal dysplasia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Congenital retrognathism	greenberg dysplasia	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Congenital retrognathism	regressive spondylometaphyseal dysplasia	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Congenital retrognathism	Reynolds syndrome	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Congenital retrognathism	Rhizomelic skeletal dysplasia with or without pelger-huet anomaly	0.143	1	3.90e-4	8.52e-4 ✓ sig.

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