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Cluster 314

7 diseases · 12 shared-gene connections

7 Diseases

7 Unique genes

0.260 Avg. similarity score

Cortical occipital malformations Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Abnormal cortical gyration 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.

Abnormal cortical gyration Cortical occipital malformations Intellectual developmental disorder autism speech Developmental delay with language impairment and movement disorder Intellectual developmental disorder speech autism dysmorphic Intellectual developmental disorder with autistic features and language delay, with or without seizures

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cortical occipital malformations	5	5	2
Intellectual developmental disorder autism speech	5	5	2
Abnormal cortical gyration	4	4	1
Developmental delay with language impairment and movement disorder	4	4	2
Intellectual developmental disorder speech autism dysmorphic	4	4	4
Intellectual developmental disorder with autistic features and language delay, with or without seizures	1	1	1
Occipital pachygyria and polymicrogyria	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
TBR1	5 / 7	Abnormal cortical gyration, Cortical occipital malformations, Developmental delay with language impairment and movement disorder, Intellectual developmental disorder autism speech and 1 more
LAMC3	2 / 7	Cortical occipital malformations, Occipital pachygyria and polymicrogyria
TANC2	2 / 7	Intellectual developmental disorder autism speech, Intellectual developmental disorder with autistic features and language delay, with or without seizures

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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain CNOT3	Reactome	1 / 20	85.8×	1.16e-2	6.22e-2
Deadenylation of mRNA CNOT3	Reactome	1 / 24	71.5×	1.39e-2	6.94e-2
Laminin interactions LAMC3	Reactome	1 / 28	61.3×	1.62e-2	7.59e-2
MET activates PTK2 signaling LAMC3	Reactome	1 / 30	57.2×	1.74e-2	7.88e-2
Nuclear Receptor transcription pathway NR4A2	Reactome	1 / 52	33.0×	2.99e-2	1.08e-1
RNA degradation CNOT3	KEGG	1 / 78	22.0×	4.46e-2	1.36e-1
ECM-receptor interaction LAMC3	KEGG	1 / 89	19.3×	5.07e-2	1.46e-1
Small cell lung cancer LAMC3	KEGG	1 / 93	18.4×	5.30e-2	1.49e-1
Aldosterone synthesis and secretion NR4A2	KEGG	1 / 98	17.5×	5.58e-2	1.54e-1
Amoebiasis LAMC3	KEGG	1 / 103	16.7×	5.85e-2	1.58e-1
Toxoplasmosis LAMC3	KEGG	1 / 112	15.3×	6.35e-2	1.66e-1
Parathyroid hormone synthesis, secretion and action NR4A2	KEGG	1 / 115	14.9×	6.51e-2	1.69e-1
Estrogen-dependent gene expression CHD1	Reactome	1 / 150	11.4×	8.42e-2	1.95e-1
Focal adhesion LAMC3	KEGG	1 / 203	8.5×	1.13e-1	2.32e-1
Human papillomavirus infection LAMC3	KEGG	1 / 333	5.2×	1.79e-1	3.08e-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 ⇵
general adaptation syndrome NR4A2	GO:0051866	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
specification of animal organ identity TBR1	GO:0010092	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
conditioned taste aversion TBR1	GO:0001661	1 / 3	890×	1.12e-3	1.55e-2 ✓ sig.
habenula development NR4A2	GO:0021986	1 / 3	890×	1.12e-3	1.55e-2 ✓ sig.
amygdala development TBR1	GO:0021764	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.
dense core granule cytoskeletal transport TANC2	GO:0099519	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.
cellular response to corticotropin-releasing hormone stimulus NR4A2	GO:0071376	1 / 5	534×	1.87e-3	2.05e-2 ✓ sig.
nucleosome organization CHD1	GO:0034728	1 / 6	445×	2.25e-3	2.24e-2 ✓ sig.
commitment of neuronal cell to specific neuron type in forebrain TBR1	GO:0021902	1 / 6	445×	2.25e-3	2.24e-2 ✓ sig.
regulation of axon guidance TBR1	GO:1902667	1 / 6	445×	2.25e-3	2.24e-2 ✓ sig.
regulation of respiratory gaseous exchange NR4A2	GO:0043576	1 / 6	445×	2.25e-3	2.24e-2 ✓ sig.
dopamine biosynthetic process NR4A2	GO:0042416	1 / 9	297×	3.37e-3	2.76e-2 ✓ sig.
regulation of dopamine metabolic process NR4A2	GO:0042053	1 / 9	297×	3.37e-3	2.76e-2 ✓ sig.
central nervous system projection neuron axonogenesis NR4A2	GO:0021952	1 / 9	297×	3.37e-3	2.76e-2 ✓ sig.
regulation of dendritic spine development TANC2	GO:0060998	1 / 10	267×	3.74e-3	2.90e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Abnormal cortical gyration	Cortical occipital malformations	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Abnormal cortical gyration	Developmental delay with language impairment and movement disorder	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Abnormal cortical gyration	Intellectual developmental disorder autism speech	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cortical occipital malformations	Occipital pachygyria and polymicrogyria	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Intellectual developmental disorder autism speech	Intellectual developmental disorder with autistic features and language delay, with or without seizures	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cortical occipital malformations	Developmental delay with language impairment and movement disorder	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Cortical occipital malformations	Intellectual developmental disorder autism speech	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Developmental delay with language impairment and movement disorder	Intellectual developmental disorder autism speech	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Abnormal cortical gyration	Intellectual developmental disorder speech autism dysmorphic	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Cortical occipital malformations	Intellectual developmental disorder speech autism dysmorphic	0.167	1	5.16e-4	9.13e-4 ✓ sig.
Intellectual developmental disorder autism speech	Intellectual developmental disorder speech autism dysmorphic	0.167	1	5.16e-4	9.13e-4 ✓ sig.
Developmental delay with language impairment and movement disorder	Intellectual developmental disorder speech autism dysmorphic	0.167	1	5.16e-4	9.13e-4 ✓ sig.

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