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Cluster 628

5 diseases · 10 shared-gene connections

5 Diseases

7 Unique genes

0.305 Avg. similarity score

Cutis laxa, autosomal dominant, 2 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.

Cutis laxa, autosomal dominant, 2 Cutis laxa, autosomal recessive, 1a Cutis laxa, autosomal recessive, type ia Demyelinating hereditary motor and sensory neuropathy Proximal spinal muscular atrophy

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cutis laxa, autosomal dominant, 2	4	4	1
Cutis laxa, autosomal recessive, 1a	4	4	1
Cutis laxa, autosomal recessive, type ia	4	4	1
Demyelinating hereditary motor and sensory neuropathy	4	4	2
Proximal spinal muscular atrophy	4	4	6

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

Gene ⇵	Member diseases ⇵	Linked diseases
FBLN5	5 / 5	Cutis laxa, autosomal dominant, 2, Cutis laxa, autosomal recessive, 1a, Cutis laxa, autosomal recessive, type ia, Demyelinating hereditary motor and sensory neuropathy and 1 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 ⇵
snRNP Assembly SMN1, SMN2	Reactome	2 / 53	64.7×	3.96e-4	5.58e-3 ✓ sig.
Synthesis of PIPs at the ER membrane MTMR2	Reactome	1 / 5	343×	2.91e-3	2.49e-2 ✓ sig.
Synthesis of PIPs at the late endosome membrane MTMR2	Reactome	1 / 10	172×	5.82e-3	4.03e-2 ✓ sig.
Synthesis of PIPs at the early endosome membrane MTMR2	Reactome	1 / 15	114×	8.71e-3	5.22e-2
Processing of SMDT1 SPG7	Reactome	1 / 16	107×	9.29e-3	5.43e-2
Elastic fibre formation FBLN5	Reactome	1 / 18	95.3×	1.04e-2	5.84e-2
Molecules associated with elastic fibres FBLN5	Reactome	1 / 38	45.2×	2.19e-2	9.03e-2
Legionellosis NAIP	KEGG	1 / 56	30.6×	3.22e-2	1.13e-1
Inositol phosphate metabolism MTMR2	KEGG	1 / 73	23.5×	4.18e-2	1.31e-1
Phosphatidylinositol signaling system MTMR2	KEGG	1 / 98	17.5×	5.58e-2	1.54e-1
NOD-like receptor signaling pathway NAIP	KEGG	1 / 187	9.2×	1.04e-1	2.21e-1
Pathogenic Escherichia coli infection NAIP	KEGG	1 / 200	8.6×	1.11e-1	2.30e-1
Salmonella infection NAIP	KEGG	1 / 248	6.9×	1.36e-1	2.60e-1
Shigellosis NAIP	KEGG	1 / 250	6.9×	1.37e-1	2.61e-1
Amyotrophic lateral sclerosis SETX	KEGG	1 / 368	4.7×	1.96e-1	3.27e-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 ⇵
DNA-templated transcription termination SETX, SMN1, SMN2	GO:0006353	3 / 13	616×	9.19e-9	1.64e-6 ✓ sig.
nervous system development SETX, SPG7, NAIP, SMN1, SMN2	GO:0007399	5 / 631	21.2×	8.58e-7	7.55e-5 ✓ sig.
spliceosomal complex assembly SMN1, SMN2	GO:0000245	2 / 28	191×	4.53e-5	1.71e-3 ✓ sig.
spliceosomal snRNP assembly SMN1, SMN2	GO:0000387	2 / 29	184×	4.86e-5	1.81e-3 ✓ sig.
RNA splicing, via transesterification reactions SMN1, SMN2	GO:0000375	2 / 30	178×	5.21e-5	1.90e-3 ✓ sig.
negative regulation of receptor catabolic process MTMR2	GO:2000645	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
positive regulation of termination of DNA-templated transcription SETX	GO:0060566	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
intramembranous bone growth FBLN5	GO:0098867	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
mitochondrial outer membrane permeabilization involved in programmed cell death SPG7	GO:1902686	1 / 2	1,335×	7.49e-4	1.23e-2 ✓ sig.
positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled SETX	GO:2000806	1 / 3	890×	1.12e-3	1.55e-2 ✓ sig.
regulation of calcium import into the mitochondrion SPG7	GO:0110097	1 / 3	890×	1.12e-3	1.55e-2 ✓ sig.
regulation of phosphatidylinositol dephosphorylation MTMR2	GO:0060304	1 / 5	534×	1.87e-3	2.05e-2 ✓ sig.
mitochondrial protein processing SPG7	GO:0034982	1 / 6	445×	2.25e-3	2.24e-2 ✓ sig.
regulation of removal of superoxide radicals FBLN5	GO:2000121	1 / 7	381×	2.62e-3	2.44e-2 ✓ sig.
myelin assembly MTMR2	GO:0032288	1 / 7	381×	2.62e-3	2.44e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Cutis laxa, autosomal dominant, 2	Cutis laxa, autosomal recessive, type ia	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cutis laxa, autosomal dominant, 2	Cutis laxa, autosomal recessive, 1a	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cutis laxa, autosomal recessive, 1a	Cutis laxa, autosomal recessive, type ia	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cutis laxa, autosomal dominant, 2	Demyelinating hereditary motor and sensory neuropathy	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cutis laxa, autosomal recessive, 1a	Demyelinating hereditary motor and sensory neuropathy	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cutis laxa, autosomal recessive, type ia	Demyelinating hereditary motor and sensory neuropathy	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cutis laxa, autosomal dominant, 2	Proximal spinal muscular atrophy	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Cutis laxa, autosomal recessive, 1a	Proximal spinal muscular atrophy	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Cutis laxa, autosomal recessive, type ia	Proximal spinal muscular atrophy	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Demyelinating hereditary motor and sensory neuropathy	Proximal spinal muscular atrophy	0.125	1	7.75e-4	1.25e-3 ✓ sig.

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