Coexpression cluster:C1570

Full id: C1570_Hepatocyte_liver_left_heart_skeletal_tongue_diaphragm

Phase1 CAGE Peaks

Hg19::chr10:13342051..13342071,-	p1@PHYH
Hg19::chr12:121163602..121163682,+	p1@ACADS
Hg19::chr16:75150620..75150634,-	p3@LDHD
Hg19::chr16:75150636..75150660,-	p2@LDHD
Hg19::chr16:75150665..75150699,-	p1@LDHD

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:0050660	FAD binding	0.00131077638607208
GO:0016898	oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor	0.00131077638607208
GO:0004085	butyryl-CoA dehydrogenase activity	0.00131077638607208
GO:0048244	phytanoyl-CoA dioxygenase activity	0.00131077638607208
GO:0004458	D-lactate dehydrogenase (cytochrome) activity	0.00131077638607208
GO:0016491	oxidoreductase activity	0.00131077638607208
GO:0050662	coenzyme binding	0.00252025744769239
GO:0048037	cofactor binding	0.00480635273047931
GO:0004457	lactate dehydrogenase activity	0.00784192485112926
GO:0051384	response to glucocorticoid stimulus	0.00784192485112926
GO:0042594	response to starvation	0.00784192485112926
GO:0031960	response to corticosteroid stimulus	0.00784192485112926
GO:0006635	fatty acid beta-oxidation	0.0103388688314331
GO:0000062	acyl-CoA binding	0.0103388688314331
GO:0031418	L-ascorbic acid binding	0.0106139469702964
GO:0006629	lipid metabolic process	0.0110433382966838
GO:0044444	cytoplasmic part	0.0110433382966838
GO:0005739	mitochondrion	0.0110433382966838
GO:0019395	fatty acid oxidation	0.0110433382966838
GO:0005504	fatty acid binding	0.0112140400163391
GO:0003995	acyl-CoA dehydrogenase activity	0.0113684032972744
GO:0048545	response to steroid hormone stimulus	0.0121655770979493
GO:0031667	response to nutrient levels	0.0188574475442301
GO:0009991	response to extracellular stimulus	0.0198753797249594
GO:0009725	response to hormone stimulus	0.0219648576348286
GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	0.0230605676661953
GO:0042579	microbody	0.0257863391494672
GO:0005777	peroxisome	0.0257863391494672
GO:0005737	cytoplasm	0.0301974184667569
GO:0050954	sensory perception of mechanical stimulus	0.0307149913056266
GO:0007605	sensory perception of sound	0.0307149913056266
GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	0.0371577689188984
GO:0031980	mitochondrial lumen	0.0387665654934522
GO:0005759	mitochondrial matrix	0.0387665654934522
GO:0006631	fatty acid metabolic process	0.0388668101039779
GO:0043231	intracellular membrane-bound organelle	0.0388668101039779
GO:0043227	membrane-bound organelle	0.0388668101039779
GO:0007601	visual perception	0.0411351438598265
GO:0050953	sensory perception of light stimulus	0.0411351438598265
GO:0030554	adenyl nucleotide binding	0.0429608724425231
GO:0019842	vitamin binding	0.0429608724425231
GO:0009055	electron carrier activity	0.0432971760442599
GO:0032787	monocarboxylic acid metabolic process	0.0479254241381839

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
fat cell	3.90e-08	15

Uber Anatomy

Ontology term	p-value	n
adult organism	3.33e-33	114
neural tube	2.64e-13	56
neural rod	2.64e-13	56
future spinal cord	2.64e-13	56
neural keel	2.64e-13	56
regional part of nervous system	2.47e-12	53
regional part of brain	2.47e-12	53
organ system subdivision	1.34e-11	223
central nervous system	6.44e-11	81
brain	1.12e-10	68
future brain	1.12e-10	68
neural plate	4.14e-10	82
presumptive neural plate	4.14e-10	82
nervous system	4.49e-10	89
regional part of forebrain	6.09e-10	41
forebrain	6.09e-10	41
anterior neural tube	6.09e-10	41
future forebrain	6.09e-10	41
telencephalon	5.03e-09	34
brain grey matter	5.18e-09	34
gray matter	5.18e-09	34
multi-cellular organism	8.21e-09	656
organ	1.02e-08	503
neurectoderm	1.39e-08	86
cerebral hemisphere	3.46e-08	32
regional part of telencephalon	3.77e-08	32
multi-tissue structure	5.51e-08	342
anatomical cluster	2.25e-07	373
structure with developmental contribution from neural crest	5.48e-07	132
ecto-epithelium	6.19e-07	104
regional part of cerebral cortex	8.47e-07	22

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
FOSL2#2355	3	10.158120362737	0.00188199070341543	0.0110890396092527
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00673459517845598
MAX#4149	4	5.1620444072057	0.00252630900948518	0.0139926382393733
RFX5#5993	3	7.22874649631706	0.0050291827895866	0.0234619565534299
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00247681076548664
SP1#6667	4	4.55870510251272	0.0040757356578168	0.01947324929625
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135088661421922
TAF7#6879	3	6.85984164295435	0.00584328640701904	0.0262390140623726
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00917585503571807

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.