Coexpression cluster:C2684

Full id: C2684_adrenal_occipital_parietal_temporal_amygdala_hippocampus_putamen

Phase1 CAGE Peaks

Hg19::chr2:210288760..210288849,+	p1@MAP2
Hg19::chr2:213403485..213403534,-	p3@ERBB4
Hg19::chr2:213403573..213403584,-	p11@ERBB4
Hg19::chr2:213403690..213403704,-	p6@ERBB4

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0007026	negative regulation of microtubule depolymerization	0.0295010355120949
GO:0031114	regulation of microtubule depolymerization	0.0295010355120949
GO:0007019	microtubule depolymerization	0.0295010355120949
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0295010355120949
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0295010355120949
GO:0031109	microtubule polymerization or depolymerization	0.0295010355120949
GO:0051261	protein depolymerization	0.0359437983519393
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0359437983519393
GO:0051128	regulation of cellular component organization and biogenesis	0.0463264455314587
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0463264455314587
GO:0051248	negative regulation of protein metabolic process	0.0463264455314587
GO:0046982	protein heterodimerization activity	0.0463264455314587
GO:0004714	transmembrane receptor protein tyrosine kinase activity	0.0463264455314587

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	7.10e-65	114
neural tube	1.77e-50	56
neural rod	1.77e-50	56
future spinal cord	1.77e-50	56
neural keel	1.77e-50	56
regional part of nervous system	1.97e-47	53
regional part of brain	1.97e-47	53
central nervous system	3.17e-46	81
neural plate	3.23e-44	82
presumptive neural plate	3.23e-44	82
regional part of forebrain	1.83e-43	41
forebrain	1.83e-43	41
anterior neural tube	1.83e-43	41
future forebrain	1.83e-43	41
nervous system	2.63e-43	89
neurectoderm	2.57e-42	86
brain	6.46e-40	68
future brain	6.46e-40	68
telencephalon	1.05e-36	34
brain grey matter	1.25e-36	34
gray matter	1.25e-36	34
pre-chordal neural plate	4.87e-36	61
cerebral hemisphere	7.11e-35	32
regional part of telencephalon	1.13e-34	32
ecto-epithelium	3.32e-34	104
structure with developmental contribution from neural crest	3.73e-30	132
ectoderm-derived structure	2.47e-29	171
ectoderm	2.47e-29	171
presumptive ectoderm	2.47e-29	171
cerebral cortex	1.26e-27	25
pallium	1.26e-27	25
regional part of cerebral cortex	1.85e-26	22
neocortex	2.95e-24	20
organ system subdivision	5.37e-21	223
anatomical cluster	1.51e-19	373
anatomical conduit	4.61e-16	240
tube	8.85e-16	192
multi-tissue structure	8.51e-14	342
organ part	1.26e-12	218
multi-cellular organism	5.55e-11	656
basal ganglion	1.82e-10	9
nuclear complex of neuraxis	1.82e-10	9
aggregate regional part of brain	1.82e-10	9
collection of basal ganglia	1.82e-10	9
cerebral subcortex	1.82e-10	9
neural nucleus	2.42e-10	9
nucleus of brain	2.42e-10	9
epithelium	3.09e-10	306
cell layer	7.11e-10	309
organ	1.05e-09	503
posterior neural tube	8.52e-09	15
chordal neural plate	8.52e-09	15
temporal lobe	1.04e-08	6
embryo	1.15e-08	592
telencephalic nucleus	1.82e-08	7
developing anatomical structure	2.16e-08	581
anatomical system	2.93e-08	624
anatomical group	3.57e-08	625
gyrus	3.84e-08	6
diencephalon	4.73e-08	7
future diencephalon	4.73e-08	7
parietal lobe	3.46e-07	5
occipital lobe	4.04e-07	5
brainstem	5.03e-07	6
segmental subdivision of nervous system	5.69e-07	13
limbic system	7.10e-07	5

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
SUZ12#23512	3	37.5868356832972	3.12785741999833e-05	0.000632101975787936

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.