Coexpression cluster:C672

Full id: C672_CD14_Smooth_Mesenchymal_Placental_Fibroblast_mesenchymal_Alveolar

Phase1 CAGE Peaks

Hg19::chr6:36646476..36646498,+	p1@CDKN1A
Hg19::chr6:36646510..36646519,+	p2@CDKN1A
Hg19::chr6:36652080..36652094,+	p1@BC037414
Hg19::chr6:36652270..36652284,+	p4@BC037414
Hg19::chr6:36652291..36652299,+	p5@BC037414
Hg19::chr6:36653519..36653558,+	p@chr6:36653519..36653558 +
Hg19::chr6:36653561..36653579,+	p@chr6:36653561..36653579 +
Hg19::chr6:36653603..36653637,+	p@chr6:36653603..36653637 +
Hg19::chr6:36653937..36653958,+	p@chr6:36653937..36653958 +
Hg19::chr6:36653968..36653983,+	p@chr6:36653968..36653983 +
Hg19::chr6:36654158..36654169,+	p@chr6:36654158..36654169 +
Hg19::chr6:36654222..36654237,+	p@chr6:36654222..36654237 +
Hg19::chr6:36654635..36654646,+	p@chr6:36654635..36654646 +

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:0043071	positive regulation of non-apoptotic programmed cell death	0.00326739667961851
GO:0016244	non-apoptotic programmed cell death	0.00326739667961851
GO:0030332	cyclin binding	0.00326739667961851
GO:0043070	regulation of non-apoptotic programmed cell death	0.00326739667961851
GO:0000307	cyclin-dependent protein kinase holoenzyme complex	0.00435652890615801
GO:0045736	negative regulation of cyclin-dependent protein kinase activity	0.00435652890615801
GO:0030890	positive regulation of B cell proliferation	0.00435652890615801
GO:0030888	regulation of B cell proliferation	0.00435652890615801
GO:0048146	positive regulation of fibroblast proliferation	0.00435652890615801
GO:0048145	regulation of fibroblast proliferation	0.00435652890615801
GO:0048144	fibroblast proliferation	0.00435652890615801
GO:0042326	negative regulation of phosphorylation	0.00435652890615801
GO:0045936	negative regulation of phosphate metabolic process	0.00435652890615801
GO:0031668	cellular response to extracellular stimulus	0.00435652890615801
GO:0004861	cyclin-dependent protein kinase inhibitor activity	0.00435652890615801
GO:0000086	G2/M transition of mitotic cell cycle	0.00435652890615801
GO:0050871	positive regulation of B cell activation	0.00435652890615801
GO:0042100	B cell proliferation	0.00435652890615801
GO:0051716	cellular response to stimulus	0.00544566113269752
GO:0050864	regulation of B cell activation	0.00544566113269752
GO:0032946	positive regulation of mononuclear cell proliferation	0.00594072123567002
GO:0050671	positive regulation of lymphocyte proliferation	0.00594072123567002
GO:0009411	response to UV	0.00617174928372385
GO:0000082	G1/S transition of mitotic cell cycle	0.00617174928372385
GO:0008629	induction of apoptosis by intracellular signals	0.00627340162486754
GO:0004860	protein kinase inhibitor activity	0.00630945565719436
GO:0019210	kinase inhibitor activity	0.00630945565719436
GO:0050670	regulation of lymphocyte proliferation	0.00630945565719436
GO:0032944	regulation of mononuclear cell proliferation	0.00630945565719436
GO:0000079	regulation of cyclin-dependent protein kinase activity	0.00664370658189097
GO:0051251	positive regulation of lymphocyte activation	0.00664370658189097
GO:0032943	mononuclear cell proliferation	0.00664370658189097
GO:0030308	negative regulation of cell growth	0.00664370658189097
GO:0046651	lymphocyte proliferation	0.00664370658189097
GO:0045792	negative regulation of cell size	0.00664370658189097
GO:0006469	negative regulation of protein kinase activity	0.00664370658189097
GO:0033673	negative regulation of kinase activity	0.00664370658189097
GO:0051348	negative regulation of transferase activity	0.00664370658189097
GO:0042113	B cell activation	0.00664370658189097
GO:0045926	negative regulation of growth	0.00664370658189097
GO:0042325	regulation of phosphorylation	0.00680043536571006
GO:0009991	response to extracellular stimulus	0.00683182942102052
GO:0051174	regulation of phosphorus metabolic process	0.00683182942102052
GO:0019220	regulation of phosphate metabolic process	0.00683182942102052
GO:0051249	regulation of lymphocyte activation	0.00735769326373353
GO:0050865	regulation of cell activation	0.0075080604552936
GO:0009416	response to light stimulus	0.0075080604552936
GO:0051329	interphase of mitotic cell cycle	0.00771468660465481
GO:0043086	negative regulation of catalytic activity	0.00773506152726014
GO:0051325	interphase	0.00784175203108442
GO:0009314	response to radiation	0.00846171960619152
GO:0007050	cell cycle arrest	0.00846171960619152
GO:0019887	protein kinase regulator activity	0.00863085915370927
GO:0019207	kinase regulator activity	0.0098425282694681
GO:0046649	lymphocyte activation	0.012277490553718
GO:0001558	regulation of cell growth	0.0126028157642428
GO:0009628	response to abiotic stimulus	0.0126110047283521
GO:0045321	leukocyte activation	0.0135202621225593
GO:0016049	cell growth	0.0144990727658071
GO:0040008	regulation of growth	0.0144990727658071
GO:0008361	regulation of cell size	0.0144990727658071
GO:0001775	cell activation	0.0144990727658071
GO:0006917	induction of apoptosis	0.0144990727658071
GO:0012502	induction of programmed cell death	0.0144990727658071
GO:0045786	negative regulation of progression through cell cycle	0.0147111773207944
GO:0008285	negative regulation of cell proliferation	0.0147111773207944
GO:0043066	negative regulation of apoptosis	0.0147111773207944
GO:0043069	negative regulation of programmed cell death	0.0147111773207944
GO:0008284	positive regulation of cell proliferation	0.0147111773207944
GO:0045859	regulation of protein kinase activity	0.0147499621537064
GO:0043549	regulation of kinase activity	0.0148490140181724
GO:0051338	regulation of transferase activity	0.0149453144419587
GO:0043065	positive regulation of apoptosis	0.0151889791593077
GO:0043068	positive regulation of programmed cell death	0.0151889791593077
GO:0051239	regulation of multicellular organismal process	0.0160901134267436
GO:0000278	mitotic cell cycle	0.0186872160974673
GO:0000074	regulation of progression through cell cycle	0.0199721390113478
GO:0051726	regulation of cell cycle	0.0200512035552657
GO:0022403	cell cycle phase	0.0203488502072444
GO:0031324	negative regulation of cellular metabolic process	0.0207479689155775
GO:0004857	enzyme inhibitor activity	0.0215675073008563
GO:0009892	negative regulation of metabolic process	0.0231639829644499
GO:0006974	response to DNA damage stimulus	0.0235147584332384
GO:0042127	regulation of cell proliferation	0.0242141955481806
GO:0000902	cell morphogenesis	0.0242141955481806
GO:0032989	cellular structure morphogenesis	0.0242141955481806
GO:0009719	response to endogenous stimulus	0.0264896987512366
GO:0005829	cytosol	0.0278817849994113
GO:0042981	regulation of apoptosis	0.0278817849994113
GO:0043067	regulation of programmed cell death	0.0278817849994113
GO:0050790	regulation of catalytic activity	0.0289637361343472
GO:0022402	cell cycle process	0.0295959844168343
GO:0009605	response to external stimulus	0.0296525031999787
GO:0065009	regulation of a molecular function	0.0310982010216173
GO:0008283	cell proliferation	0.0341643582640812
GO:0007049	cell cycle	0.0380742474194434
GO:0006915	apoptosis	0.0383196726235531
GO:0012501	programmed cell death	0.0383196726235531
GO:0008219	cell death	0.0395572824679148
GO:0016265	death	0.0395572824679148
GO:0065008	regulation of biological quality	0.0407463585928896
GO:0048522	positive regulation of cellular process	0.0407463585928896
GO:0009653	anatomical structure morphogenesis	0.0442843278130819
GO:0048518	positive regulation of biological process	0.0444868624840366
GO:0048523	negative regulation of cellular process	0.0471749844409682
GO:0004672	protein kinase activity	0.0475930233333111
GO:0048519	negative regulation of biological process	0.0481253940848483
GO:0006950	response to stress	0.0492933178085657
GO:0048468	cell development	0.0496404486371399

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
somatic cell	1.14e-34	588
animal cell	1.48e-28	679
eukaryotic cell	1.48e-28	679
stuff accumulating cell	6.20e-19	87
defensive cell	4.44e-18	48
phagocyte	4.44e-18	48
classical monocyte	8.64e-18	42
CD14-positive, CD16-negative classical monocyte	8.64e-18	42
native cell	6.19e-17	722
somatic stem cell	1.57e-16	433
multi fate stem cell	4.88e-16	427
stem cell	6.45e-15	441
macrophage dendritic cell progenitor	1.66e-13	61
monopoietic cell	7.10e-13	59
monocyte	7.10e-13	59
monoblast	7.10e-13	59
promonocyte	7.10e-13	59
granulocyte monocyte progenitor cell	1.87e-12	67
myeloid lineage restricted progenitor cell	2.91e-11	66
myeloid leukocyte	4.95e-11	72
smooth muscle cell	1.14e-09	43
smooth muscle myoblast	1.14e-09	43
connective tissue cell	1.66e-09	361
mesenchymal cell	9.97e-09	354
embryonic cell	4.13e-08	250
contractile cell	4.34e-08	59
fibroblast	6.18e-08	76
mesodermal cell	9.29e-08	121
muscle precursor cell	1.84e-07	58
myoblast	1.84e-07	58
multi-potent skeletal muscle stem cell	1.84e-07	58
muscle cell	1.86e-07	55
vascular associated smooth muscle cell	2.29e-07	32
motile cell	9.81e-07	386

Uber Anatomy

Ontology term	p-value	n
mesoderm	8.95e-21	315
mesoderm-derived structure	8.95e-21	315
presumptive mesoderm	8.95e-21	315
musculoskeletal system	1.39e-19	167
lateral plate mesoderm	3.15e-15	203
bone marrow	8.70e-12	76
skeletal element	1.14e-11	90
skeletal system	2.97e-11	100
bone element	1.53e-10	82
immune system	3.44e-09	93
connective tissue	5.29e-09	371
multilaminar epithelium	2.95e-08	83
multi-cellular organism	3.75e-08	656
artery	3.87e-08	42
arterial blood vessel	3.87e-08	42
arterial system	3.87e-08	42
anatomical system	4.55e-08	624
anatomical group	4.88e-08	625
vessel	2.45e-07	68
muscle tissue	3.50e-07	64
musculature	3.50e-07	64
musculature of body	3.50e-07	64
skeletal muscle tissue	4.03e-07	62
striated muscle tissue	4.03e-07	62
myotome	4.03e-07	62
hemolymphoid system	4.28e-07	108
epithelial vesicle	4.49e-07	78
splanchnic layer of lateral plate mesoderm	6.43e-07	83
systemic artery	6.43e-07	33
systemic arterial system	6.43e-07	33
somite	6.84e-07	71
presomitic mesoderm	6.84e-07	71
presumptive segmental plate	6.84e-07	71
dermomyotome	6.84e-07	71
trunk paraxial mesoderm	6.84e-07	71
dense mesenchyme tissue	7.13e-07	73
hematopoietic system	8.54e-07	98
blood island	8.54e-07	98
vasculature	9.88e-07	78
vascular system	9.88e-07	78

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
JUNB#3726	3	7.06399215226642	0.007792750127433	0.0320180585608787
POLR2A#5430	13	2.14745317655807	4.83928878402115e-05	0.000841089168437984
POU2F2#5452	5	3.50235540682405	0.00961613860265682	0.0361909873701937
ZBTB33#10009	3	7.30724423768796	0.00709817327748382	0.0295974016419984

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.