Coexpression cluster:C562

Full id: C562_Smooth_Fibroblast_Preadipocyte_Hepatic_Alveolar_Adipocyte_Mesenchymal

Phase1 CAGE Peaks

Hg19::chr11:66056544..66056560,-	p4@YIF1A
Hg19::chr11:66056564..66056579,-	p2@YIF1A
Hg19::chr11:68039364..68039457,-	p1@C11orf24
Hg19::chr14:24664776..24664904,-	p3@TM9SF1
Hg19::chr19:4670345..4670382,-	p1@C19orf10
Hg19::chr1:2323260..2323307,+	p1@RER1
Hg19::chr2:220363579..220363641,+	p1@GMPPA
Hg19::chr2:27255806..27255879,+	p1@TMEM214
Hg19::chr3:10362736..10362809,-	p1@SEC13
Hg19::chr3:128968437..128968505,+	p1@COPG
Hg19::chr6:33168637..33168704,+	p1@SLC39A7
Hg19::chr7:6523755..6523829,-	p1@DAGLB p1@KDELR2
Hg19::chr9:136242894..136242905,-	p4@SURF4
Hg19::chr9:136242909..136242953,-	p1@SURF4
Hg19::chr9:136242956..136242976,-	p2@SURF4
Hg19::chrX:54835499..54835584,+	p2@MAGED2

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:0005793	ER-Golgi intermediate compartment	0.00833926739920197
GO:0000139	Golgi membrane	0.00833926739920197
GO:0012505	endomembrane system	0.00833926739920197
GO:0044431	Golgi apparatus part	0.00833926739920197
GO:0044425	membrane part	0.0139153532669686
GO:0016192	vesicle-mediated transport	0.0161922944162981
GO:0031090	organelle membrane	0.0165749186817612
GO:0005794	Golgi apparatus	0.0180427800933964
GO:0016021	integral to membrane	0.0214975997088356
GO:0031224	intrinsic to membrane	0.0214975997088356
GO:0015031	protein transport	0.0227785891077271
GO:0005783	endoplasmic reticulum	0.0227785891077271
GO:0046907	intracellular transport	0.0227785891077271
GO:0045184	establishment of protein localization	0.0227785891077271
GO:0008104	protein localization	0.0227785891077271
GO:0016020	membrane	0.0227785891077271
GO:0033036	macromolecule localization	0.0248064161649225
GO:0006890	retrograde vesicle-mediated transport, Golgi to ER	0.0249997241602398
GO:0051649	establishment of cellular localization	0.0258787183563686
GO:0030126	COPI vesicle coat	0.0258787183563686
GO:0030663	COPI coated vesicle membrane	0.0258787183563686
GO:0051641	cellular localization	0.0258787183563686
GO:0004806	triacylglycerol lipase activity	0.0265426724499683
GO:0030137	COPI-coated vesicle	0.0265426724499683
GO:0006810	transport	0.0272165256352636
GO:0051234	establishment of localization	0.0291079438701855
GO:0006829	zinc ion transport	0.0318924360004973
GO:0005789	endoplasmic reticulum membrane	0.0368909860600387
GO:0051179	localization	0.0368909860600387
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0369405361170417
GO:0044432	endoplasmic reticulum part	0.0439203538946573
GO:0006886	intracellular protein transport	0.0439649120519745

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
animal cell	8.40e-27	679
eukaryotic cell	8.40e-27	679
mesodermal cell	1.99e-24	121
contractile cell	2.86e-23	59
embryonic cell	3.02e-23	250
muscle precursor cell	4.08e-22	58
myoblast	4.08e-22	58
multi-potent skeletal muscle stem cell	4.08e-22	58
somatic cell	7.62e-22	588
muscle cell	3.16e-21	55
fibroblast	2.13e-20	76
smooth muscle cell	5.28e-20	43
smooth muscle myoblast	5.28e-20	43
non-terminally differentiated cell	2.23e-18	106
electrically responsive cell	1.46e-17	61
electrically active cell	1.46e-17	61
vascular associated smooth muscle cell	1.13e-16	32
native cell	2.46e-11	722
epithelial cell	7.91e-08	253
multi fate stem cell	7.48e-07	427
cardiocyte	8.01e-07	16
skin fibroblast	8.22e-07	23

Uber Anatomy

Ontology term	p-value	n
mesenchyme	4.25e-26	160
entire embryonic mesenchyme	4.25e-26	160
trunk mesenchyme	8.46e-26	122
unilaminar epithelium	8.67e-26	148
epithelial vesicle	2.29e-24	78
epithelial tube	2.71e-24	117
trunk	1.29e-23	199
organism subdivision	1.34e-21	264
somite	1.49e-21	71
presomitic mesoderm	1.49e-21	71
presumptive segmental plate	1.49e-21	71
dermomyotome	1.49e-21	71
trunk paraxial mesoderm	1.49e-21	71
multilaminar epithelium	3.43e-21	83
dense mesenchyme tissue	3.61e-21	73
paraxial mesoderm	1.11e-20	72
presumptive paraxial mesoderm	1.11e-20	72
skeletal muscle tissue	5.28e-19	62
striated muscle tissue	5.28e-19	62
myotome	5.28e-19	62
muscle tissue	3.83e-18	64
musculature	3.83e-18	64
musculature of body	3.83e-18	64
vasculature	8.27e-18	78
vascular system	8.27e-18	78
splanchnic layer of lateral plate mesoderm	5.33e-17	83
artery	8.56e-17	42
arterial blood vessel	8.56e-17	42
arterial system	8.56e-17	42
vessel	1.68e-15	68
epithelial tube open at both ends	4.69e-15	59
blood vessel	4.69e-15	59
blood vasculature	4.69e-15	59
vascular cord	4.69e-15	59
systemic artery	2.65e-13	33
systemic arterial system	2.65e-13	33
cell layer	2.56e-12	309
cardiovascular system	7.50e-12	109
epithelium	8.43e-12	306
circulatory system	3.02e-11	112
multi-tissue structure	1.88e-10	342
subdivision of trunk	2.51e-10	112
surface structure	1.24e-09	99
multi-cellular organism	4.21e-09	656
integument	8.37e-09	46
integumental system	8.37e-09	46
anatomical group	5.73e-08	625
anatomical system	7.41e-08	624
abdominal segment of trunk	9.29e-08	60
abdomen	9.29e-08	60
primordium	2.14e-07	160
skin of body	4.27e-07	41
anatomical cluster	5.50e-07	373
mesoderm	7.91e-07	315
mesoderm-derived structure	7.91e-07	315
presumptive mesoderm	7.91e-07	315
adipose tissue	8.05e-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
ATF3#467	4	5.61579363150219	0.00464141212767522	0.0219123244373145
BRCA1#672	4	5.04605766080594	0.00677897669640447	0.0287730450782649
CCNT2#905	12	4.75215118272197	2.31381839264867e-07	1.21985299904005e-05
CHD2#1106	6	3.87900856279382	0.00277317152827015	0.0151923657805815
CTCFL#140690	6	7.40492788461538	8.67296992239919e-05	0.0012991914884186
E2F1#1869	9	2.76040643336962	0.00169642820214106	0.0105996568952085
E2F4#1874	5	3.95876884852639	0.00638275993940918	0.0277846392677541
E2F6#1876	13	4.07643903200413	2.37289564027328e-07	1.2459670576898e-05
EBF1#1879	7	3.89657924537394	0.00102115841479567	0.00724368428192929
ELF1#1997	15	3.99196683638207	4.54061180224701e-09	3.66757119887761e-07
ELK4#2005	11	11.1620311401968	1.57457980886855e-10	1.65941009746137e-08
ESR1#2099	3	5.76911311802897	0.0139904224229487	0.0491157930495255
ETS1#2113	15	9.12071336456469	2.17334805334434e-14	3.66100479585854e-12
GABPB1#2553	12	5.30076287713663	6.68540345520611e-08	4.06886277073585e-06
HEY1#23462	16	4.04011104310571	1.98084199021544e-10	2.05031869788018e-08
HMGN3#9324	8	4.0892738616753	0.000257285293595512	0.00276816923640896
IRF1#3659	11	5.25055008057518	4.46896063357945e-07	2.12731895902645e-05
JUND#3727	11	4.80883146003633	1.10371712893257e-06	4.57788376602813e-05
MAX#4149	9	3.62956247381651	0.000207178817062783	0.00243501558352689
MXI1#4601	9	5.6033840411771	6.10807177715345e-06	0.000181640349753454
MYC#4609	13	4.24310402068264	1.44725283711898e-07	8.17909302250373e-06
NFKB1#4790	8	2.74403171209692	0.00385616313935589	0.0190246975346587
NFYA#4800	4	4.60639517495763	0.00932026722368585	0.0352055911090646
NFYB#4801	7	7.3324095484222	1.90141463325496e-05	0.000430669795884872
NRF1#4899	8	6.10513972385545	1.42402144556288e-05	0.00034063988949414
PAX5#5079	12	5.00217414838337	1.2934425150475e-07	7.37770851059781e-06
POLR2A#5430	16	2.14745317655807	4.88536678567824e-06	0.000151042872033585
POU2F2#5452	10	5.69132753608908	1.08661015877248e-06	4.51589647322081e-05
REST#5978	7	4.22188756330601	0.000627281365604383	0.0051633542356838
RXRA#6256	4	5.01865428478332	0.00690995175201785	0.0292576198422522
SIN3A#25942	15	5.07082943138919	1.3297899225369e-10	1.42297059139172e-08
SIX5#147912	9	9.61127738744569	6.29588488815385e-08	3.88614611012943e-06
SP1#6667	13	4.62993486973948	4.9106978951726e-08	3.16195053929674e-06
SPI1#6688	9	4.61493197354403	3.01826774164688e-05	0.000620643561074736
SRF#6722	8	6.8985891310839	5.75315050227476e-06	0.000172857677015844
TAF1#6872	15	3.13410589288621	1.57946317760101e-07	8.84016906781733e-06
TAF7#6879	7	5.00196786465421	0.000219506557872768	0.00248752662735178
TBP#6908	15	3.47509751915286	3.48271765686805e-08	2.32564929261919e-06
TCF12#6938	6	3.98792433831991	0.00240605767871516	0.0135669073484144
TCF7L2#6934	6	4.0388162111765	0.00225404522645573	0.0128037762104759
THAP1#55145	6	11.7634292260692	6.36151165140569e-06	0.000187627764857712
YY1#7528	13	3.99032623425626	3.08644499595592e-07	1.54973667756077e-05
ZNF263#10127	6	3.083190613879	0.00873468672710712	0.0331832944269885

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.