Coexpression cluster:C938

Full id: C938_leiomyoma_Smooth_Preadipocyte_hepatic_basal_Adipocyte_Ewing

Phase1 CAGE Peaks

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Hg19::chr22:38864041..38864150,+	p1@KDELR3
Hg19::chr2:242212239..242212257,-	p1@HDLBP
Hg19::chr2:47142884..47142955,-	p1@MCFD2
Hg19::chr3:57583064..57583079,-	p1@ARF4
Hg19::chr3:57583085..57583121,-	p2@ARF4
Hg19::chr3:57583130..57583152,-	p3@ARF4
Hg19::chr4:38869366..38869387,+	p3@FAM114A1
Hg19::chr4:38869393..38869404,+	p2@FAM114A1
Hg19::chr4:38869410..38869435,+	p1@FAM114A1
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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:0016192	vesicle-mediated transport	0.00428373742142871
GO:0015031	protein transport	0.00428373742142871
GO:0045184	establishment of protein localization	0.00428373742142871
GO:0008104	protein localization	0.00428373742142871
GO:0033036	macromolecule localization	0.00428373742142871
GO:0005737	cytoplasm	0.00733327368124839
GO:0006810	transport	0.00972679873071346
GO:0051234	establishment of localization	0.00972679873071346
GO:0046923	ER retention sequence binding	0.00972679873071346
GO:0006621	protein retention in ER	0.0104499899438909
GO:0051179	localization	0.0104499899438909
GO:0005048	signal sequence binding	0.0213109713755608
GO:0032507	maintenance of cellular protein localization	0.0213109713755608
GO:0051651	maintenance of cellular localization	0.0213109713755608
GO:0045185	maintenance of protein localization	0.0213109713755608
GO:0005794	Golgi apparatus	0.0213109713755608
GO:0051235	maintenance of localization	0.0298119136755056
GO:0005793	ER-Golgi intermediate compartment	0.0298119136755056
GO:0005783	endoplasmic reticulum	0.0301261191994913
GO:0044424	intracellular part	0.0342977698170602
GO:0008203	cholesterol metabolic process	0.0462566618772057

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
fibroblast	1.14e-23	76
mesodermal cell	4.53e-22	121
muscle precursor cell	6.69e-22	58
myoblast	6.69e-22	58
multi-potent skeletal muscle stem cell	6.69e-22	58
contractile cell	5.56e-21	59
muscle cell	6.07e-21	55
smooth muscle cell	3.86e-19	43
smooth muscle myoblast	3.86e-19	43
embryonic cell	3.71e-18	250
electrically responsive cell	2.18e-17	61
electrically active cell	2.18e-17	61
non-terminally differentiated cell	2.37e-17	106
vascular associated smooth muscle cell	8.65e-17	32
somatic cell	5.78e-13	588
animal cell	8.60e-13	679
eukaryotic cell	8.60e-13	679
skin fibroblast	2.87e-08	23
preadipocyte	1.83e-07	12
stromal cell	2.10e-07	28
cardiocyte	7.55e-07	16

Uber Anatomy

Ontology term	p-value	n
unilaminar epithelium	7.81e-24	148
trunk mesenchyme	5.73e-23	122
organism subdivision	7.31e-23	264
somite	8.00e-23	71
presomitic mesoderm	8.00e-23	71
presumptive segmental plate	8.00e-23	71
dermomyotome	8.00e-23	71
trunk paraxial mesoderm	8.00e-23	71
mesenchyme	1.00e-22	160
entire embryonic mesenchyme	1.00e-22	160
dense mesenchyme tissue	1.19e-22	73
epithelial vesicle	1.36e-22	78
multilaminar epithelium	1.94e-22	83
paraxial mesoderm	4.31e-22	72
presumptive paraxial mesoderm	4.31e-22	72
trunk	1.99e-20	199
skeletal muscle tissue	2.77e-20	62
striated muscle tissue	2.77e-20	62
myotome	2.77e-20	62
epithelial tube	3.17e-20	117
vasculature	1.28e-19	78
vascular system	1.28e-19	78
muscle tissue	1.73e-19	64
musculature	1.73e-19	64
musculature of body	1.73e-19	64
splanchnic layer of lateral plate mesoderm	5.82e-19	83
artery	2.15e-17	42
arterial blood vessel	2.15e-17	42
arterial system	2.15e-17	42
vessel	4.36e-17	68
epithelial tube open at both ends	5.69e-17	59
blood vessel	5.69e-17	59
blood vasculature	5.69e-17	59
vascular cord	5.69e-17	59
multi-cellular organism	2.45e-15	656
systemic artery	1.20e-14	33
systemic arterial system	1.20e-14	33
cardiovascular system	1.99e-13	109
cell layer	4.74e-13	309
circulatory system	5.87e-13	112
anatomical system	6.01e-13	624
anatomical group	6.53e-13	625
multi-tissue structure	9.62e-13	342
surface structure	1.00e-12	99
epithelium	2.15e-12	306
integument	3.61e-09	46
integumental system	3.61e-09	46
anatomical cluster	4.44e-09	373
mesoderm	1.12e-08	315
mesoderm-derived structure	1.12e-08	315
presumptive mesoderm	1.12e-08	315
anatomical conduit	1.86e-08	240
skin of body	5.42e-08	41
aorta	6.63e-08	21
aortic system	6.63e-08	21
embryonic structure	6.37e-07	564
organ component layer	8.41e-07	66
developing anatomical structure	8.41e-07	581

Disease

Ontology term	p-value	n
ovarian cancer	2.36e-07	14

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)
MA0003.1	4.50329
MA0004.1	0.415381
MA0006.1	1.34805
MA0007.1	0.397529
MA0009.1	0.870971
MA0014.1	2.77991
MA0017.1	0.301634
MA0019.1	0.558663
MA0024.1	0.766783
MA0025.1	1.00397
MA0027.1	2.48103
MA0028.1	1.40203
MA0029.1	0.785955
MA0030.1	0.774581
MA0031.1	0.710608
MA0038.1	0.514558
MA0040.1	0.791764
MA0041.1	0.433167
MA0042.1	0.402577
MA0043.1	2.02319
MA0046.1	0.860127
MA0048.1	0.0764047
MA0050.1	0.403421
MA0051.1	0.510444
MA0052.1	0.795605
MA0055.1	0.42489
MA0056.1	0
MA0057.1	0.253359
MA0058.1	0.325084
MA0059.1	0.323879
MA0060.1	0.9464
MA0061.1	0.851955
MA0063.1	0
MA0066.1	1.28137
MA0067.1	1.18766
MA0068.1	1.18425
MA0069.1	0.856287
MA0070.1	0.845142
MA0071.1	0.47692
MA0072.1	0.840664
MA0073.1	1.74484
MA0074.1	2.19307
MA0076.1	1.61616
MA0077.1	0.832987
MA0078.1	0.607575
MA0081.1	0.324031
MA0083.1	2.03788
MA0084.1	1.37471
MA0087.1	0.838229
MA0088.1	1.92658
MA0089.1	0
MA0090.1	0.353576
MA0091.1	0.417885
MA0092.1	0.381858
MA0093.1	0.73976
MA0095.1	0
MA0098.1	0
MA0100.1	0.528088
MA0101.1	2.10501
MA0103.1	0.257174
MA0105.1	2.36395
MA0106.1	0.554855
MA0107.1	1.11943
MA0108.2	1.68573
MA0109.1	0
MA0111.1	0.959847
MA0113.1	0.57094
MA0114.1	0.200901
MA0115.1	1.11137
MA0116.1	0.599942
MA0117.1	0.908433
MA0119.1	0.308914
MA0122.1	0.934245
MA0124.1	1.06995
MA0125.1	0.986127
MA0130.1	0
MA0131.1	0.625452
MA0132.1	0
MA0133.1	0
MA0135.1	0.90122
MA0136.1	0.521435
MA0139.1	1.31371
MA0140.1	0.474342
MA0141.1	0.322254
MA0142.1	0.679161
MA0143.1	0.571113
MA0144.1	0.552298
MA0145.1	1.53859
MA0146.1	0.51271
MA0147.1	1.14329
MA0148.1	0.439278
MA0149.1	0.464973
MA0062.2	1.95022
MA0035.2	0.473658
MA0039.2	1.7915
MA0138.2	0.608783
MA0002.2	0.152495
MA0137.2	0.28622
MA0104.2	2.15714
MA0047.2	0.542971
MA0112.2	0.674448
MA0065.2	0.0483532
MA0150.1	2.48541
MA0151.1	0
MA0152.1	1.20819
MA0153.1	0.969315
MA0154.1	0.842081
MA0155.1	0.0402662
MA0156.1	0.288314
MA0157.1	0.652111
MA0158.1	0
MA0159.1	0.212043
MA0160.1	0.453945
MA0161.1	0
MA0162.1	2.79665
MA0163.1	0.873334
MA0164.1	0.583138
MA0080.2	0.268439
MA0018.2	0.556211
MA0099.2	0.481058
MA0079.2	8.0379
MA0102.2	1.41188
MA0258.1	0.180288
MA0259.1	1.17199
MA0442.1	0

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	3	7.48772484200292	0.00605035742055281	0.0268411043515893
BATF#10538	3	8.11926726410121	0.00482144889581715	0.0226242216484812
BRCA1#672	3	6.72807688107459	0.00814933356720095	0.0321804389150371
CCNT2#905	8	5.63217917952234	2.97597445628313e-06	0.000101075706094229
CHD2#1106	4	4.59734348182971	0.00737935839755762	0.0304971236469677
CTCFL#140690	3	6.58215811965812	0.00865951196291493	0.032961249722825
E2F1#1869	8	4.3621237465594	2.18983367577486e-05	0.000481380844589036
E2F4#1874	4	5.63024902901531	0.00353657181596461	0.0179473286631452
E2F6#1876	7	3.90223223576463	0.000306742359949273	0.00316341121069835
EGR1#1958	7	3.879694851519	0.000318655785854229	0.00326275408027744
ELK4#2005	4	7.21585851487468	0.00140953905898738	0.00916573375142164
ETS1#2113	7	7.56681405060182	3.61164439627206e-06	0.000118689908465153
GABPB1#2553	5	3.92649102010121	0.00433797609228731	0.0205868080657243
HEY1#23462	9	4.04011104310571	3.4850025352467e-06	0.000116024921829337
HMGN3#9324	7	6.36109267371713	1.17234969197953e-05	0.000298122789093379
MAFF#23764	3	18.7717854966484	0.000433693426399023	0.00404921399603858
MAFK#7975	3	9.03357771260997	0.00356785471281375	0.0180841144553048
MEF2A#4205	3	6.24774363654802	0.0100000500846256	0.0374993799428462
NFYB#4801	3	5.58659775117882	0.0135850027711194	0.0479536318117056
NRF1#4899	4	5.42679086564929	0.00404669891206852	0.0193672984913172
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00728936559028337
REST#5978	4	4.28890165161245	0.00945702594596283	0.0356692789010622
RFX5#5993	4	5.35462703430893	0.00424944502767474	0.0202217974778021
SIX5#147912	3	5.695571785153	0.0128879469903482	0.0463563953617915
SRF#6722	6	9.1981188414452	1.00386889165062e-05	0.000263094261418065
TAF1#6872	9	3.34304628574529	1.91655056102793e-05	0.000433627868377809
TFAP2C#7022	4	4.80410160438232	0.00629930343474712	0.0277885090357573
THAP1#55145	3	10.4563815342838	0.00235392350402662	0.0133413695575534
ZBTB7A#51341	5	4.08439405993105	0.00363499031283399	0.0183753510785126
ZEB1#6935	3	5.62947733918129	0.0133048823634195	0.047039560228611

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.