Coexpression cluster:C1499

Full id: C1499_mature_Hepatocyte_lung_aorta_heart_pancreas_thyroid

Phase1 CAGE Peaks

Hg19::chr2:165697717..165697784,-	p4@COBLL1
Hg19::chr2:211090039..211090059,-	p3@ACADL
Hg19::chr2:211090073..211090085,-	p4@ACADL
Hg19::chr2:211090089..211090121,-	p1@ACADL
Hg19::chr2:211090139..211090150,-	p5@ACADL
Hg19::chr2:211090162..211090179,-	p2@ACADL

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:0004466	long-chain-acyl-CoA dehydrogenase activity	0.00217826445307901
GO:0003995	acyl-CoA dehydrogenase activity	0.0179706817379018
GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	0.0297177507527207
GO:0050660	FAD binding	0.0297177507527207
GO:0031980	mitochondrial lumen	0.0297177507527207
GO:0005759	mitochondrial matrix	0.0297177507527207
GO:0006631	fatty acid metabolic process	0.0297177507527207
GO:0032787	monocarboxylic acid metabolic process	0.0349732459411018
GO:0050662	coenzyme binding	0.0349732459411018
GO:0048037	cofactor binding	0.0465059460732368

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	4.03e-08	15

Uber Anatomy

Ontology term	p-value	n
adult organism	4.04e-61	114
neural tube	2.18e-25	56
neural rod	2.18e-25	56
future spinal cord	2.18e-25	56
neural keel	2.18e-25	56
regional part of nervous system	9.98e-23	53
regional part of brain	9.98e-23	53
neural plate	1.55e-20	82
presumptive neural plate	1.55e-20	82
regional part of forebrain	1.60e-20	41
forebrain	1.60e-20	41
anterior neural tube	1.60e-20	41
future forebrain	1.60e-20	41
central nervous system	5.86e-19	81
neurectoderm	7.22e-19	86
telencephalon	5.29e-18	34
brain grey matter	5.56e-18	34
gray matter	5.56e-18	34
nervous system	1.33e-17	89
brain	1.53e-16	68
future brain	1.53e-16	68
regional part of telencephalon	1.76e-16	32
cerebral hemisphere	2.32e-16	32
organ system subdivision	1.12e-15	223
ecto-epithelium	1.23e-14	104
pre-chordal neural plate	1.98e-14	61
structure with developmental contribution from neural crest	1.21e-13	132
cerebral cortex	8.71e-13	25
pallium	8.71e-13	25
anatomical cluster	2.34e-11	373
multi-tissue structure	3.33e-11	342
regional part of cerebral cortex	7.15e-11	22
neocortex	1.03e-10	20
ectoderm-derived structure	1.45e-10	171
ectoderm	1.45e-10	171
presumptive ectoderm	1.45e-10	171
anatomical conduit	1.32e-09	240
organ	2.52e-09	503
tube	1.34e-08	192
multi-cellular organism	6.06e-08	656
omentum	6.85e-08	6
peritoneum	6.85e-08	6
abdominal cavity	6.85e-08	6
visceral peritoneum	6.85e-08	6
organ part	2.40e-07	218
brainstem	6.95e-07	6
neural nucleus	9.71e-07	9
nucleus of brain	9.71e-07	9

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
E2F1#1869	6	4.90738921487932	7.15746523583771e-05	0.0011276489844104
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380554454509405
ZNF263#10127	6	8.22184163701068	3.23542093046082e-06	0.000108790768369735

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.