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Cluster 418

6 diseases · 5 shared-gene connections

6 Diseases

20 Unique genes

0.048 Avg. similarity score

Autosomal recessive mental retardation Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Neurodevelopmental disorder with progressive movement abnormalities 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.

Neurodevelopmental disorder with progressive movement abnormalities Autosomal recessive mental retardation Li-campeau syndrome Mental retardation, autosomal recessive 27 Mental retardation, autosomal recessive 39 Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Autosomal recessive mental retardation	5	5	20
Li-campeau syndrome	1	1	1
Mental retardation, autosomal recessive 27	1	1	1
Mental retardation, autosomal recessive 39	1	1	1
Neurodevelopmental disorder with progressive movement abnormalities	1	1	1
Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
LHX4-AS1	2 / 6	Autosomal recessive mental retardation, Neurodevelopmental disorder with progressive movement abnormalities
LINS1	2 / 6	Autosomal recessive mental retardation, Mental retardation, autosomal recessive 27
TTI2	2 / 6	Autosomal recessive mental retardation, Mental retardation, autosomal recessive 39
UBR7	2 / 6	Autosomal recessive mental retardation, Li-campeau syndrome
WDR45B	2 / 6	Autosomal recessive mental retardation, Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures

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 MAN1B1 causes MRT15 MAN1B1	Reactome	1 / 1	601×	1.67e-3	1.66e-2 ✓ sig.
Signaling by plasma membrane FGFR1 fusions ERLIN2	Reactome	1 / 3	200×	4.99e-3	3.64e-2 ✓ sig.
Eukaryotic Translation Elongation EEF1B2	Reactome	1 / 4	150×	6.65e-3	4.39e-2 ✓ sig.
Metal ion SLC transporters SLC31A1	Reactome	1 / 9	66.7×	1.49e-2	7.22e-2
Synthesis of IP2, IP, and Ins in the cytosol INPP4A	Reactome	1 / 12	50.0×	1.98e-2	8.52e-2
Synthesis of PIPs at the early endosome membrane INPP4A	Reactome	1 / 15	40.0×	2.47e-2	9.67e-2
ER Quality Control Compartment (ERQC) MAN1B1	Reactome	1 / 21	28.6×	3.44e-2	1.17e-1
Cytosolic sensors of pathogen-associated DNA POLR3B	Reactome	1 / 22	27.3×	3.60e-2	1.20e-1
Glycosaminoglycan biosynthesis - heparan sulfate / heparin NDST1	KEGG	1 / 24	25.0×	3.92e-2	1.26e-1
RNA Polymerase III Transcription Initiation From Type 2 Promoter POLR3B	Reactome	1 / 27	22.2×	4.40e-2	1.35e-1
RNA Polymerase III Transcription Initiation From Type 3 Promoter POLR3B	Reactome	1 / 28	21.4×	4.56e-2	1.37e-1
Laminin interactions LAMA1	Reactome	1 / 28	21.4×	4.56e-2	1.37e-1
RNA Polymerase III Transcription Initiation From Type 1 Promoter POLR3B	Reactome	1 / 28	21.4×	4.56e-2	1.37e-1
HS-GAG biosynthesis NDST1	Reactome	1 / 30	20.0×	4.88e-2	1.43e-1
MET activates PTK2 signaling LAMA1	Reactome	1 / 30	20.0×	4.88e-2	1.43e-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 smoothened signaling pathway NDST1, KIF7	GO:0045880	2 / 39	47.9×	7.87e-4	1.27e-2 ✓ sig.
SA node cell to atrial cardiac muscle cell signaling CACNA1G	GO:0086018	1 / 1	934×	1.07e-3	1.51e-2 ✓ sig.
AV node cell to bundle of His cell signaling CACNA1G	GO:0086027	1 / 1	934×	1.07e-3	1.51e-2 ✓ sig.
protein alpha-1,2-demannosylation MAN1B1	GO:0036508	1 / 1	934×	1.07e-3	1.51e-2 ✓ sig.
negative regulation of short-term synaptic potentiation PRRT2	GO:1905513	1 / 1	934×	1.07e-3	1.51e-2 ✓ sig.
plasma membrane copper ion transport SLC31A1	GO:0015679	1 / 1	934×	1.07e-3	1.51e-2 ✓ sig.
silver ion transmembrane transport SLC31A1	GO:1902601	1 / 1	934×	1.07e-3	1.51e-2 ✓ sig.
response to nickel cation CACNA1G	GO:0010045	1 / 2	467×	2.14e-3	2.19e-2 ✓ sig.
regulation of calcium-dependent activation of synaptic vesicle fusion PRRT2	GO:0150037	1 / 2	467×	2.14e-3	2.19e-2 ✓ sig.
negative regulation of SNARE complex assembly PRRT2	GO:0035544	1 / 2	467×	2.14e-3	2.19e-2 ✓ sig.
retina development in camera-type eye SCAPER, LAMA1	GO:0060041	2 / 85	22.0×	3.68e-3	2.89e-2 ✓ sig.
AV node cell action potential CACNA1G	GO:0086016	1 / 4	234×	4.27e-3	3.09e-2 ✓ sig.
positive regulation of DNA damage checkpoint TTI2	GO:2000003	1 / 4	234×	4.27e-3	3.09e-2 ✓ sig.
ERAD pathway MAN1B1, ERLIN2	GO:0036503	2 / 96	19.5×	4.67e-3	3.25e-2 ✓ sig.
membrane depolarization during SA node cell action potential CACNA1G	GO:0086046	1 / 5	187×	5.34e-3	3.43e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Autosomal recessive mental retardation	Li-campeau syndrome	0.048	1	1.29e-3	1.89e-3 ✓ sig.
Autosomal recessive mental retardation	Mental retardation, autosomal recessive 27	0.048	1	1.29e-3	1.89e-3 ✓ sig.
Autosomal recessive mental retardation	Mental retardation, autosomal recessive 39	0.048	1	1.29e-3	1.89e-3 ✓ sig.
Autosomal recessive mental retardation	Neurodevelopmental disorder with progressive movement abnormalities	0.048	1	1.29e-3	1.89e-3 ✓ sig.
Autosomal recessive mental retardation	Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	0.048	1	1.29e-3	1.89e-3 ✓ sig.

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