Coexpression cluster:C1220

Full id: C1220_Mesenchymal_Fibroblast_Renal_Alveolar_Trabecular_Smooth_Hepatic

Phase1 CAGE Peaks

Hg19::chr16:31483374..31483390,+	p2@TGFB1I1
Hg19::chr19:4400432..4400570,-	p1@SH3GL1
Hg19::chr8:22423168..22423206,+	p4@SORBS3
Hg19::chr8:22423219..22423330,+	p1@SORBS3
Hg19::chr8:22423457..22423476,+	p9@SORBS3
Hg19::chr8:22423479..22423528,+	p2@SORBS3
Hg19::chr8:22423529..22423543,+	p7@SORBS3

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:0051496	positive regulation of stress fiber formation	0.00953586230242861
GO:0051495	positive regulation of cytoskeleton organization and biogenesis	0.00953586230242861
GO:0032233	positive regulation of actin filament bundle formation	0.00953586230242861
GO:0017166	vinculin binding	0.00953586230242861
GO:0030054	cell junction	0.00953586230242861
GO:0008134	transcription factor binding	0.00953586230242861
GO:0051492	regulation of stress fiber formation	0.00953586230242861
GO:0032231	regulation of actin filament bundle formation	0.00953586230242861
GO:0043149	stress fiber formation	0.00988875127094105
GO:0043410	positive regulation of MAPKKK cascade	0.0101709875930319
GO:0006366	transcription from RNA polymerase II promoter	0.0137426466736377
GO:0051130	positive regulation of cellular component organization and biogenesis	0.0146666708048605
GO:0043408	regulation of MAPKKK cascade	0.0146666708048605
GO:0031901	early endosome membrane	0.0154340161621278
GO:0051017	actin filament bundle formation	0.016098849256612
GO:0050681	androgen receptor binding	0.0174741809876831
GO:0048522	positive regulation of cellular process	0.0177970360144775
GO:0022610	biological adhesion	0.0177970360144775
GO:0007155	cell adhesion	0.0177970360144775
GO:0035258	steroid hormone receptor binding	0.0179571336086724
GO:0048518	positive regulation of biological process	0.0179571336086724
GO:0030521	androgen receptor signaling pathway	0.0179571336086724
GO:0005925	focal adhesion	0.0179571336086724
GO:0048523	negative regulation of cellular process	0.0179571336086724
GO:0005924	cell-substrate adherens junction	0.0179571336086724
GO:0007165	signal transduction	0.0179571336086724
GO:0030055	cell-matrix junction	0.0179571336086724
GO:0048519	negative regulation of biological process	0.0179571336086724
GO:0007015	actin filament organization	0.0179571336086724
GO:0016363	nuclear matrix	0.0182556209063587
GO:0005769	early endosome	0.0182556209063587
GO:0007154	cell communication	0.0182556209063587
GO:0030518	steroid hormone receptor signaling pathway	0.0182556209063587
GO:0005912	adherens junction	0.0182556209063587
GO:0030522	intracellular receptor-mediated signaling pathway	0.0182556209063587
GO:0035257	nuclear hormone receptor binding	0.0182556209063587
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.0182556209063587
GO:0033043	regulation of organelle organization and biogenesis	0.0182556209063587
GO:0051427	hormone receptor binding	0.0182556209063587
GO:0005856	cytoskeleton	0.0182556209063587
GO:0005200	structural constituent of cytoskeleton	0.0247925546529704
GO:0016323	basolateral plasma membrane	0.0247925546529704
GO:0044440	endosomal part	0.0247925546529704
GO:0010008	endosome membrane	0.0247925546529704
GO:0051128	regulation of cellular component organization and biogenesis	0.028176292534052
GO:0031589	cell-substrate adhesion	0.0283881677841821
GO:0007242	intracellular signaling cascade	0.0295528142016561
GO:0005737	cytoplasm	0.0320387244708274
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.032836619654347
GO:0016055	Wnt receptor signaling pathway	0.036521136109633
GO:0044459	plasma membrane part	0.036521136109633
GO:0000165	MAPKKK cascade	0.036521136109633
GO:0009967	positive regulation of signal transduction	0.036545466937897
GO:0003713	transcription coactivator activity	0.0427683417257407
GO:0005768	endosome	0.0427683417257407
GO:0010324	membrane invagination	0.0427683417257407
GO:0006897	endocytosis	0.0427683417257407
GO:0043231	intracellular membrane-bound organelle	0.0427683417257407
GO:0043227	membrane-bound organelle	0.0427683417257407
GO:0045892	negative regulation of transcription, DNA-dependent	0.0427683417257407
GO:0005515	protein binding	0.0439555903333185
GO:0045893	positive regulation of transcription, DNA-dependent	0.0451167438222109
GO:0008285	negative regulation of cell proliferation	0.0451167438222109
GO:0007417	central nervous system development	0.0455739196306436
GO:0043232	intracellular non-membrane-bound organelle	0.0455739196306436
GO:0043228	non-membrane-bound organelle	0.0455739196306436
GO:0030036	actin cytoskeleton organization and biogenesis	0.0465410336754617
GO:0030029	actin filament-based process	0.0482515979559621
GO:0016020	membrane	0.0492796510940489

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
non-terminally differentiated cell	6.99e-37	180
mesodermal cell	1.20e-28	119
embryonic cell	1.87e-26	248
contractile cell	2.40e-21	59
muscle precursor cell	2.29e-19	57
myoblast	2.29e-19	57
multi-potent skeletal muscle stem cell	2.29e-19	57
muscle cell	4.65e-19	54
fibroblast	9.97e-18	75
smooth muscle cell	1.87e-16	42
smooth muscle myoblast	1.87e-16	42
electrically responsive cell	2.10e-16	60
electrically active cell	2.10e-16	60
somatic cell	5.86e-13	591
vascular associated smooth muscle cell	6.64e-13	32
meso-epithelial cell	2.93e-10	44
animal cell	2.20e-09	679
eukaryotic cell	2.20e-09	679
endothelial cell	2.25e-09	35
lining cell	3.25e-09	57
barrier cell	3.25e-09	57
blood vessel endothelial cell	1.03e-08	18
embryonic blood vessel endothelial progenitor cell	1.03e-08	18
endothelial cell of vascular tree	3.26e-08	24
cardiocyte	3.84e-07	16

Uber Anatomy

Ontology term	p-value	n
splanchnic layer of lateral plate mesoderm	1.43e-25	84
vasculature	4.94e-24	79
vascular system	4.94e-24	79
somite	9.65e-23	83
paraxial mesoderm	9.65e-23	83
presomitic mesoderm	9.65e-23	83
presumptive segmental plate	9.65e-23	83
trunk paraxial mesoderm	9.65e-23	83
presumptive paraxial mesoderm	9.65e-23	83
epithelial tube	8.52e-22	118
trunk mesenchyme	1.17e-21	143
blood vessel	2.19e-21	60
epithelial tube open at both ends	2.19e-21	60
blood vasculature	2.19e-21	60
vascular cord	2.19e-21	60
vessel	2.63e-21	69
dermomyotome	1.52e-20	70
multilaminar epithelium	2.31e-20	82
trunk	1.23e-18	216
cardiovascular system	3.01e-18	110
circulatory system	4.85e-18	113
skeletal muscle tissue	5.67e-18	61
striated muscle tissue	5.67e-18	61
myotome	5.67e-18	61
organism subdivision	1.11e-17	365
cell layer	1.42e-17	312
unilaminar epithelium	1.72e-17	138
muscle tissue	2.31e-17	63
musculature	2.31e-17	63
musculature of body	2.31e-17	63
artery	3.84e-17	42
arterial blood vessel	3.84e-17	42
arterial system	3.84e-17	42
epithelium	5.18e-17	309
multi-cellular organism	3.51e-15	659
mesenchyme	4.74e-15	238
entire embryonic mesenchyme	4.74e-15	238
multi-tissue structure	9.46e-15	347
anatomical system	1.54e-12	625
systemic artery	1.62e-12	33
systemic arterial system	1.62e-12	33
anatomical group	3.14e-12	626
anatomical cluster	5.00e-11	286
surface structure	1.77e-10	95
anatomical conduit	9.67e-10	241
compound organ	1.84e-09	69
embryonic structure	4.33e-09	605
developing anatomical structure	4.33e-09	605
embryo	5.24e-09	612
mesoderm	6.12e-09	448
mesoderm-derived structure	6.12e-09	448
presumptive mesoderm	6.12e-09	448
germ layer	6.70e-09	604
embryonic tissue	6.70e-09	604
presumptive structure	6.70e-09	604
epiblast (generic)	6.70e-09	604
endothelium	1.03e-08	18
blood vessel endothelium	1.03e-08	18
cardiovascular system endothelium	1.03e-08	18
squamous epithelium	2.33e-08	25
simple squamous epithelium	3.53e-08	22
tube	7.04e-08	194
integument	1.76e-07	45
integumental system	1.76e-07	45
aorta	3.35e-07	21
aortic system	3.35e-07	21

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
CCNT2#905	5	4.52585826925902	0.0015515733062647	0.009856737502006
E2F1#1869	6	4.20633361275371	0.000413523201700764	0.00393799121568579
FOSL1#8061	5	28.3668426545522	2.03338323682158e-07	1.09862654873466e-05
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223431147689244
ZBTB7A#51341	6	6.30163654960791	3.91424956694869e-05	0.000731437306356332
ZNF143#7702	6	11.5721799019096	1.08146108094101e-06	4.49986907698796e-05

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.