Disease Clusters | GeDiPNet

← Back to all clusters

Cluster 580

5 diseases · 10 shared-gene connections

5 Diseases

4 Unique genes

0.380 Avg. similarity score

Ayme-gripp syndrome 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.

Ayme-gripp syndrome Cataract 21, multiple types Cataract, pulverulent or cerulean, with or without microcornea Cataract-multisystem syndrome Cataracts, congenital, with sensorineural deafness, down syndrome-like facial appearance, short stature, and mental retardation

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Ayme-gripp syndrome	4	4	1
Cataract 21, multiple types	4	4	1
Cataract, pulverulent or cerulean, with or without microcornea	4	4	1
Cataract-multisystem syndrome	4	4	4
Cataracts, congenital, with sensorineural deafness, down syndrome-like facial appearance, short stature, and mental retardation	4	4	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
MAF	5 / 5	Ayme-gripp syndrome, Cataract 21, multiple types, Cataract, pulverulent or cerulean, with or without microcornea, Cataract-multisystem syndrome 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 ⇵
rRNA modification in the nucleus and cytosol DKC1, NOP10	Reactome	2 / 12	500×	5.49e-6	1.77e-4 ✓ sig.
Telomere Extension By Telomerase DKC1, NOP10	Reactome	2 / 16	375×	9.97e-6	2.91e-4 ✓ sig.
Ribosome biogenesis in eukaryotes DKC1, NOP10	KEGG	2 / 125	48.0×	6.36e-4	8.05e-3 ✓ sig.
Fructose catabolism TKFC	Reactome	1 / 5	601×	1.66e-3	1.66e-2 ✓ sig.
DDX58/IFIH1-mediated induction of interferon-alpha/beta TKFC	Reactome	1 / 17	177×	5.65e-3	3.96e-2 ✓ sig.
Fructose and mannose metabolism TKFC	KEGG	1 / 34	88.3×	1.13e-2	6.12e-2
Glycerolipid metabolism TKFC	KEGG	1 / 64	46.9×	2.11e-2	8.84e-2
Inflammatory bowel disease MAF	KEGG	1 / 66	45.5×	2.18e-2	9.01e-2
RIG-I-like receptor signaling pathway TKFC	KEGG	1 / 72	41.7×	2.38e-2	9.47e-2
Th1 and Th2 cell differentiation MAF	KEGG	1 / 93	32.3×	3.06e-2	1.10e-1
Carbon metabolism TKFC	KEGG	1 / 115	26.1×	3.78e-2	1.23e-1
Transcriptional misregulation in cancer MAF	KEGG	1 / 198	15.2×	6.43e-2	1.67e-1
Metabolic pathways TKFC	KEGG	1 / 1,563	1.9×	4.28e-1	5.52e-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 ⇵
snRNA pseudouridine synthesis DKC1, NOP10	GO:0031120	2 / 3	3,115×	1.03e-7	1.30e-5 ✓ sig.
rRNA pseudouridine synthesis DKC1, NOP10	GO:0031118	2 / 4	2,336×	2.06e-7	2.32e-5 ✓ sig.
pseudouridine synthesis DKC1, NOP10	GO:0001522	2 / 16	584×	4.12e-6	2.71e-4 ✓ sig.
telomere maintenance via telomerase DKC1, NOP10	GO:0007004	2 / 24	389×	9.47e-6	5.21e-4 ✓ sig.
box H/ACA sno(s)RNA metabolic process DKC1	GO:0033979	1 / 1	4,672×	2.14e-4	5.31e-3 ✓ sig.
ribosome biogenesis DKC1, NOP10	GO:0042254	2 / 122	76.6×	2.51e-4	5.98e-3 ✓ sig.
box H/ACA sno(s)RNA 3'-end processing DKC1	GO:0000495	1 / 2	2,336×	4.28e-4	8.53e-3 ✓ sig.
protein localization to Cajal body DKC1	GO:1904867	1 / 2	2,336×	4.28e-4	8.53e-3 ✓ sig.
rRNA processing DKC1, NOP10	GO:0006364	2 / 162	57.7×	4.43e-4	8.75e-3 ✓ sig.
fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate TKFC	GO:0061624	1 / 3	1,557×	6.42e-4	1.11e-2 ✓ sig.
negative regulation of MDA-5 signaling pathway TKFC	GO:0039534	1 / 4	1,168×	8.56e-4	1.33e-2 ✓ sig.
telomerase RNA stabilization DKC1	GO:0090669	1 / 4	1,168×	8.56e-4	1.33e-2 ✓ sig.
regulation of telomerase RNA localization to Cajal body DKC1	GO:1904872	1 / 4	1,168×	8.56e-4	1.33e-2 ✓ sig.
enzyme-directed rRNA pseudouridine synthesis DKC1	GO:0000455	1 / 4	1,168×	8.56e-4	1.33e-2 ✓ sig.
scaRNA localization to Cajal body DKC1	GO:0090666	1 / 5	934×	1.07e-3	1.51e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Ayme-gripp syndrome	Cataract 21, multiple types	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Ayme-gripp syndrome	Cataract, pulverulent or cerulean, with or without microcornea	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Ayme-gripp syndrome	Cataracts, congenital, with sensorineural deafness, down syndrome-like facial appearance, short stature, and mental retardation	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cataract 21, multiple types	Cataract, pulverulent or cerulean, with or without microcornea	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cataract 21, multiple types	Cataracts, congenital, with sensorineural deafness, down syndrome-like facial appearance, short stature, and mental retardation	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cataract, pulverulent or cerulean, with or without microcornea	Cataracts, congenital, with sensorineural deafness, down syndrome-like facial appearance, short stature, and mental retardation	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Ayme-gripp syndrome	Cataract-multisystem syndrome	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Cataract 21, multiple types	Cataract-multisystem syndrome	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Cataract-multisystem syndrome	Cataract, pulverulent or cerulean, with or without microcornea	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Cataract-multisystem syndrome	Cataracts, congenital, with sensorineural deafness, down syndrome-like facial appearance, short stature, and mental retardation	0.200	1	2.58e-4	5.38e-4 ✓ sig.

Disease Clusters?