Coexpression cluster:C4740

Full id: C4740_granulosa_caudate_putamen_occipital_neuroepithelioma_stomach_Hepatocyte

Phase1 CAGE Peaks

Hg19::chr8:18871159..18871201,-	p3@PSD3
Hg19::chr8:18871203..18871275,-	p1@PSD3
Hg19::chr8:18871287..18871316,-	p5@PSD3

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	5.84e-10	180
muscle cell	6.72e-07	54

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	2.88e-22	347
epithelium	4.44e-22	309
cell layer	1.08e-21	312
organism subdivision	7.42e-21	365
multi-cellular organism	6.34e-19	659
embryo	2.75e-18	612
anatomical conduit	1.28e-17	241
regional part of nervous system	1.90e-17	94
nervous system	1.90e-17	94
anatomical system	2.00e-17	625
embryonic structure	2.09e-17	605
developing anatomical structure	2.09e-17	605
germ layer	2.81e-17	604
embryonic tissue	2.81e-17	604
presumptive structure	2.81e-17	604
epiblast (generic)	2.81e-17	604
anatomical group	4.86e-17	626
tube	6.66e-17	194
anatomical cluster	2.91e-16	286
central nervous system	1.50e-14	82
brain	3.97e-14	69
future brain	3.97e-14	69
ectoderm	5.42e-14	173
presumptive ectoderm	5.42e-14	173
head	1.76e-13	123
ectoderm-derived structure	2.29e-13	169
anterior region of body	1.77e-12	129
craniocervical region	1.77e-12	129
neurectoderm	5.19e-12	90
regional part of brain	1.15e-11	59
neural tube	2.05e-11	57
neural rod	2.05e-11	57
future spinal cord	2.05e-11	57
neural keel	2.05e-11	57
neural plate	2.12e-11	86
presumptive neural plate	2.12e-11	86
pre-chordal neural plate	1.19e-10	61
organ	2.07e-10	511
regional part of forebrain	5.96e-10	41
forebrain	5.96e-10	41
future forebrain	5.96e-10	41
gray matter	6.53e-10	34
brain grey matter	6.53e-10	34
regional part of telencephalon	6.68e-10	33
telencephalon	7.10e-10	34
anterior neural tube	9.23e-10	42
cerebral hemisphere	1.37e-09	32
primordium	6.29e-09	168
unilaminar epithelium	4.54e-07	138
cerebral cortex	5.10e-07	25
pallium	5.10e-07	25
trunk mesenchyme	8.89e-07	143

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	0.0281450761186175
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172388347174877
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327899680389007
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324497299617005
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187467064835715
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00668940900527135
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310968226245656
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545957115183967
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00249595130345174
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00619153134360552

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.