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Cluster 328

7 diseases · 11 shared-gene connections

7 Diseases

19 Unique genes

0.213 Avg. similarity score

Blindness Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Microphthalmia/coloboma 3 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.

Microphthalmia/coloboma 3 Blindness Microphthalmia with cataracts and iris abnormalities Microphthalmia, isolated 2 Retinal disorder Epileptic encephalopathy, early infantile, 38

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Blindness	4	4	14
Microphthalmia with cataracts and iris abnormalities	4	4	1
Microphthalmia, isolated 2	4	4	1
Microphthalmia/coloboma 3	4	4	1
Retinal disorder	4	4	6
Epileptic encephalopathy, early infantile, 38	1	1	1
Hereditary spastic paraplegia 11	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
VSX2	5 / 7	Blindness, Microphthalmia with cataracts and iris abnormalities, Microphthalmia, isolated 2, Microphthalmia/coloboma 3 and 1 more
ARV1	2 / 7	Blindness, Epileptic encephalopathy, early infantile, 38
SPG11	2 / 7	Hereditary spastic paraplegia 11, Retinal disorder

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 ⇵
The canonical retinoid cycle in rods (twilight vision) ABCA4, RHO, RPE65	Reactome	3 / 20	94.8×	3.76e-6	1.30e-4 ✓ sig.
Defective CYP2U1 causes Spastic paraplegia 56, autosomal recessive (SPG56) CYP2U1	Reactome	1 / 1	632×	1.58e-3	1.60e-2 ✓ sig.
Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) CYP2U1	Reactome	1 / 9	70.2×	1.42e-2	7.00e-2
Activation of the phototransduction cascade RHO	Reactome	1 / 9	70.2×	1.42e-2	7.00e-2
Opsins RHO	Reactome	1 / 10	63.2×	1.57e-2	7.46e-2
Purine ribonucleoside monophosphate biosynthesis ATIC	Reactome	1 / 12	52.7×	1.88e-2	8.28e-2
Miscellaneous substrates CYP2U1	Reactome	1 / 12	52.7×	1.88e-2	8.28e-2
Passive transport by Aquaporins AQP4	Reactome	1 / 12	52.7×	1.88e-2	8.28e-2
Retinoid cycle disease events ABCA4	Reactome	1 / 13	48.6×	2.04e-2	8.67e-2
Processing of SMDT1 PMPCA	Reactome	1 / 16	39.5×	2.50e-2	9.76e-2
G0 and Early G1 DYRK1A	Reactome	1 / 18	35.1×	2.81e-2	1.04e-1
VxPx cargo-targeting to cilium RHO	Reactome	1 / 21	30.1×	3.27e-2	1.14e-1
Cholesterol biosynthesis ARV1	Reactome	1 / 21	30.1×	3.27e-2	1.14e-1
Phototransduction RHO	KEGG	1 / 29	21.8×	4.49e-2	1.36e-1
Antifolate resistance ATIC	KEGG	1 / 30	21.1×	4.64e-2	1.39e-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 ⇵
visual perception ABCA4, EFEMP1, RHO, RPE65, USH2A, AIPL1, VSX2, UNC119	GO:0007601	8 / 215	36.6×	1.83e-11	6.57e-9 ✓ sig.
photoreceptor cell maintenance ABCA4, LCA5, RHO, USH2A	GO:0045494	4 / 45	87.4×	1.11e-7	1.38e-5 ✓ sig.
phototransduction, visible light ABCA4, RHO, AIPL1	GO:0007603	3 / 13	227×	2.53e-7	2.76e-5 ✓ sig.
camera-type eye development CEP290, EFEMP1, RPE65, VSX2	GO:0043010	4 / 74	53.2×	8.39e-7	7.43e-5 ✓ sig.
sensory perception of light stimulus RHO, USH2A	GO:0050953	2 / 13	151×	7.59e-5	2.52e-3 ✓ sig.
retina homeostasis RPE65, AIPL1	GO:0001895	2 / 15	131×	1.02e-4	3.14e-3 ✓ sig.
retinal metabolic process ABCA4, RPE65	GO:0042574	2 / 19	104×	1.66e-4	4.44e-3 ✓ sig.
response to light stimulus RHO, RPE65	GO:0009416	2 / 28	70.3×	3.64e-4	7.70e-3 ✓ sig.
phototransduction RHO, UNC119	GO:0007602	2 / 34	57.9×	5.39e-4	9.93e-3 ✓ sig.
retinoid metabolic process ABCA4, RPE65	GO:0001523	2 / 38	51.8×	6.74e-4	1.16e-2 ✓ sig.
peptidyl-tyrosine phosphorylation EFEMP1, DYRK1A	GO:0018108	2 / 39	50.4×	7.10e-4	1.19e-2 ✓ sig.
phagosome-lysosome fusion involved in apoptotic cell clearance SPG11	GO:0090389	1 / 1	984×	1.02e-3	1.48e-2 ✓ sig.
zeaxanthin biosynthetic process RPE65	GO:1901827	1 / 1	984×	1.02e-3	1.48e-2 ✓ sig.
regulation of plasma membrane sterol distribution ARV1	GO:0097036	1 / 1	984×	1.02e-3	1.48e-2 ✓ sig.
ciliary basal body-plasma membrane docking CEP290	GO:0097711	1 / 2	492×	2.03e-3	2.14e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Microphthalmia with cataracts and iris abnormalities	Microphthalmia/coloboma 3	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Microphthalmia with cataracts and iris abnormalities	Microphthalmia, isolated 2	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Microphthalmia, isolated 2	Microphthalmia/coloboma 3	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Hereditary spastic paraplegia 11	Retinal disorder	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Microphthalmia with cataracts and iris abnormalities	Retinal disorder	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Microphthalmia, isolated 2	Retinal disorder	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Microphthalmia/coloboma 3	Retinal disorder	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Blindness	Epileptic encephalopathy, early infantile, 38	0.067	1	9.04e-4	1.41e-3 ✓ sig.
Blindness	Microphthalmia with cataracts and iris abnormalities	0.067	1	9.04e-4	1.41e-3 ✓ sig.
Blindness	Microphthalmia, isolated 2	0.067	1	9.04e-4	1.41e-3 ✓ sig.
Blindness	Microphthalmia/coloboma 3	0.067	1	9.04e-4	1.41e-3 ✓ sig.

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