Coexpression cluster:C401

Full id: C401_Cardiac_pineal_occipital_globus_Hepatocyte_Osteoblast_hippocampus

Phase1 CAGE Peaks

Hg19::chr11:57367366..57367382,+	p11@SERPING1
Hg19::chr11:57367449..57367472,+	p10@SERPING1
Hg19::chr11:57382197..57382297,+	p@chr11:57382197..57382297 +
Hg19::chr11:65200782..65200798,+	p@chr11:65200782..65200798 +
Hg19::chr11:85195246..85195257,+	p@chr11:85195246..85195257 +
Hg19::chr12:105258734..105258750,+	p@chr12:105258734..105258750 +
Hg19::chr12:2912416..2912428,+	p@chr12:2912416..2912428 +
Hg19::chr14:20811496..20811529,-	p2@RPPH1
Hg19::chr14:69256272..69256281,-	p@chr14:69256272..69256281 -
Hg19::chr17:1680785..1680829,+	p@chr17:1680785..1680829 +
Hg19::chr19:41809934..41809945,+	p@chr19:41809934..41809945 +
Hg19::chr19:45409845..45409890,+	p2@APOE
Hg19::chr19:45412352..45412385,+	p3@AJ249921
Hg19::chr19:45412497..45412513,+	p5@AJ249921
Hg19::chr19:45412590..45412628,+	p1@AJ249921
Hg19::chr19:6690736..6690743,-	p@chr19:6690736..6690743 -
Hg19::chr22:36697071..36697092,-	p37@MYH9
Hg19::chr2:189872602..189872638,+	p14@COL3A1
Hg19::chr2:189876643..189876662,+	p8@AF130082
Hg19::chr2:216253018..216253020,-	p@chr2:216253018..216253020 -
Hg19::chr2:56149525..56149590,-	p5@EFEMP1
Hg19::chr3:112324173..112324209,-	p@chr3:112324173..112324209 -
Hg19::chr3:112324210..112324254,-	p@chr3:112324210..112324254 -
Hg19::chr4:124323702..124323741,+	p12@SPRY1
Hg19::chr5:40968730..40968733,+	p@chr5:40968730..40968733 +
Hg19::chr6:132269474..132269484,-	p@chr6:132269474..132269484 -

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0008015	blood circulation	0.000419219703150404
GO:0003013	circulatory system process	0.000419219703150404
GO:0003008	system process	0.000419219703150404
GO:0032501	multicellular organismal process	0.00108973671533384
GO:0009653	anatomical structure morphogenesis	0.00198778520051913
GO:0009887	organ morphogenesis	0.00231233490456949
GO:0031252	leading edge	0.00450041737435283
GO:0042157	lipoprotein metabolic process	0.00536433127423976
GO:0048731	system development	0.00540490358575841
GO:0005319	lipid transporter activity	0.00540490358575841
GO:0043495	protein anchor	0.00540490358575841
GO:0050749	apolipoprotein E receptor binding	0.00540490358575841
GO:0005586	collagen type III	0.00540490358575841
GO:0006869	lipid transport	0.00780639350888681
GO:0048856	anatomical structure development	0.00780639350888681
GO:0048156	tau protein binding	0.00780639350888681
GO:0030220	platelet formation	0.00780639350888681
GO:0005826	contractile ring	0.00780639350888681
GO:0031232	extrinsic to external side of plasma membrane	0.00961154805122228
GO:0032154	cleavage furrow	0.00961154805122228
GO:0044421	extracellular region part	0.00961154805122228
GO:0007275	multicellular organismal development	0.00961154805122228
GO:0032153	cell division site	0.0108069435902759
GO:0043534	blood vessel endothelial cell migration	0.0108069435902759
GO:0030224	monocyte differentiation	0.0108069435902759
GO:0032155	cell division site part	0.0108069435902759
GO:0050793	regulation of developmental process	0.0124559386413484
GO:0048513	organ development	0.014530909143863
GO:0033344	cholesterol efflux	0.014530909143863
GO:0010092	specification of organ identity	0.0147832261379335
GO:0001759	induction of an organ	0.0147832261379335
GO:0050877	neurological system process	0.0147832261379335
GO:0031128	induction	0.0147832261379335
GO:0045168	cell-cell signaling during cell fate commitment	0.0147832261379335
GO:0042627	chylomicron	0.0147832261379335
GO:0031532	actin cytoskeleton reorganization	0.0147832261379335
GO:0050750	low-density lipoprotein receptor binding	0.0147832261379335
GO:0045471	response to ethanol	0.0147832261379335
GO:0042995	cell projection	0.0150458835817061
GO:0006707	cholesterol catabolic process	0.0150458835817061
GO:0016127	sterol catabolic process	0.0150458835817061
GO:0048168	regulation of neuronal synaptic plasticity	0.0150458835817061
GO:0001540	beta-amyloid binding	0.0163274240036984
GO:0032432	actin filament bundle	0.0164301906435854
GO:0005583	fibrillar collagen	0.0164301906435854
GO:0017127	cholesterol transporter activity	0.0164301906435854
GO:0001725	stress fiber	0.0164301906435854
GO:0007271	synaptic transmission, cholinergic	0.0168469259304954
GO:0043542	endothelial cell migration	0.0168469259304954
GO:0030516	regulation of axon extension	0.0168469259304954
GO:0032502	developmental process	0.0168974304224498
GO:0015248	sterol transporter activity	0.0168974304224498
GO:0033619	membrane protein proteolysis	0.0168974304224498
GO:0006509	membrane protein ectodomain proteolysis	0.0168974304224498
GO:0042632	cholesterol homeostasis	0.0181532546775641
GO:0000146	microfilament motor activity	0.0181532546775641
GO:0055092	sterol homeostasis	0.0181532546775641
GO:0005578	proteinaceous extracellular matrix	0.0181532546775641
GO:0030048	actin filament-based movement	0.0186374556962015
GO:0048167	regulation of synaptic plasticity	0.0186374556962015
GO:0006706	steroid catabolic process	0.0186374556962015
GO:0051262	protein tetramerization	0.0186374556962015
GO:0048675	axon extension	0.0186374556962015
GO:0055088	lipid homeostasis	0.0186374556962015
GO:0015918	sterol transport	0.0188485102725415
GO:0050803	regulation of synapse structure and activity	0.0188485102725415
GO:0030301	cholesterol transport	0.0188485102725415
GO:0042311	vasodilation	0.0190151302149179
GO:0001657	ureteric bud development	0.0190151302149179
GO:0032989	cellular structure morphogenesis	0.0190151302149179
GO:0000902	cell morphogenesis	0.0190151302149179
GO:0048869	cellular developmental process	0.02099236082885
GO:0030154	cell differentiation	0.02099236082885
GO:0043407	negative regulation of MAP kinase activity	0.0224387791240267
GO:0001656	metanephros development	0.0224387791240267
GO:0006810	transport	0.0231720613631511
GO:0050770	regulation of axonogenesis	0.0236731024067316
GO:0000302	response to reactive oxygen species	0.0242662892719579
GO:0051234	establishment of localization	0.0243968322304056
GO:0006958	complement activation, classical pathway	0.0245337484807454
GO:0008034	lipoprotein binding	0.0250940349738294
GO:0002573	myeloid leukocyte differentiation	0.0252749891205452
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0252749891205452
GO:0008092	cytoskeletal protein binding	0.0252749891205452
GO:0050900	leukocyte migration	0.025557807841472
GO:0000910	cytokinesis	0.0273925062569107
GO:0007267	cell-cell signaling	0.0273925062569107
GO:0005737	cytoplasm	0.0281269809152259
GO:0001822	kidney development	0.0283335906023209
GO:0051179	localization	0.0284490305427894
GO:0050767	regulation of neurogenesis	0.0284490305427894
GO:0007010	cytoskeleton organization and biogenesis	0.0284490305427894
GO:0002541	activation of plasma proteins during acute inflammatory response	0.0284490305427894
GO:0030027	lamellipodium	0.0284490305427894
GO:0006956	complement activation	0.0284490305427894
GO:0051015	actin filament binding	0.0284490305427894
GO:0001655	urogenital system development	0.0288275807188739
GO:0022603	regulation of anatomical structure morphogenesis	0.0288275807188739
GO:0022604	regulation of cell morphogenesis	0.0288275807188739
GO:0035150	regulation of tube size	0.0288275807188739
GO:0008360	regulation of cell shape	0.0288275807188739
GO:0050880	regulation of blood vessel size	0.0288275807188739
GO:0001726	ruffle	0.0289438204544674
GO:0003018	vascular process in circulatory system	0.0289438204544674
GO:0007611	learning and/or memory	0.0293322770254043
GO:0044448	cell cortex part	0.0297132878901067
GO:0044242	cellular lipid catabolic process	0.031389652619269
GO:0019897	extrinsic to plasma membrane	0.0320919334640991
GO:0009897	external side of plasma membrane	0.0320919334640991
GO:0016064	immunoglobulin mediated immune response	0.03243332931013
GO:0019724	B cell mediated immunity	0.0327684628976585
GO:0005581	collagen	0.0337190066691928
GO:0042158	lipoprotein biosynthetic process	0.0337379382312679
GO:0008305	integrin complex	0.0337379382312679
GO:0006469	negative regulation of protein kinase activity	0.0343558659292324
GO:0033673	negative regulation of kinase activity	0.0343558659292324
GO:0051348	negative regulation of transferase activity	0.0352511684169105
GO:0051259	protein oligomerization	0.0364113765646222
GO:0010033	response to organic substance	0.0364113765646222
GO:0005938	cell cortex	0.0372661420881728
GO:0046907	intracellular transport	0.0387880511005239
GO:0045165	cell fate commitment	0.0403088713670378
GO:0002253	activation of immune response	0.0403088713670378
GO:0002449	lymphocyte mediated immunity	0.0403603889076714
GO:0006629	lipid metabolic process	0.0403603889076714
GO:0007600	sensory perception	0.0403603889076714
GO:0065008	regulation of biological quality	0.0403603889076714
GO:0006959	humoral immune response	0.0404946883957359
GO:0008201	heparin binding	0.0404946883957359
GO:0002250	adaptive immune response	0.0404946883957359
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0404946883957359
GO:0030099	myeloid cell differentiation	0.0406227123295673
GO:0002443	leukocyte mediated immunity	0.0406227123295673
GO:0008203	cholesterol metabolic process	0.0406227123295673
GO:0002526	acute inflammatory response	0.0408351457951511
GO:0044267	cellular protein metabolic process	0.0420603796506103
GO:0035239	tube morphogenesis	0.042424566568245
GO:0050778	positive regulation of immune response	0.042424566568245
GO:0044260	cellular macromolecule metabolic process	0.042424566568245
GO:0007229	integrin-mediated signaling pathway	0.042424566568245
GO:0002684	positive regulation of immune system process	0.042424566568245
GO:0003002	regionalization	0.042424566568245
GO:0043086	negative regulation of catalytic activity	0.042424566568245
GO:0002521	leukocyte differentiation	0.0434321415613147
GO:0048518	positive regulation of biological process	0.0434321415613147
GO:0043405	regulation of MAP kinase activity	0.0443950312545569
GO:0016125	sterol metabolic process	0.044563210610377
GO:0051649	establishment of cellular localization	0.0453248758207287
GO:0019538	protein metabolic process	0.0454877976580822
GO:0050776	regulation of immune response	0.0455142610194365
GO:0007596	blood coagulation	0.0458239430195316
GO:0002682	regulation of immune system process	0.0458239430195316
GO:0051641	cellular localization	0.0459814820448974
GO:0050817	coagulation	0.0461252636618405
GO:0051240	positive regulation of multicellular organismal process	0.0468607423454333
GO:0007599	hemostasis	0.0468607423454333
GO:0019898	extrinsic to membrane	0.0471405369067976
GO:0016459	myosin complex	0.0471405369067976
GO:0043235	receptor complex	0.0475466257239393
GO:0002252	immune effector process	0.0475466257239393
GO:0005539	glycosaminoglycan binding	0.0475466257239393
GO:0007409	axonogenesis	0.0483130591651719
GO:0045087	innate immune response	0.0483130591651719
GO:0050789	regulation of biological process	0.0483130591651719
GO:0055074	calcium ion homeostasis	0.0483130591651719
GO:0006874	cellular calcium ion homeostasis	0.0483130591651719
GO:0030247	polysaccharide binding	0.0483130591651719
GO:0035295	tube development	0.048435221358892
GO:0006950	response to stress	0.0485090286102478
GO:0048667	neuron morphogenesis during differentiation	0.0485090286102478
GO:0006979	response to oxidative stress	0.0485090286102478
GO:0048812	neurite morphogenesis	0.0485090286102478
GO:0006875	cellular metal ion homeostasis	0.0488564508901125
GO:0055065	metal ion homeostasis	0.0488564508901125
GO:0005201	extracellular matrix structural constituent	0.0488564508901125
GO:0007389	pattern specification process	0.0489694878069881
GO:0050878	regulation of body fluid levels	0.049081178617439
GO:0000904	cellular morphogenesis during differentiation	0.0491915460187666
GO:0001871	pattern binding	0.0493006122010687
GO:0001525	angiogenesis	0.0497900101460195
GO:0044420	extracellular matrix part	0.0498271677129881
GO:0042060	wound healing	0.0498271677129881
GO:0050954	sensory perception of mechanical stimulus	0.0498271677129881
GO:0007605	sensory perception of sound	0.0498271677129881

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><br>uberon_data<br><br>

---

Uber Anatomy

Ontology term	p-value	n
adult organism	5.58e-45	114
neural tube	1.28e-12	56
neural rod	1.28e-12	56
future spinal cord	1.28e-12	56
neural keel	1.28e-12	56
central nervous system	2.58e-10	81
regional part of nervous system	3.13e-10	53
regional part of brain	3.13e-10	53
organ system subdivision	2.61e-09	223
brain	3.28e-09	68
future brain	3.28e-09	68
neural plate	7.42e-09	82
presumptive neural plate	7.42e-09	82
multi-cellular organism	1.02e-08	656
neurectoderm	1.38e-08	86
multi-tissue structure	1.52e-08	342
anatomical cluster	1.69e-08	373
nervous system	2.51e-08	89
brain grey matter	2.52e-08	34
gray matter	2.52e-08	34
structure with developmental contribution from neural crest	2.90e-08	132
telencephalon	4.39e-08	34
neural nucleus	5.17e-08	9
nucleus of brain	5.17e-08	9
regional part of forebrain	1.25e-07	41
forebrain	1.25e-07	41
anterior neural tube	1.25e-07	41
future forebrain	1.25e-07	41
tube	4.37e-07	192
brainstem	4.41e-07	6
regional part of telencephalon	6.02e-07	32
cerebral hemisphere	6.08e-07	32
posterior neural tube	7.31e-07	15
chordal neural plate	7.31e-07	15
ecto-epithelium	8.18e-07	104
organ	8.27e-07	503
epithelium	9.26e-07	306

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

---

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

---

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

---

This analysis result is provided for C0 - C305 clusters.