Coexpression cluster:C848

Full id: C848_Monocytederived_Mesenchymal_Hepatocyte_Adipocyte_CD14_Cardiac_liver

Phase1 CAGE Peaks

Hg19::chr19:45409042..45409061,+	p1@APOE
Hg19::chr19:45411107..45411153,+	p3@APOE
Hg19::chr19:45411165..45411180,+	p5@APOE
Hg19::chr19:45411811..45411830,+	p@chr19:45411811..45411830 +
Hg19::chr19:45411839..45411852,+	p@chr19:45411839..45411852 +
Hg19::chr19:45412009..45412026,+	p@chr19:45412009..45412026 +
Hg19::chr19:45412466..45412491,+	p2@AJ249921
Hg19::chr19:45417848..45417869,+	p2@APOC1
Hg19::chr2:219646861..219646879,+	p1@CYP27A1
Hg19::chr2:219646891..219646911,+	p3@CYP27A1

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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p.value	FDR	nGenes	nPathway	Name
2.98763831444955e-06	0.00101310581536839	2	29	Statin Pathway (Wikipathways):WP430
3.20096624129033e-06	0.00101310581536839	2	30	{SDC1,30} (Static Module):NA

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:0042157	lipoprotein metabolic process	0.00233088563653156
GO:0005319	lipid transporter activity	0.00233088563653156
GO:0006869	lipid transport	0.00307992607221813
GO:0050749	apolipoprotein E receptor binding	0.00347933592370187
GO:0047749	cholestanetriol 26-monooxygenase activity	0.00347933592370187
GO:0048156	tau protein binding	0.00579872250488911
GO:0031232	extrinsic to external side of plasma membrane	0.00745528089466088
GO:0033344	cholesterol efflux	0.0104327851320064
GO:0042627	chylomicron	0.0104327851320064
GO:0050750	low-density lipoprotein receptor binding	0.0104327851320064
GO:0045471	response to ethanol	0.0104327851320064
GO:0006707	cholesterol catabolic process	0.0104327851320064
GO:0016127	sterol catabolic process	0.0104327851320064
GO:0048168	regulation of neuronal synaptic plasticity	0.0104327851320064
GO:0001540	beta-amyloid binding	0.0104327851320064
GO:0017127	cholesterol transporter activity	0.0104327851320064
GO:0030516	regulation of axon extension	0.0104327851320064
GO:0007271	synaptic transmission, cholinergic	0.0104327851320064
GO:0015248	sterol transporter activity	0.0104327851320064
GO:0042632	cholesterol homeostasis	0.0104327851320064
GO:0008395	steroid hydroxylase activity	0.0104327851320064
GO:0055092	sterol homeostasis	0.0104327851320064
GO:0048167	regulation of synaptic plasticity	0.0104327851320064
GO:0006706	steroid catabolic process	0.0104327851320064
GO:0051262	protein tetramerization	0.0104327851320064
GO:0048675	axon extension	0.0104327851320064
GO:0055088	lipid homeostasis	0.0104327851320064
GO:0015918	sterol transport	0.0104327851320064
GO:0050803	regulation of synapse structure and activity	0.0104327851320064
GO:0030301	cholesterol transport	0.0104327851320064
GO:0042311	vasodilation	0.0106568323372062
GO:0006629	lipid metabolic process	0.0136963903325708
GO:0050770	regulation of axonogenesis	0.0136963903325708
GO:0000302	response to reactive oxygen species	0.0138044394409538
GO:0044444	cytoplasmic part	0.013892968335835
GO:0008034	lipoprotein binding	0.014002444188512
GO:0016709	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen	0.0159706137010346
GO:0050767	regulation of neurogenesis	0.017377738469733
GO:0035150	regulation of tube size	0.0182020333822998
GO:0050880	regulation of blood vessel size	0.0182020333822998
GO:0003018	vascular process in circulatory system	0.0182020333822998
GO:0007611	learning and/or memory	0.0182020333822998
GO:0044242	cellular lipid catabolic process	0.0193017759435435
GO:0019897	extrinsic to plasma membrane	0.0193017759435435
GO:0009897	external side of plasma membrane	0.0193017759435435
GO:0042158	lipoprotein biosynthetic process	0.0207673309043863
GO:0051259	protein oligomerization	0.022430385414656
GO:0010033	response to organic substance	0.022430385414656
GO:0008201	heparin binding	0.0269230771158613
GO:0008203	cholesterol metabolic process	0.0270773521657405
GO:0035239	tube morphogenesis	0.0285834033885244
GO:0022892	substrate-specific transporter activity	0.0296339091377412
GO:0016125	sterol metabolic process	0.0307700964873075
GO:0019898	extrinsic to membrane	0.0323047891962794
GO:0005539	glycosaminoglycan binding	0.0323047891962794
GO:0007409	axonogenesis	0.0323047891962794
GO:0006874	cellular calcium ion homeostasis	0.0323047891962794
GO:0055074	calcium ion homeostasis	0.0323047891962794
GO:0030247	polysaccharide binding	0.0323047891962794
GO:0035295	tube development	0.0323047891962794
GO:0048667	neuron morphogenesis during differentiation	0.0323047891962794
GO:0006979	response to oxidative stress	0.0323047891962794
GO:0048812	neurite morphogenesis	0.0323047891962794
GO:0005737	cytoplasm	0.0323047891962794
GO:0006875	cellular metal ion homeostasis	0.0323047891962794
GO:0055065	metal ion homeostasis	0.0323047891962794
GO:0000904	cellular morphogenesis during differentiation	0.0323704952536164
GO:0001871	pattern binding	0.0323704952536164
GO:0031175	neurite development	0.0339028968136092
GO:0016042	lipid catabolic process	0.0361068058286039
GO:0009986	cell surface	0.0361068058286039
GO:0048666	neuron development	0.0370422287137999
GO:0008015	blood circulation	0.0374386623722683
GO:0003013	circulatory system process	0.0374386623722683
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0408438217093907
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0409859363824008
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0411242406834246
GO:0043231	intracellular membrane-bound organelle	0.041997112304992
GO:0043227	membrane-bound organelle	0.041997112304992
GO:0030003	cellular cation homeostasis	0.041997112304992
GO:0055080	cation homeostasis	0.041997112304992
GO:0032990	cell part morphogenesis	0.041997112304992
GO:0048858	cell projection morphogenesis	0.041997112304992
GO:0030030	cell projection organization and biogenesis	0.041997112304992
GO:0030182	neuron differentiation	0.0423266215631961
GO:0006917	induction of apoptosis	0.0423266215631961
GO:0012502	induction of programmed cell death	0.0423266215631961
GO:0008202	steroid metabolic process	0.043797299095766
GO:0004497	monooxygenase activity	0.0445047405106417
GO:0050793	regulation of developmental process	0.0445047405106417
GO:0055082	cellular chemical homeostasis	0.0445047405106417
GO:0006873	cellular ion homeostasis	0.0445047405106417
GO:0048699	generation of neurons	0.0449483858556084
GO:0043065	positive regulation of apoptosis	0.0468891903292327
GO:0043068	positive regulation of programmed cell death	0.0468891903292327
GO:0022008	neurogenesis	0.0471145908048725
GO:0050801	ion homeostasis	0.0475117257202813

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
stuff accumulating cell	4.63e-08	39
pigment cell	1.58e-07	14

Uber Anatomy

Ontology term	p-value	n
adult organism	3.14e-32	115
embryo	1.46e-17	612
organ	2.95e-17	511
regional part of brain	3.43e-16	59
neural tube	3.84e-16	57
neural rod	3.84e-16	57
future spinal cord	3.84e-16	57
neural keel	3.84e-16	57
multi-cellular organism	1.10e-15	659
central nervous system	1.12e-15	82
neural plate	1.69e-15	86
presumptive neural plate	1.69e-15	86
embryonic structure	5.01e-15	605
developing anatomical structure	5.01e-15	605
germ layer	7.27e-15	604
embryonic tissue	7.27e-15	604
presumptive structure	7.27e-15	604
epiblast (generic)	7.27e-15	604
regional part of nervous system	7.43e-15	94
nervous system	7.43e-15	94
neurectoderm	1.45e-14	90
brain	3.76e-13	69
future brain	3.76e-13	69
anterior neural tube	1.55e-11	42
anatomical system	1.70e-11	625
regional part of forebrain	2.44e-11	41
forebrain	2.44e-11	41
future forebrain	2.44e-11	41
anatomical group	3.09e-11	626
head	5.12e-11	123
pre-chordal neural plate	6.62e-11	61
anterior region of body	9.08e-11	129
craniocervical region	9.08e-11	129
ectoderm-derived structure	1.42e-10	169
ectoderm	3.57e-10	173
presumptive ectoderm	3.57e-10	173
gray matter	6.89e-10	34
brain grey matter	6.89e-10	34
telencephalon	1.47e-09	34
regional part of telencephalon	2.35e-09	33
cerebral hemisphere	1.10e-08	32
multi-tissue structure	2.40e-08	347
epithelium	1.24e-07	309
cell layer	1.42e-07	312
regional part of cerebral cortex	3.47e-07	22
organism subdivision	7.96e-07	365

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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No analysis results for this cluster

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.