Coexpression cluster:C4831

Full id: C4831_smooth_aorta_optic_granulosa_colon_globus_substantia

Phase1 CAGE Peaks

Hg19::chr9:79520989..79521001,-	p3@PRUNE2
Hg19::chr9:79521006..79521040,-	p1@PRUNE2
Hg19::chr9:79521045..79521056,-	p4@PRUNE2

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>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	7.67e-13	180

Uber Anatomy

Ontology term	p-value	n
adult organism	8.31e-35	115
neural tube	5.17e-25	57
neural rod	5.17e-25	57
future spinal cord	5.17e-25	57
neural keel	5.17e-25	57
regional part of brain	2.10e-22	59
central nervous system	2.95e-22	82
neural plate	9.60e-21	86
presumptive neural plate	9.60e-21	86
brain	3.27e-20	69
future brain	3.27e-20	69
regional part of nervous system	6.05e-20	94
nervous system	6.05e-20	94
anterior neural tube	3.33e-19	42
regional part of forebrain	7.32e-19	41
forebrain	7.32e-19	41
future forebrain	7.32e-19	41
neurectoderm	1.47e-18	90
ectoderm-derived structure	3.16e-18	169
organism subdivision	5.98e-17	365
ectoderm	6.65e-17	173
presumptive ectoderm	6.65e-17	173
head	2.37e-15	123
gray matter	3.24e-15	34
brain grey matter	3.24e-15	34
telencephalon	4.76e-15	34
anterior region of body	7.80e-15	129
craniocervical region	7.80e-15	129
regional part of telencephalon	1.48e-14	33
pre-chordal neural plate	2.96e-14	61
cerebral hemisphere	9.08e-14	32
multi-tissue structure	8.89e-11	347
multi-cellular organism	1.45e-10	659
cerebral cortex	2.83e-10	25
pallium	2.83e-10	25
regional part of cerebral cortex	3.84e-10	22
organ	1.47e-09	511
neocortex	3.70e-09	20
organ part	4.82e-09	219
epithelium	1.17e-08	309
cell layer	3.07e-08	312
anatomical system	6.21e-08	625
anatomical group	9.16e-08	626
anatomical cluster	3.63e-07	286
posterior neural tube	5.17e-07	15
chordal neural plate	5.17e-07	15
embryo	7.07e-07	612

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281789957133247
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0328265109655015
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322936697209821
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296502183989384
REST#5978	3	9.65002871612802	0.00111263624711459	0.0077211041204253
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278634608410157
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00376761814518144
SUZ12#23512	3	50.1157809110629	7.93834897779404e-06	0.000223952790084233
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00546341321457847
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191387267465765
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00423457176156357
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110290178763897

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.