Coexpression cluster:C1465

Full id: C1465_Mast_Preadipocyte_Fibroblast_Smooth_Chondrocyte_basal_Osteoblast

Phase1 CAGE Peaks

Hg19::chr1:160312998..160313024,-	p2@COPA
Hg19::chr1:160313025..160313072,-	p1@COPA
Hg19::chr4:119757222..119757238,-	p2@SEC24D
Hg19::chr4:119757239..119757305,-	p1@SEC24D
Hg19::chr4:119757322..119757334,-	p3@SEC24D
Hg19::chr4:83812268..83812401,-	p1@SEC31A

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
0.000101670189141599	0.0160893074316581	2	167	Protein processing in endoplasmic reticulum (KEGG):04141
2.20782089021958e-06	0.000465850207836331	2	25	SREBP signalling (Wikipathways):WP1982
0.00031927672820075	0.040420433790215	2	296	Metabolism of proteins (Reactome):REACT_17015
4.83581548478211e-08	3.06107120186708e-05	3	105	Membrane Trafficking (Reactome):REACT_11123
8.833140910259e-07	0.000279568909809697	2	16	{SEC24B,18} (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:0030120	vesicle coat	1.59360715573632e-07
GO:0030662	coated vesicle membrane	1.59360715573632e-07
GO:0005798	Golgi-associated vesicle	2.67292367563503e-07
GO:0030659	cytoplasmic vesicle membrane	4.8489276073581e-07
GO:0044433	cytoplasmic vesicle part	4.8489276073581e-07
GO:0012506	vesicle membrane	4.8489276073581e-07
GO:0030117	membrane coat	4.8489276073581e-07
GO:0048475	coated membrane	4.8489276073581e-07
GO:0030135	coated vesicle	8.82004274168316e-07
GO:0030127	COPII vesicle coat	3.68578464954729e-06
GO:0012507	ER to Golgi transport vesicle membrane	3.68578464954729e-06
GO:0030134	ER to Golgi transport vesicle	4.54798519481905e-06
GO:0016023	cytoplasmic membrane-bound vesicle	7.87888560646397e-06
GO:0031988	membrane-bound vesicle	7.87888560646397e-06
GO:0000139	Golgi membrane	8.20133629517297e-06
GO:0046903	secretion	8.95670736238786e-06
GO:0044431	Golgi apparatus part	1.07485746738754e-05
GO:0031410	cytoplasmic vesicle	1.07485746738754e-05
GO:0031982	vesicle	1.07485746738754e-05
GO:0030658	transport vesicle membrane	1.20808507966572e-05
GO:0030660	Golgi-associated vesicle membrane	1.22723693440234e-05
GO:0006888	ER to Golgi vesicle-mediated transport	1.84191560341748e-05
GO:0016192	vesicle-mediated transport	2.45590807920104e-05
GO:0005794	Golgi apparatus	3.55255879566779e-05
GO:0030133	transport vesicle	4.05661523916162e-05
GO:0015031	protein transport	6.34964434528897e-05
GO:0005783	endoplasmic reticulum	6.7748719125613e-05
GO:0046907	intracellular transport	6.7748719125613e-05
GO:0045184	establishment of protein localization	6.7748719125613e-05
GO:0048193	Golgi vesicle transport	6.7748719125613e-05
GO:0008104	protein localization	7.27991888716605e-05
GO:0033036	macromolecule localization	8.23717077444704e-05
GO:0012505	endomembrane system	8.37282444874029e-05
GO:0051649	establishment of cellular localization	9.90411355731548e-05
GO:0051641	cellular localization	0.000103768176789829
GO:0031090	organelle membrane	0.00024395131137356
GO:0045045	secretory pathway	0.000401112297492283
GO:0032940	secretion by cell	0.000597908532731506
GO:0030157	pancreatic juice secretion	0.00113202077726421
GO:0006886	intracellular protein transport	0.00179641366272567
GO:0016043	cellular component organization and biogenesis	0.00218737270485908
GO:0030126	COPI vesicle coat	0.00307924290153726
GO:0030663	COPI coated vesicle membrane	0.00307924290153726
GO:0030137	COPI-coated vesicle	0.00341029397521763
GO:0007589	fluid secretion	0.00353055334416461
GO:0006810	transport	0.00356800737070301
GO:0022600	digestive system process	0.00356800737070301
GO:0044446	intracellular organelle part	0.00360426233566905
GO:0044422	organelle part	0.00360426233566905
GO:0051234	establishment of localization	0.00360426233566905
GO:0051179	localization	0.00449716529632016
GO:0044444	cytoplasmic part	0.0047467189745629
GO:0007586	digestion	0.0157850363922107
GO:0005737	cytoplasm	0.019776990414091
GO:0050878	regulation of body fluid levels	0.0199968336228727
GO:0044425	membrane part	0.0209982178169082
GO:0008565	protein transporter activity	0.0237513622530376
GO:0005792	microsome	0.0245486292312923
GO:0042598	vesicular fraction	0.0251701198432801
GO:0043231	intracellular membrane-bound organelle	0.0283199098597437
GO:0043227	membrane-bound organelle	0.0283199098597437
GO:0051082	unfolded protein binding	0.0283199098597437
GO:0005515	protein binding	0.0295556769216537
GO:0005179	hormone activity	0.0297519573752465
GO:0005625	soluble fraction	0.0315733359434466
GO:0016020	membrane	0.035777524468533
GO:0006461	protein complex assembly	0.0443511685631897
GO:0006457	protein folding	0.0443511685631897
GO:0043229	intracellular organelle	0.045484256688062
GO:0043226	organelle	0.045484256688062

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
multi fate stem cell	9.28e-26	427
somatic stem cell	1.61e-24	433
stem cell	4.00e-23	441
somatic cell	8.35e-22	588
fibroblast	5.00e-19	76
muscle precursor cell	5.66e-18	58
myoblast	5.66e-18	58
multi-potent skeletal muscle stem cell	5.66e-18	58
muscle cell	6.01e-17	55
smooth muscle cell	4.97e-15	43
smooth muscle myoblast	4.97e-15	43
vascular associated smooth muscle cell	1.94e-14	32
contractile cell	3.92e-14	59
mesodermal cell	9.37e-14	121
animal cell	2.23e-13	679
eukaryotic cell	2.23e-13	679
electrically responsive cell	2.35e-13	61
electrically active cell	2.35e-13	61
non-terminally differentiated cell	1.60e-11	106
connective tissue cell	2.26e-11	361
mesenchymal cell	6.64e-11	354
skin fibroblast	4.87e-10	23
motile cell	2.37e-08	386

Uber Anatomy

Ontology term	p-value	n
mesoderm	1.00e-22	315
mesoderm-derived structure	1.00e-22	315
presumptive mesoderm	1.00e-22	315
musculoskeletal system	2.23e-21	167
somite	5.99e-18	71
presomitic mesoderm	5.99e-18	71
presumptive segmental plate	5.99e-18	71
dermomyotome	5.99e-18	71
trunk paraxial mesoderm	5.99e-18	71
dense mesenchyme tissue	7.58e-18	73
paraxial mesoderm	2.36e-17	72
presumptive paraxial mesoderm	2.36e-17	72
splanchnic layer of lateral plate mesoderm	4.27e-17	83
vasculature	1.92e-16	78
vascular system	1.92e-16	78
muscle tissue	2.43e-16	64
musculature	2.43e-16	64
musculature of body	2.43e-16	64
multilaminar epithelium	4.01e-16	83
skeletal muscle tissue	4.79e-16	62
striated muscle tissue	4.79e-16	62
myotome	4.79e-16	62
unilaminar epithelium	2.03e-15	148
artery	3.19e-15	42
arterial blood vessel	3.19e-15	42
arterial system	3.19e-15	42
vessel	2.54e-14	68
epithelial tube open at both ends	3.04e-14	59
blood vessel	3.04e-14	59
blood vasculature	3.04e-14	59
vascular cord	3.04e-14	59
epithelial vesicle	3.25e-14	78
trunk mesenchyme	3.05e-13	122
systemic artery	1.68e-12	33
systemic arterial system	1.68e-12	33
cardiovascular system	2.32e-12	109
lateral plate mesoderm	1.23e-11	203
connective tissue	1.51e-11	371
circulatory system	2.62e-11	112
multi-cellular organism	7.52e-11	656
mesenchyme	1.01e-10	160
entire embryonic mesenchyme	1.01e-10	160
epithelial tube	2.44e-10	117
anatomical group	2.58e-10	625
anatomical system	4.49e-10	624
integument	6.33e-08	46
integumental system	6.33e-08	46
aorta	2.05e-07	21
aortic system	2.05e-07	21
skin of body	4.01e-07	41
embryonic structure	4.24e-07	564
surface structure	4.41e-07	99
tissue	5.62e-07	773
germ layer	8.67e-07	560
germ layer / neural crest	8.67e-07	560
embryonic tissue	8.67e-07	560
presumptive structure	8.67e-07	560
germ layer / neural crest derived structure	8.67e-07	560
epiblast (generic)	8.67e-07	560

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	10.8263238050609	0.00177235104699106	0.0108909491054777
CCNT2#905	4	4.22413438464176	0.00710980547887581	0.0296151627012448
CTCF#10664	6	5.36025637307503	4.21437267579784e-05	0.000755483810311793
E2F1#1869	6	4.90738921487932	7.15746523583771e-05	0.00112730887010354
E2F4#1874	4	8.44537354352296	0.000511119352377084	0.00443362076768358
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205306702309926
ELK4#2005	3	8.11784082923401	0.00405611313418576	0.019409686122393
ETS1#2113	6	9.72876092220234	1.17854759771003e-06	4.80430650106316e-05
GTF2B#2959	3	15.9719149671621	0.000571165371589299	0.00486755938338758
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00253218705969184
HMGN3#9324	6	8.17854772335059	3.33956428934731e-06	0.000111502798853946
MAX#4149	4	4.30170367267141	0.00664492391067637	0.0283006772819154
NFKB1#4790	6	5.48806342419384	3.65870229532191e-05	0.00070761335003912
NRF1#4899	3	6.10513972385545	0.00909016207939674	0.0344060971047047
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380418498504079
SMARCC1#6599	2	14.5544531065438	0.00739807938314051	0.0305660262954273
SMARCC2#6601	2	31.3851248089659	0.00164386901070461	0.0102847921649181
SRF#6722	3	6.8985891310839	0.0064424516893037	0.0280024642907936
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573299855773344
TAF7#6879	3	5.71653470246196	0.0109272937988966	0.0402155062746833
TBP#6908	6	3.70677068709639	0.00038541647290796	0.00377886885223756
TCF12#6938	6	10.6344649021864	6.9082259011154e-07	3.11523404527889e-05
ZBTB7A#51341	6	7.3519093078759	6.32958528301959e-06	0.000186738858015052
ZEB1#6935	3	8.44421600877193	0.00362384381073359	0.0183394206400739
ZNF143#7702	3	6.75043827611395	0.00685025920446858	0.0290413728863606

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.