Coexpression cluster:C884

Full id: C884_Mesenchymal_Alveolar_Smooth_Renal_Pericytes_Fibroblast_Hepatic

Phase1 CAGE Peaks

Hg19::chr11:62446527..62446572,-	p1@UBXN1
Hg19::chr16:76269543..76269562,-	p1@ENST00000478088
Hg19::chr19:49122427..49122447,-	p1@RPL18
Hg19::chr19:49990853..49990871,+	p1@RPL13AP5 p1@RPL13A
Hg19::chr19:54704718..54704735,+	p1@RPS9
Hg19::chr19:55897297..55897303,+	p1@RPL28
Hg19::chr19:5690297..5690316,+	p1@RPL36
Hg19::chr8:144679575..144679593,-	p1@EEF1D
Hg19::chr8:146017765..146017814,-	p1@RPL8

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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p.value	FDR	nGenes	nPathway	Name
6.50699372147126e-12	1.29778825489618e-09	5	92	Ribosome (KEGG):03010
6.8763067114908e-12	1.29778825489618e-09	5	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
8.20087364863308e-12	1.29778825489618e-09	6	296	Metabolism of proteins (Reactome):REACT_17015
1.93996305375098e-11	2.45599322604874e-09	5	114	Regulation of beta-cell development (Reactome):REACT_13698
6.86687013595479e-11	6.20961256579912e-09	6	421	Gene Expression (Reactome):REACT_71
3.11609735119595e-09	2.4656120291338e-07	5	312	Diabetes pathways (Reactome):REACT_15380
6.12526308875603e-11	6.20961256579912e-09	5	143	Influenza Infection (Reactome):REACT_6167
0.000659723985117411	0.0464005869532579	2	162	TNF alpha/NF-kB down reg. targets (Netpath):NetPath_9
7.97550775416383e-14	5.0484964083857e-11	6	138	{RPS27A,138} (Static Module):NA

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:0005830	cytosolic ribosome (sensu Eukaryota)	1.94711712698464e-11
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	7.33774794825837e-10
GO:0044445	cytosolic part	7.33774794825837e-10
GO:0033279	ribosomal subunit	1.26256280325865e-09
GO:0015934	large ribosomal subunit	1.82626324277862e-08
GO:0006412	translation	2.35185412760321e-08
GO:0005829	cytosol	7.70670491459429e-08
GO:0009059	macromolecule biosynthetic process	8.3730524348812e-08
GO:0044249	cellular biosynthetic process	2.59969019746735e-07
GO:0003735	structural constituent of ribosome	2.59969019746735e-07
GO:0005840	ribosome	3.65482119692358e-07
GO:0009058	biosynthetic process	8.35858825099753e-07
GO:0030529	ribonucleoprotein complex	1.33240308617928e-06
GO:0032991	macromolecular complex	1.12699311692551e-05
GO:0044444	cytoplasmic part	2.87888442874071e-05
GO:0003723	RNA binding	4.3211924777402e-05
GO:0019843	rRNA binding	6.73824644083435e-05
GO:0010467	gene expression	6.73824644083435e-05
GO:0044267	cellular protein metabolic process	7.35318134200805e-05
GO:0044260	cellular macromolecule metabolic process	7.54393068709226e-05
GO:0043232	intracellular non-membrane-bound organelle	8.09803016258299e-05
GO:0043228	non-membrane-bound organelle	8.09803016258299e-05
GO:0019538	protein metabolic process	8.09803016258299e-05
GO:0005737	cytoplasm	0.000337091277116998
GO:0044446	intracellular organelle part	0.000390228814677799
GO:0044422	organelle part	0.000390228814677799
GO:0003676	nucleic acid binding	0.00309843597899137
GO:0043170	macromolecule metabolic process	0.00315665668313737
GO:0044237	cellular metabolic process	0.00657747852642446
GO:0044238	primary metabolic process	0.00665292298190928
GO:0044424	intracellular part	0.00704833894383528
GO:0005853	eukaryotic translation elongation factor 1 complex	0.00938889893486113
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	0.0128883939605573
GO:0005622	intracellular	0.0148927233606149
GO:0003746	translation elongation factor activity	0.0189162263226417
GO:0006414	translational elongation	0.02115428669203
GO:0043229	intracellular organelle	0.0263794238315517
GO:0043226	organelle	0.0263794238315517
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.0314307297225802
GO:0043284	biopolymer biosynthetic process	0.0314307297225802
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.032772484148343
GO:0015935	small ribosomal subunit	0.0358088416844965
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0401259745596671
GO:0009967	positive regulation of signal transduction	0.0431192164746101
GO:0005730	nucleolus	0.0454276527307375

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
native cell	1.12e-26	722
somatic cell	1.44e-22	591
animal cell	2.17e-22	679
eukaryotic cell	2.17e-22	679
contractile cell	1.15e-10	59
stem cell	5.74e-09	444
mesodermal cell	9.36e-09	119
muscle cell	1.62e-08	54
lymphoid lineage restricted progenitor cell	2.46e-08	52
smooth muscle cell	3.52e-08	42
smooth muscle myoblast	3.52e-08	42
lymphocyte	3.57e-08	53
common lymphoid progenitor	3.57e-08	53
electrically responsive cell	3.90e-08	60
electrically active cell	3.90e-08	60
multi fate stem cell	4.69e-08	430
somatic stem cell	4.90e-08	436
muscle precursor cell	1.99e-07	57
myoblast	1.99e-07	57
multi-potent skeletal muscle stem cell	1.99e-07	57
embryonic cell	9.78e-07	248

Uber Anatomy

Ontology term	p-value	n
dermomyotome	2.93e-08	70
multilaminar epithelium	1.13e-07	82
vasculature	1.22e-07	79
vascular system	1.22e-07	79
vessel	4.91e-07	69
cardiovascular system	6.44e-07	110
skeletal muscle tissue	6.82e-07	61
striated muscle tissue	6.82e-07	61
myotome	6.82e-07	61

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	5	12.4795414033382	1.89229392694668e-05	0.000429069225871439
BCL3#602	3	11.5157009345794	0.00178591501782776	0.0109556052009934
BRCA1#672	4	8.97076917476612	0.000620269035673191	0.00514047594164993
CCNT2#905	6	4.22413438464176	0.00084033506380825	0.00633764830510325
CEBPB#1051	5	4.42841534768045	0.0025225868523706	0.0139868575214872
E2F1#1869	6	3.27159280991955	0.00338995924180989	0.0172999732839181
E2F4#1874	5	7.03781128626913	0.000294271514829666	0.00307242054756528
EGR1#1958	8	4.43393697316457	1.92853122912633e-05	0.00043530121685482
ELF1#1997	7	3.31185396796142	0.000896020581017362	0.00666900609042704
ELK4#2005	5	9.01982314359335	9.04446507305493e-05	0.00132000403544548
ETS1#2113	5	5.4048671790013	0.0010116099868046	0.00717838941513018
FOSL2#2355	6	11.2868004030411	3.04906898154755e-06	0.000103122317151504
GABPB1#2553	7	5.49708742814169	3.13640621886058e-05	0.000632727697685108
GATA1#2623	6	9.0402054292003	1.10995595465212e-05	0.000284472858767885
GTF2B#2959	7	24.84520106003	9.99944740019878e-10	9.27470947628206e-08
GTF2F1#2962	8	11.3241430015624	1.20451544008114e-08	8.97278088777707e-07
HEY1#23462	8	3.59120981609396	9.88548321897326e-05	0.00139179021556531
IRF1#3659	8	6.78859000316791	6.86477102732501e-07	3.09697547007688e-05
JUND#3727	5	3.88592441215057	0.00454408927040116	0.0214800461352144
MAX#4149	7	5.01865428478332	5.77474544696214e-05	0.000962356214672537
MXI1#4601	5	5.53420646042183	0.00090661270204698	0.00660198884319373
MYC#4609	8	4.64202833031947	1.34916872863392e-05	0.000327231381444027
NFE2#4778	2	17.1565023670287	0.00568307962110636	0.0256575088639056
NFKB1#4790	8	4.87827859928341	9.15949022225393e-06	0.000244531697168195
NFYA#4800	3	6.14186023327684	0.0104816316305809	0.0388160813370058
NR3C1#2908	4	6.6546770360769	0.00190686261501888	0.0112197647690117
NRF1#4899	6	8.14018629847394	2.03653511272495e-05	0.000451483104729105
PAX5#5079	7	5.18743985758276	4.62776729125731e-05	0.000812574626986588
POLR2A#5430	8	1.90884726805162	0.011661228959883	0.0425760213718307
POU2F2#5452	7	7.08254093379974	5.66141070992737e-06	0.000170493677374309
RDBP#7936	4	68.2837351066777	2.19241742291806e-07	1.16644871743321e-05
REST#5978	7	7.5055778903218	3.81690996642637e-06	0.000124768156489391
RFX5#5993	5	6.69328379288617	0.000372811529353423	0.00370643153870939
SIN3A#25942	6	3.60592315121009	0.00200305799133432	0.011646015340253
SIX5#147912	7	13.2896674986903	7.60830171883304e-08	4.57457353605759e-06
SMARCB1#6598	4	8.11231812495885	0.000907642378981639	0.00660764411114341
SP1#6667	7	4.4320744052207	0.000132210094074154	0.00173793455192077
SP2#6668	4	11.6237913305976	0.000230490494099578	0.00253471588009538
STAT1#6772	4	9.20292777653298	0.000562899503225266	0.00480299519749539
TAF1#6872	8	2.97159669844026	0.000423374995123481	0.00395782859968683
TAF7#6879	7	8.89238731494082	1.20106539601475e-06	4.86194065482111e-05
TBP#6908	8	3.29490727741901	0.000191885322027247	0.00231519306229248
TCF12#6938	5	5.90803605677023	0.000668943553105202	0.00546451276830303
THAP1#55145	4	13.9418420457117	0.000114286764867544	0.00156414564749068
USF1#7391	7	4.94783277116175	6.35032938033638e-05	0.00103547548813888
USF2#7392	4	5.77430994891982	0.00322324100537492	0.0167005044084115
YY1#7528	8	4.36548511098121	2.17675027117712e-05	0.000479008895009413
ZNF143#7702	5	7.50048697345995	0.000217746517580183	0.00249109744216855

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.