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Cluster 374

5 diseases · 6 shared-gene connections

5 Diseases

10 Unique genes

0.216 Avg. similarity score

IFT140-related recessive ciliopathy Most-connected disease (3 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: IFT140-related recessive ciliopathy 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.

IFT140-related recessive ciliopathy Saldino-mainzer syndrome autosomal dominant polycystic kidney disease Mainzer-saldino disease renal-hepatic-pancreatic dysplasia 2

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
IFT140-related recessive ciliopathy	3	3	1
Saldino-mainzer syndrome	3	3	2
autosomal dominant polycystic kidney disease	3	3	7
Mainzer-saldino disease	2	2	4
renal-hepatic-pancreatic dysplasia 2	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
IFT140	4 / 5	autosomal dominant polycystic kidney disease, IFT140-related recessive ciliopathy, Mainzer-saldino disease, Saldino-mainzer syndrome
IFT172	2 / 5	Mainzer-saldino disease, Saldino-mainzer syndrome
NEK8	2 / 5	autosomal dominant polycystic kidney disease, renal-hepatic-pancreatic dysplasia 2

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 ⇵
Intraflagellar transport IFT140, IFT172, WDR19	Reactome	3 / 54	66.7×	1.01e-5	3.58e-4 ✓ sig.
Hedgehog 'off' state IFT140, IFT172, WDR19	Reactome	3 / 56	64.3×	1.13e-5	3.91e-4 ✓ sig.
VxPx cargo-targeting to cilium PKD1, PKD2	Reactome	2 / 21	114×	1.30e-4	2.86e-3 ✓ sig.
Defective ALG8 causes ALG8-CDG (CDG-1h) ALG8	Reactome	1 / 1	1,201×	8.33e-4	1.22e-2 ✓ sig.
N-Glycan biosynthesis ALG5, ALG8	KEGG	2 / 55	43.7×	9.05e-4	1.30e-2 ✓ sig.
Synthesis of dolichyl-phosphate-glucose ALG5	Reactome	1 / 2	601×	1.66e-3	2.07e-2 ✓ sig.
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein ALG8	Reactome	1 / 11	109×	9.12e-3	6.71e-2
XBP1(S) activates chaperone genes DNAJB11	Reactome	1 / 50	24.0×	4.09e-2	1.58e-1
Protein processing in endoplasmic reticulum DNAJB11	KEGG	1 / 171	7.0×	1.34e-1	2.97e-1
Metabolic pathways ALG5, ALG8	KEGG	2 / 1,563	1.5×	3.81e-1	5.44e-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 ⇵
determination of left/right symmetry IFT140, IFT172, NEK8, PKD2, ALG5	GO:0007368	5 / 83	113×	3.79e-10	9.51e-8 ✓ sig.
heart development IFT140, IFT172, NEK8, PKD1, PKD2	GO:0007507	5 / 273	34.2×	1.52e-7	1.76e-5 ✓ sig.
cilium organization IFT172, WDR19, PKD2	GO:0044782	3 / 40	140×	1.08e-6	9.00e-5 ✓ sig.
metanephric ascending thin limb development PKD1, PKD2	GO:0072218	2 / 4	934×	1.55e-6	1.22e-4 ✓ sig.
neural tube development IFT172, PKD1, PKD2	GO:0021915	3 / 45	125×	1.55e-6	1.22e-4 ✓ sig.
mesonephric duct development PKD1, PKD2	GO:0072177	2 / 6	623×	3.86e-6	2.51e-4 ✓ sig.
mesonephric tubule development PKD1, PKD2	GO:0072164	2 / 7	534×	5.40e-6	3.31e-4 ✓ sig.
chordate embryonic development PKD1, PKD2	GO:0043009	2 / 11	340×	1.41e-5	7.09e-4 ✓ sig.
placenta blood vessel development PKD1, PKD2	GO:0060674	2 / 14	267×	2.34e-5	1.04e-3 ✓ sig.
intraciliary retrograde transport IFT140, WDR19	GO:0035721	2 / 14	267×	2.34e-5	1.04e-3 ✓ sig.
embryonic camera-type eye development IFT140, WDR19	GO:0031076	2 / 15	249×	2.70e-5	1.16e-3 ✓ sig.
detection of mechanical stimulus PKD1, PKD2	GO:0050982	2 / 15	249×	2.70e-5	1.16e-3 ✓ sig.
protein heterotetramerization PKD1, PKD2	GO:0051290	2 / 16	234×	3.08e-5	1.29e-3 ✓ sig.
dolichol-linked oligosaccharide biosynthetic process ALG5, ALG8	GO:0006488	2 / 19	197×	4.39e-5	1.69e-3 ✓ sig.
protein N-linked glycosylation via asparagine ALG5, ALG8	GO:0018279	2 / 24	156×	7.07e-5	2.41e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Mainzer-saldino disease	Saldino-mainzer syndrome	0.400	2	5.06e-8	3.71e-7 ✓ sig.
IFT140-related recessive ciliopathy	Saldino-mainzer syndrome	0.333	1	1.30e-4	3.93e-4 ✓ sig.
IFT140-related recessive ciliopathy	Mainzer-saldino disease	0.200	1	2.60e-4	6.51e-4 ✓ sig.
autosomal dominant polycystic kidney disease	IFT140-related recessive ciliopathy	0.125	1	4.55e-4	9.73e-4 ✓ sig.
autosomal dominant polycystic kidney disease	renal-hepatic-pancreatic dysplasia 2	0.125	1	4.55e-4	9.73e-4 ✓ sig.
autosomal dominant polycystic kidney disease	Saldino-mainzer syndrome	0.111	1	9.09e-4	1.58e-3 ✓ sig.

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