Coexpression cluster:C4104

Full id: C4104_pineal_parietal_pituitary_testis_caudate_spinal_thalamus

Phase1 CAGE Peaks

Hg19::chr22:42720402..42720435,-	p@chr22:42720402..42720435 -
Hg19::chr7:124569919..124569936,+	p1@ENST00000429134
Hg19::chr7:124569941..124569993,+	p1@ENST00000435452 p1@ENST00000449642 p1@ENST00000453342 p1@uc003vlp.2 p1@uc003vlq.1 p1@uc010lkx.1

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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No GOStat results

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
nervous system	6.32e-39	89
central nervous system	4.19e-38	81
neural tube	1.40e-37	56
neural rod	1.40e-37	56
future spinal cord	1.40e-37	56
neural keel	1.40e-37	56
regional part of nervous system	2.62e-35	53
regional part of brain	2.62e-35	53
brain	5.52e-33	68
future brain	5.52e-33	68
neurectoderm	7.96e-31	86
regional part of forebrain	1.25e-30	41
forebrain	1.25e-30	41
anterior neural tube	1.25e-30	41
future forebrain	1.25e-30	41
adult organism	5.63e-30	114
neural plate	1.35e-28	82
presumptive neural plate	1.35e-28	82
telencephalon	3.46e-25	34
brain grey matter	3.77e-25	34
gray matter	3.77e-25	34
pre-chordal neural plate	6.06e-25	61
regional part of telencephalon	1.08e-23	32
cerebral hemisphere	1.26e-23	32
ectoderm-derived structure	4.28e-21	171
ectoderm	4.28e-21	171
presumptive ectoderm	4.28e-21	171
organ system subdivision	1.61e-19	223
ecto-epithelium	5.77e-19	104
cerebral cortex	2.23e-18	25
pallium	2.23e-18	25
regional part of cerebral cortex	2.46e-17	22
structure with developmental contribution from neural crest	6.12e-17	132
neocortex	6.31e-16	20
basal ganglion	3.00e-08	9
nuclear complex of neuraxis	3.00e-08	9
aggregate regional part of brain	3.00e-08	9
collection of basal ganglia	3.00e-08	9
cerebral subcortex	3.00e-08	9
posterior neural tube	3.11e-08	15
chordal neural plate	3.11e-08	15
neural nucleus	3.17e-08	9
nucleus of brain	3.17e-08	9
anatomical cluster	3.77e-07	373
segmental subdivision of nervous system	5.98e-07	13
diencephalon	7.73e-07	7
future diencephalon	7.73e-07	7
telencephalic nucleus	8.18e-07	7

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)
{{{tfbs_overrepresentation_jaspar}}}

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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259614270004728
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296308267806398
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246782942282579
HNF4G#3174	2	19.1689483509645	0.00354398661128422	0.017975349312608
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174527842739187
SETDB1#9869	2	26.880017452007	0.00181446890796441	0.010895263512844
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.028756428640486
STAT2#6773	2	43.5091807909604	0.000696899089886823	0.00560908169302481
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329208035458198

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.