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Cluster 619

5 diseases · 4 shared-gene connections

5 Diseases

8 Unique genes

0.111 Avg. similarity score

Complex hereditary spastic paraplegia 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.

Complex hereditary spastic paraplegia Spastic paraplegia 26, autosomal recessive Spastic paraplegia 45, autosomal recessive Spastic paraplegia 46, autosomal recessive Spastic paraplegia 75, autosomal recessive

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Complex hereditary spastic paraplegia	4	4	8
Spastic paraplegia 26, autosomal recessive	1	1	1
Spastic paraplegia 45, autosomal recessive	1	1	1
Spastic paraplegia 46, autosomal recessive	1	1	1
Spastic paraplegia 75, autosomal recessive	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
B4GALNT1	2 / 5	Complex hereditary spastic paraplegia, Spastic paraplegia 26, autosomal recessive
GBA2	2 / 5	Complex hereditary spastic paraplegia, Spastic paraplegia 46, autosomal recessive
MAG	2 / 5	Complex hereditary spastic paraplegia, Spastic paraplegia 75, autosomal recessive
NT5C2	2 / 5	Complex hereditary spastic paraplegia, Spastic paraplegia 45, autosomal recessive

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 ⇵
Glycosphingolipid metabolism B4GALNT1, GBA2	Reactome	2 / 46	65.3×	3.96e-4	5.58e-3 ✓ sig.
Sphingolipid metabolism B4GALNT1, GBA2	KEGG	2 / 54	55.6×	5.46e-4	7.15e-3 ✓ sig.
Pyrimidine metabolism ENTPD1, NT5C2	KEGG	2 / 58	51.8×	6.30e-4	7.99e-3 ✓ sig.
Nucleotide metabolism ENTPD1, NT5C2	KEGG	2 / 85	35.3×	1.35e-3	1.42e-2 ✓ sig.
Signaling by plasma membrane FGFR1 fusions ERLIN2	Reactome	1 / 3	500×	2.00e-3	1.90e-2 ✓ sig.
Abacavir metabolism NT5C2	Reactome	1 / 3	500×	2.00e-3	1.90e-2 ✓ sig.
Purine metabolism ENTPD1, NT5C2	KEGG	2 / 128	23.5×	3.03e-3	2.56e-2 ✓ sig.
Phosphate bond hydrolysis by NTPDase proteins ENTPD1	Reactome	1 / 8	188×	5.32e-3	3.80e-2 ✓ sig.
Axonal growth inhibition (RHOA activation) MAG	Reactome	1 / 9	167×	5.98e-3	4.10e-2 ✓ sig.
Purine catabolism NT5C2	Reactome	1 / 12	125×	7.97e-3	4.94e-2 ✓ sig.
Membrane binding and targetting of GAG proteins VPS37A	Reactome	1 / 14	107×	9.29e-3	5.43e-2
Glycosphingolipid biosynthesis - ganglio series B4GALNT1	KEGG	1 / 15	100×	9.95e-3	5.67e-2
Other glycan degradation GBA2	KEGG	1 / 18	83.4×	1.19e-2	6.32e-2
Metabolic pathways B4GALNT1, ENTPD1, NT5C2, GBA2	KEGG	4 / 1,563	3.8×	1.29e-2	6.63e-2
Purinergic signaling in leishmaniasis infection ENTPD1	Reactome	1 / 24	62.6×	1.59e-2	7.50e-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 ⇵
sphingolipid metabolic process B4GALNT1, GBA2	GO:0006665	2 / 59	79.2×	2.71e-4	6.30e-3 ✓ sig.
GMP catabolic process to guanine NT5C2	GO:0006202	1 / 1	2,336×	4.28e-4	8.53e-3 ✓ sig.
purine ribonucleoside diphosphate catabolic process ENTPD1	GO:0009181	1 / 2	1,168×	8.56e-4	1.33e-2 ✓ sig.
cholesterol metabolic process GBA2, ERLIN2	GO:0008203	2 / 107	43.7×	8.89e-4	1.37e-2 ✓ sig.
glucosylceramide catabolic process GBA2	GO:0006680	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
dGMP metabolic process NT5C2	GO:0046054	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
ADP catabolic process ENTPD1	GO:0046032	1 / 3	779×	1.28e-3	1.67e-2 ✓ sig.
steroid metabolic process GBA2, ERLIN2	GO:0008202	2 / 135	34.6×	1.41e-3	1.77e-2 ✓ sig.
IMP metabolic process NT5C2	GO:0046040	1 / 4	584×	1.71e-3	1.96e-2 ✓ sig.
negative regulation of defense response to virus by host NT5C2	GO:0050689	1 / 4	584×	1.71e-3	1.96e-2 ✓ sig.
nucleoside diphosphate catabolic process ENTPD1	GO:0009134	1 / 4	584×	1.71e-3	1.96e-2 ✓ sig.
IMP catabolic process NT5C2	GO:0006204	1 / 5	467×	2.14e-3	2.19e-2 ✓ sig.
GMP catabolic process NT5C2	GO:0046038	1 / 5	467×	2.14e-3	2.19e-2 ✓ sig.
carbohydrate metabolic process B4GALNT1, GBA2	GO:0005975	2 / 175	26.7×	2.35e-3	2.30e-2 ✓ sig.
central nervous system myelin formation MAG	GO:0032289	1 / 6	389×	2.57e-3	2.40e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Complex hereditary spastic paraplegia	Spastic paraplegia 45, autosomal recessive	0.111	1	5.17e-4	9.13e-4 ✓ sig.
Complex hereditary spastic paraplegia	Spastic paraplegia 26, autosomal recessive	0.111	1	5.17e-4	9.13e-4 ✓ sig.
Complex hereditary spastic paraplegia	Spastic paraplegia 46, autosomal recessive	0.111	1	5.17e-4	9.13e-4 ✓ sig.
Complex hereditary spastic paraplegia	Spastic paraplegia 75, autosomal recessive	0.111	1	5.17e-4	9.13e-4 ✓ sig.

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