Coexpression cluster:C1171

Full id: C1171_Alveolar_Renal_Bronchial_Mesenchymal_Smooth_Keratinocyte_embryonic

Phase1 CAGE Peaks

Hg19::chr12:53715328..53715411,-	p1@AAAS
Hg19::chr19:49497121..49497164,+	p1@RUVBL2
Hg19::chr1:1447517..1447556,+	p1@ATAD3A
Hg19::chr1:894620..894659,-	p1@NOC2L
Hg19::chr3:47866490..47866534,+	p1@DHX30
Hg19::chr6:31763408..31763545,-	p1@VARS
Hg19::chr7:1177874..1177936,-	p2@C7orf50

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:0008026	ATP-dependent helicase activity	0.0126628131237378
GO:0017111	nucleoside-triphosphatase activity	0.0126628131237378
GO:0016462	pyrophosphatase activity	0.0126628131237378
GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.0126628131237378
GO:0016817	hydrolase activity, acting on acid anhydrides	0.0126628131237378
GO:0005524	ATP binding	0.0126628131237378
GO:0032559	adenyl ribonucleotide binding	0.0126628131237378
GO:0030554	adenyl nucleotide binding	0.0130157929178116
GO:0004386	helicase activity	0.015254011509818
GO:0035267	NuA4 histone acetyltransferase complex	0.015254011509818
GO:0043189	H4/H2A histone acetyltransferase complex	0.0159176240429507
GO:0032553	ribonucleotide binding	0.0159176240429507
GO:0032555	purine ribonucleotide binding	0.0159176240429507
GO:0017076	purine nucleotide binding	0.0170004643870686
GO:0000123	histone acetyltransferase complex	0.0194313746840619
GO:0004832	valine-tRNA ligase activity	0.0194313746840619
GO:0006438	valyl-tRNA aminoacylation	0.0194313746840619
GO:0000166	nucleotide binding	0.0240891554983028
GO:0042623	ATPase activity, coupled	0.0262980976105518
GO:0016887	ATPase activity	0.0348302374230744
GO:0046822	regulation of nucleocytoplasmic transport	0.0348302374230744
GO:0043231	intracellular membrane-bound organelle	0.0348302374230744
GO:0043227	membrane-bound organelle	0.0348302374230744
GO:0004003	ATP-dependent DNA helicase activity	0.0369966852587803
GO:0016363	nuclear matrix	0.0459929166824502
GO:0003678	DNA helicase activity	0.0459929166824502
GO:0003684	damaged DNA binding	0.0459929166824502
GO:0003725	double-stranded RNA binding	0.0479566301137395

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	2.81e-24	254
embryonic cell	1.54e-23	248
animal cell	3.05e-22	679
eukaryotic cell	3.05e-22	679
non-terminally differentiated cell	6.46e-16	180
mesodermal cell	2.15e-14	119
contractile cell	1.01e-10	59
native cell	4.89e-10	722
electrically responsive cell	8.45e-10	60
electrically active cell	8.45e-10	60
muscle cell	1.37e-08	54
muscle precursor cell	3.71e-08	57
myoblast	3.71e-08	57
multi-potent skeletal muscle stem cell	3.71e-08	57
somatic cell	4.15e-08	591
epithelial cell of nephron	9.46e-08	16
smooth muscle cell	1.72e-07	42
smooth muscle myoblast	1.72e-07	42
squamous epithelial cell	1.80e-07	62
meso-epithelial cell	5.81e-07	44
blood vessel endothelial cell	7.45e-07	18
embryonic blood vessel endothelial progenitor cell	7.45e-07	18
kidney cortical cell	7.67e-07	13
renal cortical epithelial cell	7.67e-07	13
endothelial cell	9.48e-07	35

Uber Anatomy

Ontology term	p-value	n
epithelial tube	9.30e-15	118
mesenchyme	8.64e-14	238
entire embryonic mesenchyme	8.64e-14	238
unilaminar epithelium	1.55e-11	138
cell layer	3.94e-11	312
trunk mesenchyme	8.96e-11	143
vasculature	9.14e-11	79
vascular system	9.14e-11	79
trunk	1.68e-10	216
epithelium	1.90e-10	309
blood vessel	1.93e-10	60
epithelial tube open at both ends	1.93e-10	60
blood vasculature	1.93e-10	60
vascular cord	1.93e-10	60
vessel	2.02e-10	69
multilaminar epithelium	2.88e-10	82
dermomyotome	3.96e-10	70
artery	7.01e-10	42
arterial blood vessel	7.01e-10	42
arterial system	7.01e-10	42
splanchnic layer of lateral plate mesoderm	1.61e-09	84
somite	2.29e-08	83
paraxial mesoderm	2.29e-08	83
presomitic mesoderm	2.29e-08	83
presumptive segmental plate	2.29e-08	83
trunk paraxial mesoderm	2.29e-08	83
presumptive paraxial mesoderm	2.29e-08	83
primordium	4.90e-08	168
nephron epithelium	9.46e-08	16
nephron	9.46e-08	16
uriniferous tubule	9.46e-08	16
metanephric mesenchyme	9.46e-08	16
nephrogenic mesenchyme	9.46e-08	16
skeletal muscle tissue	1.11e-07	61
striated muscle tissue	1.11e-07	61
myotome	1.11e-07	61
simple squamous epithelium	3.55e-07	22
multi-tissue structure	5.77e-07	347
excretory tube	6.83e-07	17
mesonephric epithelium	6.83e-07	17
mesonephric tubule	6.83e-07	17
nephric duct	6.83e-07	17
kidney epithelium	6.83e-07	17
renal duct	6.83e-07	17
mesonephric duct	6.83e-07	17
pronephric duct	6.83e-07	17
endothelium	7.45e-07	18
blood vessel endothelium	7.45e-07	18
cardiovascular system endothelium	7.45e-07	18
cortex of kidney	7.67e-07	13
renal parenchyma	7.67e-07	13
muscle tissue	8.04e-07	63
musculature	8.04e-07	63
musculature of body	8.04e-07	63

Disease

Ontology term	p-value	n
cancer	1.61e-17	235
disease of cellular proliferation	3.47e-17	239
hematologic cancer	1.63e-09	51
immune system cancer	1.63e-09	51
organ system cancer	1.04e-08	137
cell type cancer	1.72e-08	143
leukemia	4.37e-08	39
carcinoma	2.35e-07	106
myeloid leukemia	4.89e-07	31

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	3	9.27970611862364	0.0029949923357571	0.0159207005931764
CCNT2#905	6	5.43102992311083	9.35028339706757e-05	0.00135818393283218
CHD2#1106	5	7.3885877386549	0.000149868960082067	0.00193212743142958
CTCF#10664	5	3.82875455219645	0.00338737119268134	0.0172926806135715
CTCFL#140690	4	11.2836996336996	0.000203273626505993	0.00241356233272617
E2F1#1869	5	3.50527801062809	0.00509055358791505	0.0236879489470798
E2F4#1874	6	10.8583374131009	1.57765285246789e-06	6.00249494567919e-05
EGR1#1958	6	4.27558208126583	0.000376213061986645	0.00373633662807372
ELF1#1997	7	4.25809795880754	3.93848941900192e-05	0.000735046276681812
ELK4#2005	4	9.27753237626744	0.000432817858966577	0.00404212325606817
ETS1#2113	7	9.72876092220234	1.21106237796078e-07	6.97640064488944e-06
FOSL1#8061	2	11.3467370618209	0.0122366479067572	0.0443636362944358
GABPB1#2553	7	7.06768383618217	1.13438576906404e-06	4.65700138896537e-05
GTF2F1#2962	3	5.45985466146756	0.013298821684157	0.0470245001987972
HDAC2#3066	4	7.66606870664358	0.000898637344705782	0.00668609999599111
HEY1#23462	6	3.46295232266204	0.00126789009587212	0.00850572801405375
HMGN3#9324	5	5.84181980239328	0.000462918719129959	0.00426338343097123
IRF1#3659	4	4.36409357346509	0.0073934558242782	0.0305505492712875
IRF3#3661	2	13.4234149175685	0.0088581602305654	0.0336144682915493
MAX#4149	5	4.60896822071937	0.00142433701403361	0.00917909005360088
MXI1#4601	5	7.11540830625664	0.000179725622524823	0.00217905320302647
MYC#4609	7	5.2222818716094	9.4355989882785e-06	0.000250940800289487
NFKB1#4790	7	5.48806342419384	6.66568321176054e-06	0.000194620433031328
NFYB#4801	3	7.18276853722991	0.0061947399088996	0.0273746484448492
PAX5#5079	5	4.76397537941274	0.00121882104700747	0.00819919171197507
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223310395852986
REST#5978	4	5.51430212350173	0.00311564137576196	0.0163761685779166
SIN3A#25942	7	5.40888472681514	7.3795239773719e-06	0.000211501126419523
SIX5#147912	4	9.76383734597657	0.000355537135106872	0.00355908586728904
SMARCC1#6599	2	12.4752455198947	0.0102004731657184	0.0379890602629699
SMC3#9126	3	6.44782836211408	0.00838431128343785	0.0329451479036444
SP1#6667	6	4.88432689554934	0.000173636112229091	0.00211307176941202
SP2#6668	4	14.9448745679112	6.81071539656055e-05	0.00108795396956468
SRF#6722	4	7.88410186409589	0.000807478872809276	0.0061659929807215
STAT1#6772	3	8.87425178451394	0.00340236953269376	0.0173590655410358
TAF1#6872	7	3.34304628574529	0.000214233631962245	0.0024649494644161
TAF7#6879	4	6.53318251709938	0.0016484941094751	0.0103118756767771
TBP#6908	7	3.70677068709639	0.000103967209750511	0.00145066552025834
TFAP2A#7020	3	7.07941473130498	0.00645255447218097	0.0280288789468913
TFAP2C#7022	5	7.72087757847159	0.000121181199560433	0.00164193607951376
THAP1#55145	3	13.4439191155077	0.00102904083369238	0.00728920209102
TRIM28#10155	3	7.96736787654108	0.00462234126315646	0.0218321589717256
USF1#7391	5	4.54392805514854	0.00152278835596876	0.00970397785764972
YY1#7528	7	4.91117074985386	1.45048003565243e-05	0.000345308147808306
ZBTB7A#51341	6	6.30163654960791	3.91424956694869e-05	0.000731306458895446
ZNF143#7702	6	11.5721799019096	1.08146108094101e-06	4.4980770144324e-05
ZNF263#10127	4	4.69819522114896	0.0056412295360981	0.0254839902902612

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.