Coexpression cluster:C1147

Full id: C1147_Mesenchymal_Renal_Alveolar_Fibroblast_Placental_Pericytes_Hepatic

Phase1 CAGE Peaks

Hg19::chr11:64851666..64851728,+	p1@ZFPL1
Hg19::chr11:66056596..66056622,-	p1@YIF1A
Hg19::chr19:11039271..11039355,-	p1@YIPF2
Hg19::chr19:38806561..38806607,-	p1@YIF1B
Hg19::chr1:44444865..44444930,+	p1@B4GALT2
Hg19::chr5:180229833..180229860,-	p3@MGAT1
Hg19::chr6:43484621..43484706,-	p1@YIPF3

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
6.02832773164619e-05	0.0381593145413204	2	49	N-Glycan biosynthesis (KEGG):00510

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:0016021	integral to membrane	0.000580518378430204
GO:0031224	intrinsic to membrane	0.000580518378430204
GO:0044425	membrane part	0.00101525068808855
GO:0030133	transport vesicle	0.00171329991318636
GO:0016020	membrane	0.0031001539715636
GO:0005794	Golgi apparatus	0.00453665188376353
GO:0008194	UDP-glycosyltransferase activity	0.00470395734307677
GO:0003831	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity	0.00666117273112001
GO:0004461	lactose synthase activity	0.00666117273112001
GO:0044444	cytoplasmic part	0.00722897183027535
GO:0003945	N-acetyllactosamine synthase activity	0.00726609217133451
GO:0003827	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity	0.00832499538422828
GO:0016758	transferase activity, transferring hexosyl groups	0.0103938426317109
GO:0043231	intracellular membrane-bound organelle	0.0108150443212596
GO:0043227	membrane-bound organelle	0.0108150443212596
GO:0016023	cytoplasmic membrane-bound vesicle	0.0123942685714032
GO:0031988	membrane-bound vesicle	0.0123942685714032
GO:0000139	Golgi membrane	0.0125714635726644
GO:0044431	Golgi apparatus part	0.0147521770957566
GO:0031410	cytoplasmic vesicle	0.0147521770957566
GO:0031982	vesicle	0.0147521770957566
GO:0016757	transferase activity, transferring glycosyl groups	0.0147521770957566
GO:0035250	UDP-galactosyltransferase activity	0.0147521770957566
GO:0006023	aminoglycan biosynthetic process	0.0174578072166668
GO:0043229	intracellular organelle	0.0192729000207756
GO:0043226	organelle	0.0192729000207756
GO:0005737	cytoplasm	0.0260771053646539
GO:0008378	galactosyltransferase activity	0.0284547695479466
GO:0005793	ER-Golgi intermediate compartment	0.0295262676453299
GO:0008375	acetylglucosaminyltransferase activity	0.0298643231755696
GO:0006022	aminoglycan metabolic process	0.0319533690155563
GO:0005975	carbohydrate metabolic process	0.0319533690155563
GO:0006487	protein amino acid N-linked glycosylation	0.0319533690155563
GO:0044424	intracellular part	0.0413708282874496
GO:0012505	endomembrane system	0.0481188913306716

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
mesodermal cell	3.15e-25	121
embryonic cell	4.65e-24	250
contractile cell	7.27e-22	59
muscle precursor cell	4.67e-20	58
myoblast	4.67e-20	58
multi-potent skeletal muscle stem cell	4.67e-20	58
muscle cell	1.54e-19	55
smooth muscle cell	3.56e-18	43
smooth muscle myoblast	3.56e-18	43
non-terminally differentiated cell	1.55e-17	106
electrically responsive cell	1.42e-16	61
electrically active cell	1.42e-16	61
fibroblast	1.23e-15	76
animal cell	1.23e-15	679
eukaryotic cell	1.23e-15	679
somatic cell	8.92e-15	588
vascular associated smooth muscle cell	1.28e-14	32
epithelial cell	1.89e-08	253
extraembryonic cell	4.82e-08	19
meso-epithelial cell	6.60e-07	45

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	7.28e-23	78
mesenchyme	7.45e-22	160
entire embryonic mesenchyme	7.45e-22	160
organism subdivision	1.82e-21	264
unilaminar epithelium	9.28e-21	148
multilaminar epithelium	2.99e-20	83
dense mesenchyme tissue	7.26e-20	73
somite	8.03e-20	71
presomitic mesoderm	8.03e-20	71
presumptive segmental plate	8.03e-20	71
dermomyotome	8.03e-20	71
trunk paraxial mesoderm	8.03e-20	71
trunk	8.51e-20	199
trunk mesenchyme	1.36e-19	122
paraxial mesoderm	2.60e-19	72
presumptive paraxial mesoderm	2.60e-19	72
vasculature	3.81e-19	78
vascular system	3.81e-19	78
epithelial tube	2.27e-18	117
skeletal muscle tissue	6.06e-18	62
striated muscle tissue	6.06e-18	62
myotome	6.06e-18	62
muscle tissue	6.75e-17	64
musculature	6.75e-17	64
musculature of body	6.75e-17	64
splanchnic layer of lateral plate mesoderm	1.23e-16	83
vessel	3.43e-16	68
cell layer	7.58e-16	309
epithelium	2.33e-15	306
artery	3.43e-15	42
arterial blood vessel	3.43e-15	42
arterial system	3.43e-15	42
epithelial tube open at both ends	6.83e-15	59
blood vessel	6.83e-15	59
blood vasculature	6.83e-15	59
vascular cord	6.83e-15	59
multi-tissue structure	4.66e-13	342
cardiovascular system	1.58e-12	109
multi-cellular organism	1.67e-12	656
circulatory system	2.01e-12	112
systemic artery	1.78e-11	33
systemic arterial system	1.78e-11	33
anatomical cluster	1.40e-10	373
anatomical group	3.15e-10	625
anatomical system	4.30e-10	624
surface structure	9.97e-09	99
anatomical conduit	2.61e-08	240
subdivision of trunk	5.30e-08	112
urinary system structure	7.92e-08	47
renal system	1.41e-07	48

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	2.0712
MA0004.1	0.502801
MA0006.1	0.341337
MA0007.1	0.483857
MA0009.1	0.973289
MA0014.1	3.71689
MA0017.1	0.380797
MA0019.1	0.652951
MA0024.1	0.867125
MA0025.1	2.50576
MA0027.1	2.59001
MA0028.1	2.53091
MA0029.1	0.886702
MA0030.1	0.875089
MA0031.1	0.809638
MA0038.1	0.60704
MA0040.1	0.892629
MA0041.1	0.521615
MA0042.1	0.48922
MA0043.1	0.973609
MA0046.1	0.962263
MA0048.1	1.8235
MA0050.1	0.490116
MA0051.1	0.602745
MA0052.1	0.896548
MA0055.1	0.158296
MA0056.1	0
MA0057.1	0.369442
MA0058.1	0.406232
MA0059.1	1.04442
MA0060.1	1.19421
MA0061.1	0.198335
MA0063.1	0
MA0066.1	0.607474
MA0067.1	1.29359
MA0068.1	0.946606
MA0069.1	0.958358
MA0070.1	0.947018
MA0071.1	0.567661
MA0072.1	0.942461
MA0073.1	3.16596
MA0074.1	1.46532
MA0076.1	3.86616
MA0077.1	0.934645
MA0078.1	0.703614
MA0081.1	0.405093
MA0083.1	0.980893
MA0084.1	1.48179
MA0087.1	0.939982
MA0088.1	0.252594
MA0089.1	0
MA0090.1	0.436918
MA0091.1	0.505453
MA0092.1	0.467172
MA0093.1	0.344385
MA0095.1	0
MA0098.1	0
MA0100.1	0.621149
MA0101.1	0.347695
MA0103.1	0.332048
MA0105.1	0.340955
MA0106.1	0.648997
MA0107.1	0.274127
MA0108.2	0.806528
MA0109.1	0
MA0111.1	0.45062
MA0113.1	0.665691
MA0114.1	0.269076
MA0115.1	1.21667
MA0116.1	0.277571
MA0117.1	1.01134
MA0119.1	0.388712
MA0122.1	1.03753
MA0124.1	1.17486
MA0125.1	1.0901
MA0130.1	0
MA0131.1	0.722072
MA0132.1	0
MA0133.1	0
MA0135.1	1.00402
MA0136.1	0.614215
MA0139.1	0.547495
MA0140.1	0.564957
MA0141.1	1.04059
MA0142.1	0.777365
MA0143.1	0.66587
MA0144.1	0.708913
MA0145.1	0.276317
MA0146.1	1.97205
MA0147.1	0.768766
MA0148.1	0.528066
MA0149.1	0.555119
MA0062.2	2.39331
MA0035.2	0.564239
MA0039.2	3.10611
MA0138.2	0.704862
MA0002.2	0.213296
MA0137.2	0.36398
MA0104.2	1.19136
MA0047.2	0.636643
MA0112.2	0.556641
MA0065.2	0.591589
MA0150.1	0.430951
MA0151.1	0
MA0152.1	0.571637
MA0153.1	1.07307
MA0154.1	0.685508
MA0155.1	0.910701
MA0156.1	0.959643
MA0157.1	0.749547
MA0158.1	0
MA0159.1	0.770207
MA0160.1	0.543522
MA0161.1	0
MA0162.1	1.13878
MA0163.1	1.72058
MA0164.1	0.678332
MA0080.2	0.344472
MA0018.2	1.56673
MA0099.2	0.572
MA0079.2	3.65327
MA0102.2	1.51913
MA0258.1	0.245543
MA0259.1	1.43531
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
BRCA1#672	3	8.65038456138161	0.00365929333120223	0.0184740627552294
CCNT2#905	5	4.52585826925902	0.0015515733062647	0.00985553853138175
CEBPB#1051	4	4.55494150047132	0.00632108033306846	0.0275276169170768
E2F1#1869	6	4.20633361275371	0.000413523201700764	0.0039365554336365
E2F6#1876	6	4.30041919859776	0.00036379750429086	0.00363202825261764
EGR1#1958	5	3.56298506772153	0.00472235121105893	0.0222582199716483
ELF1#1997	5	3.04149854200538	0.00971956226937075	0.0365617837433659
ELK4#2005	4	9.27753237626744	0.000432817858966577	0.00404140048034066
ETS1#2113	5	6.94911494443024	0.000201406263333039	0.00239329488408684
GABPB1#2553	4	4.03867647781838	0.0098011349469615	0.0368447459767372
GTF2F1#2962	4	7.27980621529009	0.00109405687916472	0.00764756083281467
HDAC2#3066	3	5.74955152998268	0.0115304170404053	0.0421706550386221
HEY1#23462	7	4.04011104310571	5.68979821988558e-05	0.000949715256970801
IRF1#3659	5	5.45511696683136	0.0006415794721055	0.0052586657108167
MAX#4149	4	3.6871745765755	0.0136057064395334	0.0480137311991359
MXI1#4601	4	5.69232664500531	0.00276690540539156	0.015160423568212
MYC#4609	6	4.47624160423663	0.000288361195091082	0.00306338672099659
PAX5#5079	4	3.81118030353019	0.0120826168155519	0.043826500107645
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223280228284761
RFX5#5993	5	8.60565059085364	7.16524263203101e-05	0.00112717393469903
SIN3A#25942	6	4.63618690869869	0.000235167814635783	0.00256508526295002
SIX5#147912	4	9.76383734597657	0.000355537135106872	0.00355840372337581
SREBF1#6720	2	13.4302426972824	0.00884947602167745	0.0335912781212463
SRF#6722	4	7.88410186409589	0.000807478872809276	0.00616554218433455
TAF1#6872	6	2.86546824492454	0.00372833020747146	0.0185845302853242
TAF7#6879	4	6.53318251709938	0.0016484941094751	0.0103112580882476
YY1#7528	5	3.50797910703847	0.00507257067280898	0.023613737842545
ZBTB7A#51341	4	4.20109103307194	0.0084941066128735	0.0324250155540003

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.