Coexpression cluster:C647

Full id: C647_pineal_cerebellum_pituitary_occipital_parietal_medial_hippocampus

Phase1 CAGE Peaks

Hg19::chr10:133879140..133879164,+	p@chr10:133879140..133879164 +
Hg19::chr10:22609986..22610045,+	p1@BMI1
Hg19::chr12:1192383..1192475,+	p5@ERC1
Hg19::chr16:24621546..24621640,+	p@chr16:24621546..24621640 +
Hg19::chr16:24661163..24661168,+	p@chr16:24661163..24661168 +
Hg19::chr1:72749352..72749438,-	p@chr1:72749352..72749438 -
Hg19::chr1:78444841..78444869,+	p6@DNAJB4
Hg19::chr21:17443633..17443652,+	p23@LINC00478
Hg19::chr2:73298446..73298468,-	p5@SFXN5
Hg19::chr3:47422286..47422316,-	p1@BC036224
Hg19::chr5:146762442..146762468,+	p2@STK32A
Hg19::chr7:50850523..50850543,-	p5@GRB10
Hg19::chrX:49012602..49012631,-	p@chrX:49012602..49012631 -

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:0043522	leucine zipper domain binding	0.0312564375468493
GO:0030275	LRR domain binding	0.0312564375468493
GO:0007252	I-kappaB phosphorylation	0.0312564375468493
GO:0008385	IkappaB kinase complex	0.0338362305696425
GO:0007379	segment specification	0.0338362305696425
GO:0045768	positive regulation of anti-apoptosis	0.0338362305696425
GO:0048146	positive regulation of fibroblast proliferation	0.0338362305696425
GO:0048145	regulation of fibroblast proliferation	0.0338362305696425
GO:0048144	fibroblast proliferation	0.0338362305696425
GO:0045767	regulation of anti-apoptosis	0.0338362305696425
GO:0042734	presynaptic membrane	0.0338362305696425
GO:0009408	response to heat	0.0338362305696425

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	1.81e-76	114
neural tube	1.08e-67	56
neural rod	1.08e-67	56
future spinal cord	1.08e-67	56
neural keel	1.08e-67	56
regional part of nervous system	2.03e-63	53
regional part of brain	2.03e-63	53
central nervous system	1.13e-62	81
nervous system	3.03e-62	89
neurectoderm	5.40e-55	86
neural plate	6.10e-55	82
presumptive neural plate	6.10e-55	82
regional part of forebrain	7.92e-55	41
forebrain	7.92e-55	41
anterior neural tube	7.92e-55	41
future forebrain	7.92e-55	41
brain	1.60e-54	68
future brain	1.60e-54	68
brain grey matter	1.42e-44	34
gray matter	1.42e-44	34
telencephalon	1.97e-44	34
ecto-epithelium	3.31e-43	104
pre-chordal neural plate	4.75e-43	61
regional part of telencephalon	1.09e-41	32
cerebral hemisphere	1.50e-41	32
ectoderm-derived structure	2.91e-39	171
ectoderm	2.91e-39	171
presumptive ectoderm	2.91e-39	171
structure with developmental contribution from neural crest	8.81e-37	132
cerebral cortex	1.01e-31	25
pallium	1.01e-31	25
organ system subdivision	1.56e-29	223
regional part of cerebral cortex	4.74e-29	22
neocortex	3.16e-26	20
anatomical cluster	2.98e-21	373
tube	4.11e-18	192
anatomical conduit	3.33e-17	240
basal ganglion	2.92e-14	9
nuclear complex of neuraxis	2.92e-14	9
aggregate regional part of brain	2.92e-14	9
collection of basal ganglia	2.92e-14	9
cerebral subcortex	2.92e-14	9
neural nucleus	3.54e-14	9
nucleus of brain	3.54e-14	9
posterior neural tube	8.35e-14	15
chordal neural plate	8.35e-14	15
organ part	2.66e-13	218
multi-tissue structure	3.05e-12	342
diencephalon	1.31e-11	7
future diencephalon	1.31e-11	7
telencephalic nucleus	2.15e-11	7
segmental subdivision of nervous system	3.35e-11	13
embryo	3.49e-11	592
epithelium	1.08e-10	306
cell layer	2.22e-10	309
multi-cellular organism	3.06e-10	656
segmental subdivision of hindbrain	4.66e-10	12
hindbrain	4.66e-10	12
presumptive hindbrain	4.66e-10	12
brainstem	6.73e-10	6
germ layer	7.64e-10	560
germ layer / neural crest	7.64e-10	560
embryonic tissue	7.64e-10	560
presumptive structure	7.64e-10	560
germ layer / neural crest derived structure	7.64e-10	560
epiblast (generic)	7.64e-10	560
gyrus	1.24e-09	6
embryonic structure	1.52e-09	564
developing anatomical structure	3.39e-09	581
organ	3.73e-09	503
limbic system	9.87e-09	5
parietal lobe	3.16e-08	5
temporal lobe	3.80e-08	6
anatomical system	6.51e-08	624
occipital lobe	6.53e-08	5
anatomical group	7.58e-08	625
gland of diencephalon	1.53e-07	4
neuroendocrine gland	1.53e-07	4
regional part of diencephalon	1.90e-07	4
corpus striatum	2.75e-07	4
striatum	2.75e-07	4
ventral part of telencephalon	2.75e-07	4
future corpus striatum	2.75e-07	4

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
USF2#7392	4	3.99759919540603	0.0142546073921536	0.0499945241933349

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.