Coexpression cluster:C178

Full id: C178_spleen_liver_Hepatocyte_b_lymph_vein_thymus

Phase1 CAGE Peaks

Hg19::chr10:102890767..102890780,+	p4@TLX1
Hg19::chr10:102891007..102891008,+	p9@TLX1
Hg19::chr10:98014908..98014919,-	p@chr10:98014908..98014919 -
Hg19::chr10:98014943..98014960,-	p@chr10:98014943..98014960 -
Hg19::chr11:1891326..1891337,-	p@chr11:1891326..1891337 -
Hg19::chr11:1891472..1891476,+	p48@LSP1
Hg19::chr11:1891482..1891489,+	p42@LSP1
Hg19::chr11:56859569..56859572,-	p@chr11:56859569..56859572 -
Hg19::chr11:56859584..56859589,-	p@chr11:56859584..56859589 -
Hg19::chr11:925449..925458,+	p17@AP2A2
Hg19::chr12:101869096..101869118,+	p1@SPIC
Hg19::chr12:101882023..101882028,+	p@chr12:101882023..101882028 +
Hg19::chr12:120168462..120168466,-	p@chr12:120168462..120168466 -
Hg19::chr12:57388270..57388282,+	p1@GPR182
Hg19::chr12:57388297..57388302,+	p3@GPR182
Hg19::chr12:57388350..57388361,+	p2@GPR182
Hg19::chr12:72481040..72481051,+	p19@TRHDE
Hg19::chr12:72481055..72481060,+	p28@TRHDE
Hg19::chr14:24168655..24168686,+	p@chr14:24168655..24168686 +
Hg19::chr14:75904485..75904519,+	p12@JDP2
Hg19::chr14:81859777..81859783,-	p@chr14:81859777..81859783 -
Hg19::chr15:94899297..94899314,+	p16@MCTP2
Hg19::chr16:31404650..31404662,+	p1@ITGAD
Hg19::chr17:72313080..72313103,-	p@chr17:72313080..72313103 -
Hg19::chr17:72313399..72313408,-	p@chr17:72313399..72313408 -
Hg19::chr17:73836893..73836935,-	p@chr17:73836893..73836935 -
Hg19::chr17:78945208..78945214,-	p1@ENST00000545206 p1@uc002jyv.1
Hg19::chr19:14223454..14223463,-	p9@PRKACA
Hg19::chr1:157801226..157801230,-	p8@CD5L
Hg19::chr1:157801262..157801284,-	p10@CD5L
Hg19::chr1:157811525..157811541,-	p3@CD5L
Hg19::chr1:157811550..157811559,-	p5@CD5L
Hg19::chr1:157811563..157811585,-	p2@CD5L
Hg19::chr1:157811590..157811604,-	p1@CD5L
Hg19::chr1:157811612..157811617,-	p6@CD5L
Hg19::chr1:157811628..157811640,-	p4@CD5L
Hg19::chr1:157811772..157811796,-	p7@CD5L
Hg19::chr1:25890126..25890172,+	p9@LDLRAP1
Hg19::chr21:28820892..28820899,-	p4@ENST00000420186 p4@uc002ymh.2
Hg19::chr21:28820911..28820933,-	p1@ENST00000420186 p1@uc002ymh.2
Hg19::chr21:28820941..28820952,-	p2@ENST00000420186 p2@uc002ymh.2
Hg19::chr21:28820954..28820963,-	p3@ENST00000420186 p3@uc002ymh.2
Hg19::chr21:40181520..40181558,+	p11@ETS2
Hg19::chr21:40364741..40364783,-	p@chr21:40364741..40364783 -
Hg19::chr22:36718586..36718593,-	p@chr22:36718586..36718593 -
Hg19::chr2:1098240..1098249,+	p3@SNTG2
Hg19::chr2:128321491..128321509,+	p@chr2:128321491..128321509 +
Hg19::chr2:1418171..1418194,+	p2@TPO
Hg19::chr2:1418195..1418210,+	p6@TPO
Hg19::chr2:1507506..1507512,+	p16@TPO
Hg19::chr2:1508349..1508357,+	p@chr2:1508349..1508357 +
Hg19::chr2:1545753..1545760,-	p@chr2:1545753..1545760 -
Hg19::chr2:218142645..218142648,+	p@chr2:218142645..218142648 +
Hg19::chr2:218142682..218142730,+	p@chr2:218142682..218142730 +
Hg19::chr2:218844734..218844743,-	p@chr2:218844734..218844743 -
Hg19::chr2:218844745..218844765,-	p@chr2:218844745..218844765 -
Hg19::chr3:119466528..119466536,+	p4@C3orf15
Hg19::chr3:119466639..119466644,+	p@chr3:119466639..119466644 +
Hg19::chr3:119466654..119466656,+	p@chr3:119466654..119466656 +
Hg19::chr3:119466669..119466679,+	p@chr3:119466669..119466679 +
Hg19::chr3:46505137..46505149,-	p4@LTF
Hg19::chr3:46620614..46620623,+	p8@TDGF1
Hg19::chr4:185269050..185269068,-	p1@ENST00000511465
Hg19::chr4:186854504..186854528,-	p34@SORBS2
Hg19::chr4:76901930..76901942,+	p1@ENST00000501239
Hg19::chr5:1501865..1501869,-	p@chr5:1501865..1501869 -
Hg19::chr5:1501872..1501883,-	p@chr5:1501872..1501883 -
Hg19::chr5:1501941..1501953,-	p@chr5:1501941..1501953 -
Hg19::chr5:152069112..152069147,-	p1@ENST00000506723 p1@uc003luw.1
Hg19::chr5:76249436..76249479,+	p2@CRHBP
Hg19::chr5:76249493..76249508,+	p6@CRHBP
Hg19::chr6:36172477..36172497,+	p@chr6:36172477..36172497 +
Hg19::chr6:56707958..56707979,-	p44@DST
Hg19::chr7:100420483..100420489,-	p12@EPHB4
Hg19::chr7:151070957..151070988,+	p@chr7:151070957..151070988 +
Hg19::chr7:22259740..22259751,-	p19@RAPGEF5
Hg19::chr7:84736120..84736124,-	p@chr7:84736120..84736124 -
Hg19::chr8:22424709..22424716,-	p2@ENST00000517384
Hg19::chr8:22424743..22424759,-	p1@ENST00000517384
Hg19::chr8:22436248..22436259,+	p11@PDLIM2
Hg19::chr8:47834174..47834213,+	p1@ENST00000524012
Hg19::chr9:124516729..124516752,+	p@chr9:124516729..124516752 +
Hg19::chr9:126579213..126579224,-	p@chr9:126579213..126579224 -
Hg19::chr9:127260615..127260651,-	p@chr9:127260615..127260651 -
Hg19::chr9:127263337..127263341,-	p9@NR5A1
Hg19::chr9:127267367..127267383,+	p@chr9:127267367..127267383 +
Hg19::chr9:127269434..127269438,-	p8@NR5A1
Hg19::chr9:127269462..127269484,-	p2@NR5A1
Hg19::chr9:127269488..127269495,-	p5@NR5A1
Hg19::chr9:133973310..133973321,+	p18@AIF1L
Hg19::chr9:133973327..133973338,+	p17@AIF1L
Hg19::chr9:138596697..138596714,+	p@chr9:138596697..138596714 +
Hg19::chr9:79223787..79223821,+	p@chr9:79223787..79223821 +
Hg19::chr9:79894775..79894780,+	p12@VPS13A
Hg19::chr9:79894790..79894797,+	p10@VPS13A
Hg19::chrX:69645652..69645664,+	p7@GDPD2

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
7.1885277451996e-05	0.0455033806271134	2	13	{ETS1,13} (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:0030669	clathrin-coated endocytic vesicle membrane	0.000992071849670377
GO:0030128	clathrin coat of endocytic vesicle	0.000992071849670377
GO:0030122	AP-2 adaptor complex	0.000992071849670377
GO:0030666	endocytic vesicle membrane	0.00111553331382684
GO:0045334	clathrin-coated endocytic vesicle	0.0012487844173176
GO:0030132	clathrin coat of coated pit	0.00385392387092292
GO:0005886	plasma membrane	0.00578149704885549
GO:0030125	clathrin vesicle coat	0.00746363347430808
GO:0030139	endocytic vesicle	0.00746363347430808
GO:0030665	clathrin coated vesicle membrane	0.00746363347430808
GO:0048731	system development	0.00890381700236304
GO:0009986	cell surface	0.00896187838544101
GO:0044459	plasma membrane part	0.0108793621863433
GO:0005905	coated pit	0.0173244936324337
GO:0043565	sequence-specific DNA binding	0.0173244936324337
GO:0030120	vesicle coat	0.0173244936324337
GO:0030662	coated vesicle membrane	0.0173244936324337
GO:0048856	anatomical structure development	0.0173244936324337
GO:0035103	sterol regulatory element binding protein cleavage	0.0173244936324337
GO:0048645	organ formation	0.0173244936324337
GO:0006992	sterol depletion response, sterol regulatory element binding protein cleavage	0.0173244936324337
GO:0017047	adrenocorticotropin-releasing hormone binding	0.0173244936324337
GO:0030131	clathrin adaptor complex	0.0173244936324337
GO:0030119	AP-type membrane coat adaptor complex	0.0173244936324337
GO:0044464	cell part	0.0192221274731382
GO:0030118	clathrin coat	0.0228993724109768
GO:0006968	cellular defense response	0.0228993724109768
GO:0030967	ER-nuclear sterol response pathway	0.0228993724109768
GO:0007538	primary sex determination	0.0228993724109768
GO:0004447	iodide peroxidase activity	0.0228993724109768
GO:0016013	syntrophin complex	0.0228993724109768
GO:0016921	pyroglutamyl-peptidase II activity	0.0228993724109768
GO:0017034	Rap guanyl-nucleotide exchange factor activity	0.0228993724109768
GO:0015460	transport accessory protein activity	0.0228993724109768
GO:0007275	multicellular organismal development	0.0240168502532878
GO:0048513	organ development	0.025140756393618
GO:0042445	hormone metabolic process	0.0295648481646199
GO:0032933	SREBP-mediated signaling pathway	0.0299338749298829
GO:0006991	response to sterol depletion	0.0299338749298829
GO:0030659	cytoplasmic vesicle membrane	0.0361852549088417
GO:0048260	positive regulation of receptor-mediated endocytosis	0.0361852549088417
GO:0048536	spleen development	0.0361852549088417
GO:0016920	pyroglutamyl-peptidase activity	0.0361852549088417
GO:0044433	cytoplasmic vesicle part	0.0364903709871873
GO:0032502	developmental process	0.0373887191819808
GO:0012506	vesicle membrane	0.0373887191819808
GO:0030136	clathrin-coated vesicle	0.0373887191819808
GO:0030117	membrane coat	0.0373887191819808
GO:0048475	coated membrane	0.0373887191819808
GO:0030121	AP-1 adaptor complex	0.0373887191819808
GO:0050810	regulation of steroid biosynthetic process	0.0373887191819808
GO:0001784	phosphotyrosine binding	0.0373887191819808
GO:0007165	signal transduction	0.040892928832658
GO:0005856	cytoskeleton	0.0424029754600826
GO:0045309	protein phosphorylated amino acid binding	0.0424029754600826
GO:0003779	actin binding	0.0424971396615758
GO:0044421	extracellular region part	0.0424971396615758
GO:0007350	blastoderm segmentation	0.0424971396615758
GO:0008242	omega peptidase activity	0.0424971396615758
GO:0000578	embryonic axis specification	0.0424971396615758
GO:0008595	determination of anterior/posterior axis, embryo	0.0424971396615758
GO:0006895	Golgi to endosome transport	0.0424971396615758
GO:0007351	tripartite regional subdivision	0.0424971396615758
GO:0048259	regulation of receptor-mediated endocytosis	0.0424971396615758
GO:0005515	protein binding	0.0426672972879588
GO:0003700	transcription factor activity	0.044239107836448
GO:0030135	coated vesicle	0.0444686533011773
GO:0046890	regulation of lipid biosynthetic process	0.0450314997123685
GO:0004691	cAMP-dependent protein kinase activity	0.0450314997123685
GO:0048646	anatomical structure formation	0.0459858650514926
GO:0017046	peptide hormone binding	0.0485310207523525
GO:0006590	thyroid hormone generation	0.0485310207523525

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>

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Uber Anatomy

Ontology term	p-value	n
adult organism	8.71e-40	115
neural tube	3.77e-17	57
neural rod	3.77e-17	57
future spinal cord	3.77e-17	57
neural keel	3.77e-17	57
regional part of brain	9.13e-16	59
anterior neural tube	2.93e-15	42
regional part of forebrain	7.22e-15	41
forebrain	7.22e-15	41
future forebrain	7.22e-15	41
telencephalon	3.00e-14	34
neural plate	3.87e-14	86
presumptive neural plate	3.87e-14	86
gray matter	4.13e-14	34
brain grey matter	4.13e-14	34
central nervous system	7.40e-14	82
regional part of telencephalon	8.87e-14	33
brain	2.28e-13	69
future brain	2.28e-13	69
cerebral hemisphere	3.42e-13	32
neurectoderm	8.76e-13	90
regional part of nervous system	6.45e-12	94
nervous system	6.45e-12	94
organ	6.54e-11	511
pre-chordal neural plate	1.07e-10	61
regional part of cerebral cortex	1.13e-10	22
cerebral cortex	6.11e-10	25
pallium	6.11e-10	25
neocortex	9.03e-10	20
anatomical system	7.84e-08	625
anatomical group	9.94e-08	626
multi-cellular organism	1.07e-07	659
anterior region of body	1.13e-07	129
craniocervical region	1.13e-07	129
immune system	2.59e-07	115
head	4.43e-07	123
ectoderm-derived structure	6.31e-07	169
embryo	9.93e-07	612

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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