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Cluster 595

5 diseases · 10 shared-gene connections

5 Diseases

3 Unique genes

0.400 Avg. similarity score

Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy 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.

Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy Cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1 Inherited thrombocytopenia Lateral meningocele syndrome Myofibromatosis, infantile 2

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy	4	4	3
Cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1	4	4	1
Inherited thrombocytopenia	4	4	1
Lateral meningocele syndrome	4	4	1
Myofibromatosis, infantile 2	4	4	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
NOTCH3	5 / 5	Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy, Cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1, Inherited thrombocytopenia, Lateral meningocele 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 ⇵
Defective LFNG causes SCDO3 NOTCH3	Reactome	1 / 5	801×	1.25e-3	1.34e-2 ✓ sig.
Pre-NOTCH Processing in Golgi NOTCH3	Reactome	1 / 6	667×	1.50e-3	1.54e-2 ✓ sig.
Noncanonical activation of NOTCH3 NOTCH3	Reactome	1 / 8	500×	2.00e-3	1.90e-2 ✓ sig.
NOTCH3 Intracellular Domain Regulates Transcription NOTCH3	Reactome	1 / 18	222×	4.49e-3	3.39e-2 ✓ sig.
NOTCH3 Activation and Transmission of Signal to the Nucleus NOTCH3	Reactome	1 / 19	211×	4.74e-3	3.52e-2 ✓ sig.
Notch-HLH transcription pathway NOTCH3	Reactome	1 / 28	143×	6.98e-3	4.53e-2 ✓ sig.
Pre-NOTCH Transcription and Translation NOTCH3	Reactome	1 / 31	129×	7.72e-3	4.84e-2 ✓ sig.
Notch signaling pathway NOTCH3	KEGG	1 / 62	64.6×	1.54e-2	7.38e-2
Degradation of the extracellular matrix HTRA1	Reactome	1 / 70	57.2×	1.74e-2	7.89e-2
Th1 and Th2 cell differentiation NOTCH3	KEGG	1 / 93	43.0×	2.31e-2	9.30e-2
Endocrine resistance NOTCH3	KEGG	1 / 99	40.4×	2.45e-2	9.64e-2
Thyroid hormone signaling pathway NOTCH3	KEGG	1 / 122	32.8×	3.02e-2	1.09e-1
Apelin signaling pathway NOTCH3	KEGG	1 / 140	28.6×	3.46e-2	1.17e-1
Breast cancer NOTCH3	KEGG	1 / 148	27.0×	3.65e-2	1.21e-1
MicroRNAs in cancer NOTCH3	KEGG	1 / 311	12.9×	7.57e-2	1.84e-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 ⇵
glomerular capillary formation NOTCH3	GO:0072104	1 / 3	2,076×	4.82e-4	9.24e-3 ✓ sig.
chorionic trophoblast cell differentiation HTRA1	GO:0060718	1 / 6	1,038×	9.63e-4	1.42e-2 ✓ sig.
neuroblast differentiation NOTCH3	GO:0014016	1 / 7	890×	1.12e-3	1.55e-2 ✓ sig.
retina homeostasis ARMS2	GO:0001895	1 / 15	415×	2.41e-3	2.32e-2 ✓ sig.
artery morphogenesis NOTCH3	GO:0048844	1 / 27	231×	4.33e-3	3.11e-2 ✓ sig.
regulation of developmental process NOTCH3	GO:0050793	1 / 32	195×	5.13e-3	3.37e-2 ✓ sig.
neuron fate commitment NOTCH3	GO:0048663	1 / 33	189×	5.29e-3	3.43e-2 ✓ sig.
programmed cell death HTRA1	GO:0012501	1 / 42	148×	6.73e-3	3.84e-2 ✓ sig.
placenta development HTRA1	GO:0001890	1 / 48	130×	7.69e-3	4.09e-2 ✓ sig.
positive regulation of smooth muscle cell proliferation NOTCH3	GO:0048661	1 / 52	120×	8.33e-3	4.25e-2 ✓ sig.
positive regulation of miRNA transcription NOTCH3	GO:1902895	1 / 56	111×	8.96e-3	4.41e-2 ✓ sig.
negative regulation of neuron differentiation NOTCH3	GO:0045665	1 / 63	98.9×	1.01e-2	4.67e-2 ✓ sig.
negative regulation of cell differentiation NOTCH3	GO:0045596	1 / 75	83.1×	1.20e-2	5.06e-2
negative regulation of BMP signaling pathway HTRA1	GO:0030514	1 / 75	83.1×	1.20e-2	5.06e-2
forebrain development NOTCH3	GO:0030900	1 / 76	82.0×	1.22e-2	5.10e-2

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1	Inherited thrombocytopenia	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1	Lateral meningocele syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1	Myofibromatosis, infantile 2	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Inherited thrombocytopenia	Lateral meningocele syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Inherited thrombocytopenia	Myofibromatosis, infantile 2	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Lateral meningocele syndrome	Myofibromatosis, infantile 2	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy	Inherited thrombocytopenia	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy	Cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy	Lateral meningocele syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy	Myofibromatosis, infantile 2	0.250	1	1.94e-4	4.41e-4 ✓ sig.

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