Coexpression cluster:C1714

Full id: C1714_Hepatocyte_mature_liver_Synoviocyte_parotid_tenocyte_breast

Phase1 CAGE Peaks

Hg19::chr14:21152706..21152783,+	p1@ANG p1@RNASE4
Hg19::chr4:185726679..185726692,-	p6@ACSL1
Hg19::chr4:77227797..77227808,+	p4@STBD1
Hg19::chr4:77227809..77227820,+	p5@STBD1
Hg19::chr4:77227845..77227860,+	p3@STBD1

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:0032148	activation of protein kinase B	0.0104828061310714
GO:0032311	angiogenin-PRI complex	0.0104828061310714
GO:0032429	regulation of phospholipase A2 activity	0.0104828061310714
GO:0001556	oocyte maturation	0.0104828061310714
GO:0032431	activation of phospholipase A2	0.0104828061310714
GO:0006651	diacylglycerol biosynthetic process	0.0104828061310714
GO:0032430	positive regulation of phospholipase A2 activity	0.0104828061310714
GO:0048662	negative regulation of smooth muscle cell proliferation	0.0114132670918778
GO:0001938	positive regulation of endothelial cell proliferation	0.0114132670918778
GO:0048599	oocyte development	0.0114132670918778
GO:0030246	carbohydrate binding	0.0114132670918778
GO:0046460	neutral lipid biosynthetic process	0.0114132670918778
GO:0009994	oocyte differentiation	0.0114132670918778
GO:0046339	diacylglycerol metabolic process	0.0114132670918778
GO:0046463	acylglycerol biosynthetic process	0.0114132670918778
GO:0046504	glycerol ether biosynthetic process	0.0115088380852527
GO:0045017	glycerolipid biosynthetic process	0.0115088380852527
GO:0004467	long-chain-fatty-acid-CoA ligase activity	0.0128709689544981
GO:0015645	fatty-acid ligase activity	0.0128709689544981
GO:0048660	regulation of smooth muscle cell proliferation	0.0129699268652264
GO:0009303	rRNA transcription	0.0129699268652264
GO:0005624	membrane fraction	0.0129699268652264
GO:0048659	smooth muscle cell proliferation	0.0129699268652264
GO:0001890	placenta development	0.0129699268652264
GO:0007202	phospholipase C activation	0.0129699268652264
GO:0050714	positive regulation of protein secretion	0.0129699268652264
GO:0032501	multicellular organismal process	0.0129699268652264
GO:0001936	regulation of endothelial cell proliferation	0.0129699268652264
GO:0048477	oogenesis	0.0129699268652264
GO:0044255	cellular lipid metabolic process	0.0129699268652264
GO:0001541	ovarian follicle development	0.0129699268652264
GO:0030426	growth cone	0.0129699268652264
GO:0007281	germ cell development	0.0129699268652264
GO:0030427	site of polarized growth	0.0129699268652264
GO:0001935	endothelial cell proliferation	0.0129699268652264
GO:0033002	muscle cell proliferation	0.0129699268652264
GO:0051047	positive regulation of secretion	0.0129699268652264
GO:0004522	pancreatic ribonuclease activity	0.0129699268652264
GO:0042327	positive regulation of phosphorylation	0.0129699268652264
GO:0006638	neutral lipid metabolic process	0.0129699268652264
GO:0006639	acylglycerol metabolic process	0.0129699268652264
GO:0000267	cell fraction	0.0129699268652264
GO:0046486	glycerolipid metabolic process	0.0129699268652264
GO:0022601	menstrual cycle phase	0.0129699268652264
GO:0045937	positive regulation of phosphate metabolic process	0.0129699268652264
GO:0022602	menstrual cycle process	0.0129699268652264
GO:0006662	glycerol ether metabolic process	0.0129699268652264
GO:0006629	lipid metabolic process	0.0129699268652264
GO:0050708	regulation of protein secretion	0.0129699268652264
GO:0008585	female gonad development	0.0131258106267946
GO:0016892	endoribonuclease activity, producing 3'-phosphomonoesters	0.0131258106267946
GO:0016877	ligase activity, forming carbon-sulfur bonds	0.0131258106267946
GO:0046660	female sex differentiation	0.0131258106267946
GO:0046545	development of primary female sexual characteristics	0.0131258106267946
GO:0016894	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters	0.013331151788889
GO:0030041	actin filament polymerization	0.0135291336434057
GO:0042698	menstrual cycle	0.0141484813821663
GO:0043025	cell soma	0.0144964345499042
GO:0007292	female gamete generation	0.0144964345499042
GO:0019843	rRNA binding	0.0146616763370218
GO:0005605	basal lamina	0.0160218026441832
GO:0017148	negative regulation of translation	0.0161569953268891
GO:0031327	negative regulation of cellular biosynthetic process	0.0166565806400099
GO:0005778	peroxisomal membrane	0.0166565806400099
GO:0048469	cell maturation	0.0166565806400099
GO:0031903	microbody membrane	0.0166565806400099
GO:0044439	peroxisomal part	0.016884205859888
GO:0044438	microbody part	0.016884205859888
GO:0001666	response to hypoxia	0.0169930388304039
GO:0009890	negative regulation of biosynthetic process	0.0176400003007381
GO:0048608	reproductive structure development	0.0176400003007381
GO:0008406	gonad development	0.0176400003007381
GO:0021700	developmental maturation	0.017732417975579
GO:0009306	protein secretion	0.0188107850763081
GO:0051046	regulation of secretion	0.0188545148732673
GO:0045137	development of primary sexual characteristics	0.0188545148732673
GO:0008154	actin polymerization and/or depolymerization	0.0188545148732673
GO:0048609	reproductive process in a multicellular organism	0.0188545148732673
GO:0032504	multicellular organism reproduction	0.0188545148732673
GO:0042325	regulation of phosphorylation	0.0195327876836674
GO:0051174	regulation of phosphorus metabolic process	0.0205421321007198
GO:0019220	regulation of phosphate metabolic process	0.0205421321007198
GO:0032147	activation of protein kinase activity	0.0205881552272556
GO:0004521	endoribonuclease activity	0.0209230556606885
GO:0005604	basement membrane	0.0210790797008298
GO:0009725	response to hormone stimulus	0.0210790797008298
GO:0008201	heparin binding	0.0210790797008298
GO:0051345	positive regulation of hydrolase activity	0.0210790797008298
GO:0007548	sex differentiation	0.0222101641048811
GO:0005741	mitochondrial outer membrane	0.0222338823698106
GO:0003006	reproductive developmental process	0.0233269439938313
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0233379140418386
GO:0031968	organelle outer membrane	0.0243951342809688
GO:0007586	digestion	0.024636467903827
GO:0019867	outer membrane	0.024636467903827
GO:0051258	protein polymerization	0.024636467903827
GO:0042579	microbody	0.024636467903827
GO:0004540	ribonuclease activity	0.024636467903827
GO:0005777	peroxisome	0.024636467903827
GO:0051248	negative regulation of protein metabolic process	0.0253627177922908
GO:0005539	glycosaminoglycan binding	0.0265556523991351
GO:0030247	polysaccharide binding	0.0276913871447646
GO:0005507	copper ion binding	0.0276913871447646
GO:0001871	pattern binding	0.0296569389378297
GO:0048015	phosphoinositide-mediated signaling	0.0296569389378297
GO:0001525	angiogenesis	0.0296569389378297
GO:0044420	extracellular matrix part	0.0298335129112542
GO:0045860	positive regulation of protein kinase activity	0.0318041813116468
GO:0033674	positive regulation of kinase activity	0.0321800304860929
GO:0051347	positive regulation of transferase activity	0.0322556951144632
GO:0048514	blood vessel morphogenesis	0.0322556951144632
GO:0004519	endonuclease activity	0.032833695199742
GO:0048646	anatomical structure formation	0.032972222229306
GO:0005792	microsome	0.0339570459220793
GO:0001568	blood vessel development	0.0339570459220793
GO:0003012	muscle system process	0.0339570459220793
GO:0006936	muscle contraction	0.0339570459220793
GO:0005730	nucleolus	0.0339570459220793
GO:0001944	vasculature development	0.0339570459220793
GO:0042598	vesicular fraction	0.0342796057165606
GO:0006417	regulation of translation	0.0369973583403696
GO:0006631	fatty acid metabolic process	0.0380822101533051
GO:0031326	regulation of cellular biosynthetic process	0.0393454125919087
GO:0042277	peptide binding	0.0407823737579117
GO:0009889	regulation of biosynthetic process	0.0421954160278696
GO:0008285	negative regulation of cell proliferation	0.0433935348567793
GO:0008284	positive regulation of cell proliferation	0.0442238454679207
GO:0016477	cell migration	0.0442238454679207
GO:0045859	regulation of protein kinase activity	0.0446290798871913
GO:0043549	regulation of kinase activity	0.0450999918537434
GO:0004518	nuclease activity	0.0450999918537434
GO:0030036	actin cytoskeleton organization and biogenesis	0.0450999918537434
GO:0051338	regulation of transferase activity	0.0450999918537434
GO:0043085	positive regulation of catalytic activity	0.046382160641243
GO:0030029	actin filament-based process	0.0467524227931329
GO:0007276	gamete generation	0.0471170717781419
GO:0019932	second-messenger-mediated signaling	0.0474762305321381

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	2.20e-08	15

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	2.87e-18	656
anatomical system	4.92e-15	624
anatomical group	1.04e-14	625
organ	5.58e-12	503
multi-tissue structure	1.06e-09	342
embryo	1.44e-09	592
organism subdivision	1.50e-09	264
developing anatomical structure	7.08e-09	581
embryonic structure	2.01e-08	564
germ layer	6.48e-08	560
germ layer / neural crest	6.48e-08	560
embryonic tissue	6.48e-08	560
presumptive structure	6.48e-08	560
germ layer / neural crest derived structure	6.48e-08	560
epiblast (generic)	6.48e-08	560
mesenchyme	9.09e-08	160
entire embryonic mesenchyme	9.09e-08	160
adult organism	9.81e-08	114
trunk	1.18e-07	199
endoderm-derived structure	7.52e-07	160
endoderm	7.52e-07	160
presumptive endoderm	7.52e-07	160

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)
MA0003.1	4.3611
MA0004.1	1.51734
MA0006.1	1.14863
MA0007.1	0.606704
MA0009.1	1.11255
MA0014.1	4.38573
MA0017.1	1.24112
MA0019.1	0.784036
MA0024.1	1.00439
MA0025.1	1.24931
MA0027.1	2.73598
MA0028.1	0.470679
MA0029.1	1.02437
MA0030.1	1.01252
MA0031.1	0.945567
MA0038.1	0.736268
MA0040.1	1.03042
MA0041.1	0.64667
MA0042.1	0.612397
MA0043.1	1.11288
MA0046.1	1.10134
MA0048.1	1.7027
MA0050.1	0.613347
MA0051.1	0.731787
MA0052.1	1.03442
MA0055.1	1.01397
MA0056.1	0
MA0057.1	0.189508
MA0058.1	1.29981
MA0059.1	0.522232
MA0060.1	0.321781
MA0061.1	0.291022
MA0063.1	0
MA0066.1	0.736721
MA0067.1	1.43651
MA0068.1	0.247962
MA0069.1	1.09737
MA0070.1	1.08584
MA0071.1	0.695094
MA0072.1	1.0812
MA0073.1	0.362215
MA0074.1	0.730989
MA0076.1	0.540943
MA0077.1	1.07324
MA0078.1	0.836493
MA0081.1	0.522409
MA0083.1	1.12028
MA0084.1	1.62584
MA0087.1	1.07867
MA0088.1	0.132006
MA0089.1	0
MA0090.1	0.556637
MA0091.1	0.629594
MA0092.1	0.588959
MA0093.1	2.99362
MA0095.1	0
MA0098.1	0
MA0100.1	1.77562
MA0101.1	0.459973
MA0103.1	0.442769
MA0105.1	0.175503
MA0106.1	0.779931
MA0107.1	0.378225
MA0108.2	0.94238
MA0109.1	0
MA0111.1	0.5713
MA0113.1	0.797251
MA0114.1	0.372523
MA0115.1	1.35895
MA0116.1	0.382106
MA0117.1	1.1512
MA0119.1	0.504689
MA0122.1	1.17777
MA0124.1	1.31673
MA0125.1	1.23103
MA0130.1	0
MA0131.1	0.855546
MA0132.1	0
MA0133.1	0
MA0135.1	1.14377
MA0136.1	0.743749
MA0139.1	0.277033
MA0140.1	0.692258
MA0141.1	0.520334
MA0142.1	0.912455
MA0143.1	0.797437
MA0144.1	0.356507
MA0145.1	0.442008
MA0146.1	0.946108
MA0147.1	1.77656
MA0148.1	0.653474
MA0149.1	0.681935
MA0062.2	0.284987
MA0035.2	0.691506
MA0039.2	2.38271
MA0138.2	0.837782
MA0002.2	0.30855
MA0137.2	0.47779
MA0104.2	0.858845
MA0047.2	0.767096
MA0112.2	0.136971
MA0065.2	0.880827
MA0150.1	0.550239
MA0151.1	0
MA0152.1	0.69926
MA0153.1	1.21379
MA0154.1	1.57192
MA0155.1	0.813062
MA0156.1	0.480289
MA0157.1	0.883854
MA0158.1	0
MA0159.1	0.386729
MA0160.1	0.669748
MA0161.1	0
MA0162.1	0.0592265
MA0163.1	0.382496
MA0164.1	0.810347
MA0080.2	0.456437
MA0018.2	0.781393
MA0099.2	0.699641
MA0079.2	2.12087
MA0102.2	1.66336
MA0258.1	0.345771
MA0259.1	1.02361
MA0442.1	0

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	4	3.92591137190346	0.00721498454710636	0.0298745498598597
ZNF263#10127	4	6.57747330960854	0.000987510323790016	0.00709072469620526

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.