Coexpression cluster:C1236

Full id: C1236_acute_Mesenchymal_iPS_Skeletal_Bronchial_chronic_embryonic

Phase1 CAGE Peaks

Hg19::chr18:47018869..47018896,-	p2@RPL17
Hg19::chr18:47018897..47018922,-	p3@RPL17
Hg19::chr1:45241186..45241289,+	p1@RPS8
Hg19::chr2:3622817..3622828,+	p4@RPS7
Hg19::chr2:3622829..3622838,+	p5@RPS7
Hg19::chr2:3622840..3622882,+	p1@RPS7
Hg19::chr4:109541684..109541697,+	p4@RPL34

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
1.01011768964648e-10	3.34070889167409e-08	4	92	Ribosome (KEGG):03010
1.05551623749576e-10	3.34070889167409e-08	4	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.133023502997e-08	1.19533979566183e-06	4	296	Metabolism of proteins (Reactome):REACT_17015
2.41231788802606e-10	5.08999074373498e-08	4	114	Regulation of beta-cell development (Reactome):REACT_13698
4.66478822294209e-08	3.69101368140293e-06	4	421	Gene Expression (Reactome):REACT_71
1.40005596835204e-08	1.2660506113812e-06	4	312	Diabetes pathways (Reactome):REACT_15380
6.03784237646204e-10	7.64390844860094e-08	4	143	Influenza Infection (Reactome):REACT_6167
5.22856572235584e-10	7.64390844860094e-08	4	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:0033279	ribosomal subunit	8.46541406768146e-08
GO:0005830	cytosolic ribosome (sensu Eukaryota)	9.49265585536572e-07
GO:0003735	structural constituent of ribosome	4.18593866862922e-06
GO:0005840	ribosome	4.45499684263136e-06
GO:0003723	RNA binding	5.25917983946982e-06
GO:0044445	cytosolic part	5.25917983946982e-06
GO:0030529	ribonucleoprotein complex	8.23244723203298e-06
GO:0006412	translation	9.11860074703107e-06
GO:0009059	macromolecule biosynthetic process	2.28763759932242e-05
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	2.6799510277966e-05
GO:0044249	cellular biosynthetic process	4.41598008983352e-05
GO:0005829	cytosol	7.04056771737254e-05
GO:0009058	biosynthetic process	9.61263843812998e-05
GO:0043232	intracellular non-membrane-bound organelle	0.000162564217958898
GO:0043228	non-membrane-bound organelle	0.000162564217958898
GO:0015934	large ribosomal subunit	0.000162564217958898
GO:0015935	small ribosomal subunit	0.000203313742897541
GO:0032991	macromolecular complex	0.000435587953843731
GO:0044446	intracellular organelle part	0.000501752069462546
GO:0044422	organelle part	0.000501752069462546
GO:0044444	cytoplasmic part	0.000730416704183392
GO:0010467	gene expression	0.00138774622843352
GO:0044267	cellular protein metabolic process	0.00145860309969479
GO:0044260	cellular macromolecule metabolic process	0.00147134878170099
GO:0019538	protein metabolic process	0.00162540887295163
GO:0003676	nucleic acid binding	0.00219499584095007
GO:0005737	cytoplasm	0.00400598022910381
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	0.00753137890643941
GO:0043229	intracellular organelle	0.0154713065329693
GO:0043226	organelle	0.0154713065329693
GO:0043170	macromolecule metabolic process	0.0171758779144423
GO:0005730	nucleolus	0.0269440353263539
GO:0044237	cellular metabolic process	0.0269440353263539
GO:0044238	primary metabolic process	0.026953438245518
GO:0044424	intracellular part	0.0278120385522976
GO:0005622	intracellular	0.0473496982711292
GO:0043234	protein complex	0.0478253109342925

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
animal cell	1.29e-39	679
eukaryotic cell	1.29e-39	679
embryonic cell	2.58e-27	250
native cell	1.01e-25	722
epithelial cell	1.07e-19	253
somatic cell	6.65e-18	588
electrically responsive cell	7.82e-14	61
electrically active cell	7.82e-14	61
mesodermal cell	1.74e-13	121
muscle precursor cell	1.81e-13	58
myoblast	1.81e-13	58
multi-potent skeletal muscle stem cell	1.81e-13	58
muscle cell	1.06e-12	55
non-terminally differentiated cell	2.36e-12	106
contractile cell	1.05e-11	59
smooth muscle cell	8.07e-10	43
smooth muscle myoblast	8.07e-10	43
squamous epithelial cell	1.04e-07	63
vascular associated smooth muscle cell	1.11e-07	32
endo-epithelial cell	2.77e-07	42

Uber Anatomy

Ontology term	p-value	n
multilaminar epithelium	7.15e-14	83
unilaminar epithelium	7.99e-14	148
somite	2.67e-13	71
presomitic mesoderm	2.67e-13	71
presumptive segmental plate	2.67e-13	71
dermomyotome	2.67e-13	71
trunk paraxial mesoderm	2.67e-13	71
epithelial vesicle	3.04e-13	78
paraxial mesoderm	1.03e-12	72
presumptive paraxial mesoderm	1.03e-12	72
dense mesenchyme tissue	1.72e-12	73
skeletal muscle tissue	4.08e-11	62
striated muscle tissue	4.08e-11	62
myotome	4.08e-11	62
trunk	4.86e-10	199
muscle tissue	6.73e-10	64
musculature	6.73e-10	64
musculature of body	6.73e-10	64
organism subdivision	9.42e-10	264
trunk mesenchyme	1.66e-09	122
mesenchyme	6.21e-09	160
entire embryonic mesenchyme	6.21e-09	160
vasculature	1.08e-07	78
vascular system	1.08e-07	78
artery	1.50e-07	42
arterial blood vessel	1.50e-07	42
arterial system	1.50e-07	42
epithelial tube open at both ends	7.10e-07	59
blood vessel	7.10e-07	59
blood vasculature	7.10e-07	59
vascular cord	7.10e-07	59

Disease

Ontology term	p-value	n
disease of cellular proliferation	4.31e-17	239
cancer	3.37e-16	235
organ system cancer	4.40e-08	137
cell type cancer	1.21e-07	143
hematologic cancer	2.51e-07	51
immune system cancer	2.51e-07	51
carcinoma	7.99e-07	106

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
BATF#10538	3	10.4390579109873	0.0021372507929898	0.0123505967780148
BCL3#602	6	29.6118024032043	4.00448178379027e-09	3.2776181270946e-07
BCLAF1#9774	5	15.4661768643727	4.07501217827014e-06	0.000129555615490519
BRCA1#672	7	20.1842306432238	7.31084756176234e-10	6.92865343469054e-08
CHD2#1106	7	10.3440228341169	7.88338195961115e-08	4.72365191325203e-06
CTBP2#1488	3	26.8787144311406	0.000135090303129668	0.0017700032829707
E2F4#1874	4	7.23889160873397	0.00111774143052487	0.007666368770118
E2F6#1876	5	3.58368266549813	0.00459810189782724	0.0217274981498135
ELF1#1997	7	4.25809795880754	3.93848941900192e-05	0.000735440544307423
ELK4#2005	4	9.27753237626744	0.000432817858966577	0.00404284629036851
EP300#2033	6	5.80623576533417	6.3256174139893e-05	0.00103225180796817
ETS1#2113	5	6.94911494443024	0.000201406263333039	0.0023935672207828
FAM48A#55578	2	330.048214285714	1.55944547998347e-05	0.000365500283850974
FOSL2#2355	3	7.25580025909787	0.00602077509384975	0.0269872845504967
FOXA1#3169	4	6.33223985679169	0.00185468101692017	0.0109435610579732
GABPB1#2553	4	4.03867647781838	0.0098011349469615	0.036850051577713
GATA3#2625	3	11.6727927245169	0.00154910869847361	0.00984467344285538
GTF2B#2959	7	31.9438299343242	2.93605109232773e-11	3.41467973309149e-09
GTF2F1#2962	7	12.7396608767577	1.83364622006546e-08	1.31889929461031e-06
HDAC2#3066	4	7.66606870664358	0.000898637344705782	0.00668657634965283
HEY1#23462	7	4.04011104310571	5.68979821988558e-05	0.000950626837764566
HNF4A#3172	4	13.2184516359735	0.000109930254651323	0.00152855889569025
HNF4G#3174	4	16.4305271579696	4.70133893497423e-05	0.000822175380157022
IRF1#3659	5	5.45511696683136	0.0006415794721055	0.00525949124703503
IRF3#3661	2	13.4234149175685	0.0088581602305654	0.0336169112034891
IRF4#3662	4	12.5225786781395	0.000135673113103555	0.00177674786952003
JUNB#3726	3	13.1188425684948	0.0011047899931696	0.00767890071187542
JUND#3727	6	5.99542623588945	5.24232039014691e-05	0.000891407846347368
KAT2A#2648	6	528.077142857143	1.21570198874926e-16	2.44166730774968e-14
MAX#4149	7	6.45255550900712	2.14589603858566e-06	7.77098600464106e-05
MEF2A#4205	4	10.7104176626537	0.000248736097009112	0.00268282032794946
MEF2C#4208	3	17.7048662111246	0.000461134767071175	0.00424807744007642
MYC#4609	7	5.2222818716094	9.4355989882785e-06	0.000251004717966586
NANOG#79923	5	20.8891274864376	9.25196150281741e-07	3.96986691615755e-05
NFKB1#4790	7	5.48806342419384	6.66568321176054e-06	0.000194892858049569
NR2C2#7182	5	23.2961506466006	5.39462754436063e-07	2.51185691531645e-05
NR3C1#2908	3	6.41700999907416	0.00849722801565155	0.0324333746336756
PAX5#5079	6	5.71677045529528	6.92762487228137e-05	0.00109906458155278
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.022346135605569
POU2F2#5452	7	9.10612405774252	1.92426562613847e-07	1.0483483449571e-05
REST#5978	7	9.65002871612802	1.28195528172884e-07	7.32018193922787e-06
RFX5#5993	4	6.88452047268291	0.00135220703152858	0.0089032373071374
RXRA#6256	5	14.339012242238	5.91222266390468e-06	0.000177483938716741
SETDB1#9869	3	17.2800112191473	0.00049510103046179	0.00437831130570694
SIN3A#25942	6	4.63618690869869	0.000235167814635783	0.00256615728688188
SIX5#147912	7	17.086715355459	2.34744782955753e-09	2.00134778670334e-07
SMC3#9126	3	6.44782836211408	0.00838431128343785	0.0329463874682431
SP1#6667	5	4.07027241295778	0.00254920612899158	0.0141119759835552
SP2#6668	3	11.2086559259334	0.00174151533091611	0.0107178620887182
SPI1#6688	6	7.03227729301948	2.05436318006376e-05	0.000455242173058941
SRF#6722	6	11.8261527961438	9.50741412579311e-07	4.0661131199169e-05
STAT1#6772	5	14.7904196408566	5.07663030596835e-06	0.000156539177007685
STAT2#6773	3	27.9701876513317	0.00012010576817872	0.00162799822489517
TAF1#6872	7	3.34304628574529	0.000214233631962245	0.00246657990172031
TAF7#6879	7	11.4330694049239	3.91151708659369e-08	2.59045613828001e-06
TBP#6908	7	3.70677068709639	0.000103967209750511	0.00145144117352408
TCF12#6938	6	9.1152556304455	4.4461156654571e-06	0.000139151295770055
TCF7L2#6934	4	6.15438660750705	0.00206467614813804	0.0119729434889166
THAP1#55145	3	13.4439191155077	0.00102904083369238	0.00728969650885158
TRIM28#10155	3	7.96736787654108	0.00462234126315646	0.0218331463607615
WRNIP1#56897	5	78.4428316781258	1.2872343948194e-09	1.16699195278249e-07
YY1#7528	7	4.91117074985386	1.45048003565243e-05	0.000345465642972642
ZBTB33#10009	5	22.6176607357008	6.24429259373417e-07	2.86155188326899e-05
ZEB1#6935	4	9.65053258145363	0.000371891664568925	0.00369869474868241
ZNF143#7702	6	11.5721799019096	1.08146108094101e-06	4.50166256805092e-05
ZZZ3#26009	4	136.80754996299	1.04657769083544e-08	7.8976537177141e-07

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.