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Cluster 272

7 diseases · 8 shared-gene connections

7 Diseases

203 Unique genes

0.035 Avg. similarity score

Specific language disorder 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.

Specific language disorder Brain aneurysm Dyslexia Male infertility acephalic spermatozoa holocarboxylase synthetase deficiency Cortical dysplasia-focal epilepsy syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Specific language disorder	4	4	19
Brain aneurysm	3	3	87
Dyslexia	3	3	111
Male infertility acephalic spermatozoa	2	2	2
holocarboxylase synthetase deficiency	2	2	1
Cortical dysplasia-focal epilepsy syndrome	1	1	1
Trimethylaminuria	1	1	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
HLCS	3 / 7	Brain aneurysm, holocarboxylase synthetase deficiency, Specific language disorder
PMFBP1	3 / 7	Dyslexia, Male infertility acephalic spermatozoa, Specific language disorder
CCDC136	2 / 7	Dyslexia, Specific language disorder
CCDC171	2 / 7	Brain aneurysm, Dyslexia
CNTNAP2	2 / 7	Cortical dysplasia-focal epilepsy syndrome, Specific language disorder
COX6A1	2 / 7	Dyslexia, Specific language disorder
EPHA4	2 / 7	Dyslexia, Specific language disorder
ESRRG	2 / 7	Brain aneurysm, Dyslexia
FHIT	2 / 7	Brain aneurysm, Dyslexia
FMO4	2 / 7	Brain aneurysm, Trimethylaminuria
FOXP2	2 / 7	Dyslexia, Specific language disorder
HDAC9	2 / 7	Brain aneurysm, Dyslexia
INIP	2 / 7	Dyslexia, Specific language disorder
RBFOX1	2 / 7	Brain aneurysm, Dyslexia
RBFOX2	2 / 7	Dyslexia, Specific language disorder
RBMS3	2 / 7	Brain aneurysm, Dyslexia
STK24	2 / 7	Dyslexia, Specific language disorder
ZFP64	2 / 7	Dyslexia, Specific language 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 ⇵
LDL remodeling APOB, CETP	Reactome	2 / 3	39.4×	8.43e-4	1.19e-2 ✓ sig.
Cholesterol metabolism ABCG5, ANGPTL4, APOB, APOE, CETP	KEGG	5 / 51	5.8×	1.64e-3	1.98e-2 ✓ sig.
Chylomicron clearance APOB, APOE	Reactome	2 / 5	23.7×	2.75e-3	2.89e-2 ✓ sig.
Elastic fibre formation FBN1, FBN2, ITGAV	Reactome	3 / 18	9.9×	3.22e-3	3.24e-2 ✓ sig.
DARPP-32 events PDE4D, PPP1R1B, PPP2R1B	Reactome	3 / 19	9.3×	3.78e-3	3.62e-2 ✓ sig.
Scavenging by Class F Receptors SCARF1, APOB	Reactome	2 / 6	19.7×	4.08e-3	3.82e-2 ✓ sig.
Lysine degradation ALDH2, HYKK, PRDM2, KMT2E, SETDB2	KEGG	5 / 63	4.7×	4.17e-3	3.88e-2 ✓ sig.
Regulation of FOXO transcriptional activity by acetylation SIRT3, FOXO3	Reactome	2 / 7	16.9×	5.65e-3	4.75e-2 ✓ sig.
Dopaminergic synapse CAMK2B, DRD4, GNAQ, PPP1R1B, PPP2R1B, PPP2R3A, SLC6A3	KEGG	7 / 132	3.1×	7.08e-3	5.51e-2
Chylomicron remodeling APOB, APOE	Reactome	2 / 9	13.1×	9.47e-3	6.63e-2
Chylomicron assembly APOB, APOE	Reactome	2 / 9	13.1×	9.47e-3	6.63e-2
HDL remodeling APOE, CETP	Reactome	2 / 10	11.8×	1.17e-2	7.54e-2
FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes SIRT3, FOXO3	Reactome	2 / 10	11.8×	1.17e-2	7.54e-2
Scavenging by Class A Receptors APOB, APOE	Reactome	2 / 11	10.8×	1.41e-2	8.41e-2
Defective FMO3 causes Trimethylaminuria (TMAU) FMO3	Reactome	1 / 1	59.2×	1.69e-2	9.37e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
vocal learning CNTNAP2, FOXP2, HTT, NRXN1	GO:0042297	4 / 8	46.0×	9.15e-7	7.72e-5 ✓ sig.
positive regulation of synapse maturation CAMK2B, NEUROD2, NRXN1	GO:0090129	3 / 8	34.5×	6.80e-5	2.26e-3 ✓ sig.
proteoglycan biosynthetic process CHST8, CHST9, CSGALNACT1, XYLT1	GO:0030166	4 / 21	17.5×	7.00e-5	2.32e-3 ✓ sig.
positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity HTT, HAP1	GO:0031587	2 / 2	92.1×	1.17e-4	3.42e-3 ✓ sig.
low-density lipoprotein particle remodeling APOB, APOE, CETP	GO:0034374	3 / 16	17.3×	6.37e-4	1.13e-2 ✓ sig.
photoreceptor cell development RP1, RP1L1	GO:0042461	2 / 4	46.0×	6.95e-4	1.19e-2 ✓ sig.
sequestering of TGFbeta in extracellular matrix FBN1, FBN2	GO:0035583	2 / 4	46.0×	6.95e-4	1.19e-2 ✓ sig.
triglyceride homeostasis ABCG5, ANGPTL4, APOE, CETP	GO:0070328	4 / 38	9.7×	7.47e-4	1.25e-2 ✓ sig.
axon development L1CAM, MAPT, MARK2, NEUROD2	GO:0061564	4 / 40	9.2×	9.10e-4	1.42e-2 ✓ sig.
vocalization behavior CNTNAP2, FOXP2, NRXN1	GO:0071625	3 / 19	14.5×	1.08e-3	1.58e-2 ✓ sig.
cellular response to lipoprotein particle stimulus APOB, APOE	GO:0071402	2 / 5	36.8×	1.15e-3	1.65e-2 ✓ sig.
NMDA glutamate receptor clustering NRXN1, APOE	GO:0097114	2 / 5	36.8×	1.15e-3	1.65e-2 ✓ sig.
camera-type eye photoreceptor cell differentiation DSCAM, PROM1	GO:0060219	2 / 5	36.8×	1.15e-3	1.65e-2 ✓ sig.
antral ovarian follicle growth FOXO3, ESR1	GO:0001547	2 / 5	36.8×	1.15e-3	1.65e-2 ✓ sig.
positive regulation of cation channel activity EDNRA, STAC	GO:2001259	2 / 5	36.8×	1.15e-3	1.65e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Dyslexia	Specific language disorder	0.074	9	3.29e-15	5.01e-14 ✓ sig.
Brain aneurysm	Dyslexia	0.031	6	3.85e-5	1.86e-4 ✓ sig.
Cortical dysplasia-focal epilepsy syndrome	Specific language disorder	0.050	1	1.23e-3	1.97e-3 ✓ sig.
holocarboxylase synthetase deficiency	Specific language disorder	0.050	1	1.23e-3	1.97e-3 ✓ sig.
Male infertility acephalic spermatozoa	Specific language disorder	0.048	1	2.47e-3	3.36e-3 ✓ sig.
Brain aneurysm	holocarboxylase synthetase deficiency	0.011	1	5.65e-3	6.86e-3 ✓ sig.
Brain aneurysm	Trimethylaminuria	0.011	1	1.13e-2	1.27e-2 ✓ sig.
Dyslexia	Male infertility acephalic spermatozoa	0.009	1	1.44e-2	1.60e-2 ✓ sig.

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