Coexpression cluster:C895

Full id: C895_Mesenchymal_Renal_Alveolar_Fibroblast_Pericytes_Trabecular_Osteoblast

Phase1 CAGE Peaks

Hg19::chr12:53693466..53693537,+	p1@C12orf10
Hg19::chr16:2933231..2933309,+	p1@FLYWCH2
Hg19::chr17:42092313..42092389,-	p1@TMEM101
Hg19::chr19:17530838..17530885,+	p1@FAM125A
Hg19::chr19:17530888..17530938,+	p2@FAM125A
Hg19::chr19:49314305..49314316,-	p2@BCAT2
Hg19::chr19:7985198..7985257,+	p1@SNAPC2
Hg19::chr3:49055991..49056026,-	p1@DALRD3
Hg19::chr9:131133622..131133661,+	p1@URM1

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:0009098	leucine biosynthetic process	0.00653479335923701
GO:0006549	isoleucine metabolic process	0.00653479335923701
GO:0006550	isoleucine catabolic process	0.00653479335923701
GO:0009082	branched chain family amino acid biosynthetic process	0.00980074736638496
GO:0006551	leucine metabolic process	0.00980074736638496
GO:0009301	snRNA transcription	0.00980074736638496
GO:0006420	arginyl-tRNA aminoacylation	0.0130647783764645
GO:0004814	arginine-tRNA ligase activity	0.0130647783764645
GO:0004084	branched-chain-amino-acid transaminase activity	0.0130647783764645
GO:0009083	branched chain family amino acid catabolic process	0.017633557274085
GO:0006520	amino acid metabolic process	0.0261103347061558
GO:0009081	branched chain family amino acid metabolic process	0.0261103347061558
GO:0007595	lactation	0.0295901655496141
GO:0006519	amino acid and derivative metabolic process	0.0295901655496141
GO:0006383	transcription from RNA polymerase III promoter	0.0346414888684331
GO:0009308	amine metabolic process	0.0346414888684331
GO:0006807	nitrogen compound metabolic process	0.036932758980158
GO:0019752	carboxylic acid metabolic process	0.0449410093543494
GO:0006082	organic acid metabolic process	0.0449410093543494
GO:0008483	transaminase activity	0.0449410093543494

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
embryonic cell	5.25e-24	250
mesodermal cell	7.26e-20	121
non-terminally differentiated cell	9.86e-19	106
contractile cell	1.53e-16	59
animal cell	1.90e-16	679
eukaryotic cell	1.90e-16	679
electrically responsive cell	4.09e-15	61
electrically active cell	4.09e-15	61
muscle cell	2.97e-14	55
muscle precursor cell	5.79e-14	58
myoblast	5.79e-14	58
multi-potent skeletal muscle stem cell	5.79e-14	58
somatic cell	2.65e-12	588
smooth muscle cell	3.44e-12	43
smooth muscle myoblast	3.44e-12	43
epithelial cell	1.15e-10	253
native cell	3.39e-09	722
vascular associated smooth muscle cell	5.26e-09	32
ectodermal cell	1.65e-08	72
meso-epithelial cell	4.47e-08	45
fibroblast	4.94e-08	76
epithelial cell of nephron	7.13e-08	15
kidney cell	1.54e-07	17
kidney epithelial cell	1.54e-07	17
neurectodermal cell	2.01e-07	59
endothelial cell	2.38e-07	36
lining cell	7.32e-07	58
barrier cell	7.32e-07	58

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	1.39e-17	78
multilaminar epithelium	1.38e-14	83
somite	2.14e-14	71
presomitic mesoderm	2.14e-14	71
presumptive segmental plate	2.14e-14	71
dermomyotome	2.14e-14	71
trunk paraxial mesoderm	2.14e-14	71
dense mesenchyme tissue	4.56e-14	73
paraxial mesoderm	7.92e-14	72
presumptive paraxial mesoderm	7.92e-14	72
vasculature	1.31e-13	78
vascular system	1.31e-13	78
unilaminar epithelium	1.62e-13	148
organism subdivision	1.85e-12	264
skeletal muscle tissue	3.18e-12	62
striated muscle tissue	3.18e-12	62
myotome	3.18e-12	62
mesenchyme	7.02e-12	160
entire embryonic mesenchyme	7.02e-12	160
muscle tissue	3.89e-11	64
musculature	3.89e-11	64
musculature of body	3.89e-11	64
splanchnic layer of lateral plate mesoderm	3.99e-11	83
trunk	4.21e-11	199
vessel	5.16e-11	68
epithelial tube	1.06e-10	117
epithelial tube open at both ends	3.16e-10	59
blood vessel	3.16e-10	59
blood vasculature	3.16e-10	59
vascular cord	3.16e-10	59
cell layer	6.98e-10	309
artery	8.30e-10	42
arterial blood vessel	8.30e-10	42
arterial system	8.30e-10	42
epithelium	1.81e-09	306
trunk mesenchyme	4.08e-09	122
anatomical cluster	3.47e-08	373
multi-tissue structure	4.77e-08	342
cardiovascular system	5.62e-08	109
nephron epithelium	7.13e-08	15
renal tubule	7.13e-08	15
nephron tubule	7.13e-08	15
nephron	7.13e-08	15
uriniferous tubule	7.13e-08	15
nephrogenic mesenchyme	7.13e-08	15
parenchyma	2.27e-07	15
circulatory system	2.65e-07	112
excretory tube	4.60e-07	16
kidney epithelium	4.60e-07	16

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
BCLAF1#9774	6	14.4350984067479	7.2101191630514e-07	3.21527598321915e-05
CCNT2#905	6	4.22413438464176	0.00084033506380825	0.0063381059961775
CHD2#1106	5	5.74667935228714	0.000761042370922	0.00597612813358817
E2F1#1869	7	3.81685827823947	0.000354757705323757	0.00355264550640597
E2F6#1876	7	3.90223223576463	0.000306742359949273	0.00316216220814749
EGR1#1958	7	3.879694851519	0.000318655785854229	0.00326243423378393
ELF1#1997	9	4.25809795880754	2.17161853202127e-06	7.8234449074084e-05
ELK4#2005	5	9.01982314359335	9.04446507305493e-05	0.00132018852238265
ETS1#2113	8	8.64778748640208	1.01768374293787e-07	5.96441483887138e-06
FOS#2353	4	3.99909124839751	0.0121138499120048	0.0439291101027732
FOSL2#2355	3	5.64340020152056	0.0132155804190592	0.0467586558501971
GABPB1#2553	7	5.49708742814169	3.13640621886058e-05	0.000632849940285124
HEY1#23462	9	4.04011104310571	3.4850025352467e-06	0.000115950997062323
HMGN3#9324	7	6.36109267371713	1.17234969197953e-05	0.000298050217820474
IRF1#3659	8	6.78859000316791	6.86477102732501e-07	3.09831383458426e-05
MAX#4149	6	4.30170367267141	0.000759756385172366	0.00596782469246516
MXI1#4601	6	6.6410477525062	6.5621720999513e-05	0.0010635423524935
MYC#4609	6	3.4815212477396	0.00242366981145926	0.0136566307763147
NFYB#4801	3	5.58659775117882	0.0135850027711194	0.0479487700038166
NRF1#4899	6	8.14018629847394	2.03653511272495e-05	0.00045157896101461
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.0072859076369673
POLR3A#11128	2	75.3626911314985	0.000308186501582264	0.00317235265511039
REST#5978	4	4.28890165161245	0.00945702594596283	0.035662839240672
RFX5#5993	6	8.0319405514634	2.20018388626684e-05	0.000482538859508236
SIN3A#25942	8	4.80789753494679	1.02597602607548e-05	0.000267946762158783
SIX5#147912	6	11.391143570306	2.88946640975924e-06	9.93000929150529e-05
SP1#6667	5	3.1657674323005	0.0111972168609182	0.0411190622973782
SRF#6722	5	7.66509903453767	0.000196444781216345	0.00236147519629994
STAT3#6774	4	4.675317776513	0.00694682535577889	0.0293815856045111
TAF1#6872	8	2.97159669844026	0.000423374995123481	0.00395889167478747
TBP#6908	7	2.88304386774163	0.00218780200212605	0.0126161919993397
TCF7L2#6934	5	5.98343142396519	0.000630515439732144	0.0051842546063758
THAP1#55145	4	13.9418420457117	0.000114286764867544	0.00156435064692023
TRIM28#10155	3	6.19684168175417	0.010227806502978	0.0380813505655799
USF1#7391	5	3.53416626511553	0.0069229675408181	0.0293091656327983
YY1#7528	8	4.36548511098121	2.17675027117712e-05	0.000479109845250721
ZBTB7A#51341	7	5.71815168390347	2.40589727322203e-05	0.000524242656620145
ZEB1#6935	4	7.50596978557505	0.00121590332463561	0.00818272616287248
ZNF143#7702	5	7.50048697345995	0.000217746517580183	0.00249164331648479

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.