Coexpression cluster:C1780

Full id: C1780_Mesenchymal_tenocyte_Osteoblast_Smooth_mature_Synoviocyte_Chondrocyte

Phase1 CAGE Peaks

Hg19::chr17:40575190..40575206,-	p4@PTRF
Hg19::chr17:40575209..40575222,-	p2@PTRF
Hg19::chr17:40575228..40575241,-	p3@PTRF
Hg19::chr17:46115174..46115183,-	p2@COPZ2
Hg19::chr19:13106214..13106382,+	p1@NFIX

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:0042134	rRNA primary transcript binding	0.00629911987840746
GO:0003716	RNA polymerase I transcription termination factor activity	0.00629911987840746
GO:0006361	transcription initiation from RNA polymerase I promoter	0.00629911987840746
GO:0003715	transcription termination factor activity	0.00944812353844312
GO:0006353	transcription termination	0.0132262048248837
GO:0006360	transcription from RNA polymerase I promoter	0.0144102097285995
GO:0005801	cis-Golgi network	0.0144102097285995
GO:0030126	COPI vesicle coat	0.0144102097285995
GO:0030663	COPI coated vesicle membrane	0.0144102097285995
GO:0065003	macromolecular complex assembly	0.0144102097285995
GO:0030137	COPI-coated vesicle	0.0144102097285995
GO:0022607	cellular component assembly	0.0144102097285995
GO:0005783	endoplasmic reticulum	0.0144102097285995
GO:0016599	caveolar membrane	0.0144102097285995
GO:0043624	cellular protein complex disassembly	0.0144102097285995
GO:0043241	protein complex disassembly	0.0144102097285995
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0144102097285995
GO:0032984	macromolecular complex disassembly	0.0144102097285995
GO:0005901	caveola	0.0144102097285995
GO:0019843	rRNA binding	0.0169906068743104
GO:0022411	cellular component disassembly	0.0209212139325074
GO:0030120	vesicle coat	0.0209212139325074
GO:0030662	coated vesicle membrane	0.0209212139325074
GO:0005798	Golgi-associated vesicle	0.0271114120113892
GO:0006352	transcription initiation	0.0343031653617995
GO:0030659	cytoplasmic vesicle membrane	0.0364124261128975
GO:0044433	cytoplasmic vesicle part	0.0364124261128975
GO:0012506	vesicle membrane	0.0364124261128975
GO:0030117	membrane coat	0.0364124261128975
GO:0048475	coated membrane	0.0364124261128975
GO:0030135	coated vesicle	0.0446140550686479
GO:0005792	microsome	0.0476089978154376
GO:0042598	vesicular fraction	0.0481512019910992

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
mesodermal cell	8.04e-22	121
fibroblast	3.10e-21	76
muscle precursor cell	7.11e-19	58
myoblast	7.11e-19	58
multi-potent skeletal muscle stem cell	7.11e-19	58
contractile cell	5.89e-18	59
muscle cell	8.33e-18	55
non-terminally differentiated cell	8.32e-16	106
smooth muscle cell	2.84e-15	43
smooth muscle myoblast	2.84e-15	43
electrically responsive cell	8.44e-15	61
electrically active cell	8.44e-15	61
vascular associated smooth muscle cell	1.33e-12	32
embryonic cell	7.60e-12	250
fat cell	1.66e-09	15
skin fibroblast	2.34e-07	23
preadipocyte	2.98e-07	12

Uber Anatomy

Ontology term	p-value	n
dense mesenchyme tissue	4.77e-22	73
epithelial vesicle	6.82e-22	78
somite	7.14e-22	71
presomitic mesoderm	7.14e-22	71
presumptive segmental plate	7.14e-22	71
dermomyotome	7.14e-22	71
trunk paraxial mesoderm	7.14e-22	71
paraxial mesoderm	1.50e-21	72
presumptive paraxial mesoderm	1.50e-21	72
muscle tissue	1.35e-20	64
musculature	1.35e-20	64
musculature of body	1.35e-20	64
multilaminar epithelium	2.99e-20	83
skeletal muscle tissue	2.99e-20	62
striated muscle tissue	2.99e-20	62
myotome	2.99e-20	62
vasculature	3.17e-20	78
vascular system	3.17e-20	78
splanchnic layer of lateral plate mesoderm	9.82e-20	83
vessel	2.18e-18	68
epithelial tube open at both ends	2.84e-18	59
blood vessel	2.84e-18	59
blood vasculature	2.84e-18	59
vascular cord	2.84e-18	59
trunk mesenchyme	6.79e-18	122
mesenchyme	9.81e-18	160
entire embryonic mesenchyme	9.81e-18	160
organism subdivision	5.33e-17	264
artery	9.89e-17	42
arterial blood vessel	9.89e-17	42
arterial system	9.89e-17	42
unilaminar epithelium	1.21e-16	148
multi-tissue structure	4.91e-15	342
cell layer	1.41e-14	309
epithelium	1.87e-14	306
circulatory system	2.45e-14	112
multi-cellular organism	2.78e-14	656
epithelial tube	3.87e-14	117
cardiovascular system	6.33e-14	109
systemic artery	1.16e-13	33
systemic arterial system	1.16e-13	33
trunk	1.19e-13	199
anatomical cluster	4.13e-13	373
surface structure	1.34e-12	99
anatomical system	1.69e-11	624
anatomical group	3.29e-11	625
anatomical conduit	4.08e-11	240
integument	9.15e-09	46
integumental system	9.15e-09	46
aorta	1.03e-07	21
aortic system	1.03e-07	21
primary circulatory organ	1.49e-07	27
heart	2.95e-07	24
primitive heart tube	2.95e-07	24
primary heart field	2.95e-07	24
anterior lateral plate mesoderm	2.95e-07	24
heart tube	2.95e-07	24
heart primordium	2.95e-07	24
cardiac mesoderm	2.95e-07	24
cardiogenic plate	2.95e-07	24
heart rudiment	2.95e-07	24
tube	3.95e-07	192
mesoderm	4.61e-07	315
mesoderm-derived structure	4.61e-07	315
presumptive mesoderm	4.61e-07	315
skin of body	4.92e-07	41
adipose tissue	6.39e-07	14

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	4	5.06896126157011	0.00270999809128077	0.0148962889818564
CTBP2#1488	3	37.6302002035969	3.95343056005017e-05	0.000737702937754297
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0282957553917162
ETS1#2113	3	5.8372565533214	0.00925327904563143	0.0349727937700105
FOS#2353	3	5.39877318533664	0.0115389531727874	0.0421900549787406
GTF2B#2959	3	19.1662979605945	0.000292422965447241	0.00310243418207481
NANOG#79923	3	17.5468670886076	0.000379420009068183	0.00376103325048139
NFYA#4800	3	11.0553484198983	0.00147089290764443	0.0094117500540054
NFYB#4801	3	10.0558759521219	0.00193816560672546	0.0113872681031053
REST#5978	3	5.79001722967681	0.00946878869443394	0.0356994629240095
SMC3#9126	3	9.0269597069597	0.00265096444946755	0.0146380499174126
TAF7#6879	3	6.85984164295435	0.00584328640701904	0.0262457848384079

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.