Disease Clusters | GeDiPNet

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Cluster 253

7 diseases · 17 shared-gene connections

7 Diseases

7 Unique genes

0.333 Avg. similarity score

Axenfeld anomaly Most-connected disease (6 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: anterior segment dysgenesis 4 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.

anterior segment dysgenesis 4 Axenfeld anomaly Iridogoniodysgenesis Rieger syndrome Axenfeld-rieger syndrome FOXC1-related anterior segment dysgenesis

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Axenfeld anomaly	6	6	2
Iridogoniodysgenesis	6	6	2
Rieger syndrome	6	6	4
Axenfeld-rieger syndrome	4	4	6
FOXC1-related anterior segment dysgenesis	4	4	1
Ring dermoid of cornea	4	4	1
anterior segment dysgenesis 4	4	4	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
PITX2	6 / 7	anterior segment dysgenesis 4, Axenfeld anomaly, Axenfeld-rieger syndrome, Iridogoniodysgenesis and 2 more
FOXC1	5 / 7	Axenfeld anomaly, Axenfeld-rieger syndrome, FOXC1-related anterior segment dysgenesis, Iridogoniodysgenesis and 1 more
COL4A1	2 / 7	Axenfeld-rieger syndrome, Rieger syndrome

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 ⇵
Hedgehog 'off' state IFT140, PTCH1	Reactome	2 / 56	61.3×	4.42e-4	7.53e-3 ✓ sig.
TFAP2 (AP-2) family regulates transcription of other transcription factors PITX2	Reactome	1 / 4	429×	2.33e-3	2.65e-2 ✓ sig.
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) PAX6	Reactome	1 / 7	245×	4.07e-3	3.93e-2 ✓ sig.
Ligand-receptor interactions PTCH1	Reactome	1 / 7	245×	4.07e-3	3.93e-2 ✓ sig.
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) PAX6	Reactome	1 / 14	123×	8.13e-3	6.22e-2
Extracellular matrix organization COL4A1	Reactome	1 / 15	114×	8.71e-3	6.50e-2
Anchoring fibril formation COL4A1	Reactome	1 / 15	114×	8.71e-3	6.50e-2
Activation of SMO PTCH1	Reactome	1 / 18	95.3×	1.04e-2	7.29e-2
Crosslinking of collagen fibrils COL4A1	Reactome	1 / 18	95.3×	1.04e-2	7.29e-2
NCAM1 interactions COL4A1	Reactome	1 / 21	81.7×	1.22e-2	8.02e-2
Non-integrin membrane-ECM interactions COL4A1	Reactome	1 / 24	71.5×	1.39e-2	8.64e-2
Maturity onset diabetes of the young PAX6	KEGG	1 / 26	66.0×	1.51e-2	9.07e-2
Laminin interactions COL4A1	Reactome	1 / 28	61.3×	1.62e-2	9.49e-2
Signaling by PDGF COL4A1	Reactome	1 / 33	52.0×	1.91e-2	1.04e-1
Collagen chain trimerization COL4A1	Reactome	1 / 44	39.0×	2.54e-2	1.22e-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 ⇵
brain development FOXC1, COL4A1, PAX6, PTCH1	GO:0007420	4 / 244	43.8×	9.63e-7	8.18e-5 ✓ sig.
camera-type eye development FOXC1, PITX2, PAX6	GO:0043010	3 / 74	108×	2.06e-6	1.52e-4 ✓ sig.
lacrimal gland development FOXC1, PAX6	GO:0032808	2 / 7	763×	2.52e-6	1.80e-4 ✓ sig.
neural tube patterning IFT140, PTCH1	GO:0021532	2 / 8	667×	3.36e-6	2.26e-4 ✓ sig.
iris morphogenesis PITX2, PAX6	GO:0061072	2 / 9	593×	4.32e-6	2.75e-4 ✓ sig.
negative regulation of transcription by RNA polymerase II FOXC1, PITX2, PRDM5, PAX6, PTCH1	GO:0000122	5 / 1,002	13.3×	8.42e-6	4.74e-4 ✓ sig.
animal organ morphogenesis PITX2, PAX6, PTCH1	GO:0009887	3 / 130	61.6×	1.13e-5	5.94e-4 ✓ sig.
embryonic camera-type eye development PITX2, IFT140	GO:0031076	2 / 15	356×	1.26e-5	6.46e-4 ✓ sig.
cell fate determination PAX6, PTCH1	GO:0001709	2 / 18	297×	1.84e-5	8.67e-4 ✓ sig.
anatomical structure morphogenesis FOXC1, PITX2, PAX6	GO:0009653	3 / 160	50.1×	2.10e-5	9.64e-4 ✓ sig.
regulation of smoothened signaling pathway IFT140, PTCH1	GO:0008589	2 / 29	184×	4.86e-5	1.82e-3 ✓ sig.
pituitary gland development PITX2, PAX6	GO:0021983	2 / 30	178×	5.21e-5	1.92e-3 ✓ sig.
limb morphogenesis IFT140, PTCH1	GO:0035108	2 / 31	172×	5.56e-5	2.02e-3 ✓ sig.
branching involved in blood vessel morphogenesis PITX2, COL4A1	GO:0001569	2 / 33	162×	6.32e-5	2.21e-3 ✓ sig.
in utero embryonic development FOXC1, PITX2, PTCH1	GO:0001701	3 / 252	31.8×	8.15e-5	2.70e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Axenfeld-rieger syndrome	Rieger syndrome	0.375	3	1.31e-10	1.29e-9 ✓ sig.
Axenfeld anomaly	Iridogoniodysgenesis	0.667	2	8.44e-9	6.82e-8 ✓ sig.
Iridogoniodysgenesis	Rieger syndrome	0.400	2	5.06e-8	3.71e-7 ✓ sig.
Axenfeld anomaly	Rieger syndrome	0.400	2	5.06e-8	3.71e-7 ✓ sig.
Axenfeld-rieger syndrome	Iridogoniodysgenesis	0.286	2	1.27e-7	8.71e-7 ✓ sig.
Axenfeld anomaly	Axenfeld-rieger syndrome	0.286	2	1.27e-7	8.71e-7 ✓ sig.
anterior segment dysgenesis 4	Ring dermoid of cornea	0.500	1	6.49e-5	2.33e-4 ✓ sig.
anterior segment dysgenesis 4	Axenfeld anomaly	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Iridogoniodysgenesis	Ring dermoid of cornea	0.333	1	1.30e-4	3.93e-4 ✓ sig.
FOXC1-related anterior segment dysgenesis	Iridogoniodysgenesis	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Axenfeld anomaly	Ring dermoid of cornea	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Axenfeld anomaly	FOXC1-related anterior segment dysgenesis	0.333	1	1.30e-4	3.93e-4 ✓ sig.
anterior segment dysgenesis 4	Iridogoniodysgenesis	0.333	1	1.30e-4	3.93e-4 ✓ sig.
FOXC1-related anterior segment dysgenesis	Rieger syndrome	0.200	1	2.60e-4	6.51e-4 ✓ sig.
anterior segment dysgenesis 4	Rieger syndrome	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Rieger syndrome	Ring dermoid of cornea	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Axenfeld-rieger syndrome	FOXC1-related anterior segment dysgenesis	0.143	1	3.90e-4	8.67e-4 ✓ sig.

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