Coexpression cluster:C49

Full id: C49_H9_iPS_testicular_HES3GFP_teratocarcinoma_hepatoblastoma_choriocarcinoma

Phase1 CAGE Peaks

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Hg19::chr10:101673730..101673781,-	p3@DNMBP
Hg19::chr10:118085026..118085031,+	p@chr10:118085026..118085031 +
Hg19::chr10:126138622..126138638,-	p2@NKX1-2
Hg19::chr10:13390193..13390218,-	p4@SEPHS1
Hg19::chr10:13390222..13390246,-	p1@SEPHS1
Hg19::chr10:13390252..13390269,-	p5@SEPHS1
Hg19::chr10:135042855..135042873,+	p@chr10:135042855..135042873 +
Hg19::chr10:135051422..135051430,+	p2@VENTX
Hg19::chr10:21581922..21581939,-	p@chr10:21581922..21581939 -
Hg19::chr10:21581957..21581984,-	p@chr10:21581957..21581984 -
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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:0003677	DNA binding	3.95036411579275e-15
GO:0005634	nucleus	1.20737198218058e-10
GO:0019222	regulation of metabolic process	1.2954821097401e-10
GO:0031323	regulation of cellular metabolic process	1.2954821097401e-10
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	1.2954821097401e-10
GO:0050794	regulation of cellular process	1.75651419149499e-10
GO:0006355	regulation of transcription, DNA-dependent	2.65857670272778e-10
GO:0010468	regulation of gene expression	3.30540380273447e-10
GO:0050789	regulation of biological process	4.50925840855671e-10
GO:0045449	regulation of transcription	4.50925840855671e-10
GO:0006351	transcription, DNA-dependent	4.50925840855671e-10
GO:0032774	RNA biosynthetic process	4.50925840855671e-10
GO:0006350	transcription	1.85301713394524e-09
GO:0043231	intracellular membrane-bound organelle	2.16633446218497e-09
GO:0043227	membrane-bound organelle	2.16633446218497e-09
GO:0065007	biological regulation	2.44035625068062e-09
GO:0016070	RNA metabolic process	4.33394817796637e-08
GO:0043283	biopolymer metabolic process	8.20472778744412e-08
GO:0007275	multicellular organismal development	4.28603624078332e-07
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	4.72973755730249e-07
GO:0043229	intracellular organelle	5.62229326061631e-07
GO:0043226	organelle	5.62229326061631e-07
GO:0010467	gene expression	1.26337489093366e-06
GO:0003676	nucleic acid binding	1.53778188763554e-06
GO:0044424	intracellular part	1.53778188763554e-06
GO:0043565	sequence-specific DNA binding	1.30599182065928e-05
GO:0003700	transcription factor activity	2.29393153517212e-05
GO:0005622	intracellular	4.34543701848668e-05
GO:0008270	zinc ion binding	6.91704608320932e-05
GO:0043170	macromolecule metabolic process	0.00026424115832834
GO:0032502	developmental process	0.000398075066182975
GO:0046914	transition metal ion binding	0.000713132997593127
GO:0032501	multicellular organismal process	0.00531395199956216
GO:0044238	primary metabolic process	0.00566905222576778
GO:0044464	cell part	0.0104126099465675
GO:0046872	metal ion binding	0.0212378991688859
GO:0043169	cation binding	0.0212378991688859
GO:0044237	cellular metabolic process	0.0241679808359093
GO:0043167	ion binding	0.0274850187662175
GO:0009893	positive regulation of metabolic process	0.0297645329767371
GO:0010232	vascular transport	0.0297645329767371
GO:0018144	RNA-protein covalent cross-linking	0.0297645329767371
GO:0035067	negative regulation of histone acetylation	0.0297645329767371
GO:0051095	regulation of helicase activity	0.0297645329767371
GO:0051097	negative regulation of helicase activity	0.0297645329767371
GO:0018143	nucleic acid-protein covalent cross-linking	0.0297645329767371
GO:0031057	negative regulation of histone modification	0.0297645329767371
GO:0016929	SUMO-specific protease activity	0.0297645329767371
GO:0008326	site-specific DNA-methyltransferase (cytosine-specific) activity	0.0297645329767371
GO:0015326	cationic amino acid transmembrane transporter activity	0.0297645329767371
GO:0032444	activin responsive factor complex	0.0297645329767371
GO:0015819	lysine transport	0.0297645329767371
GO:0008401	retinoic acid 4-hydroxylase activity	0.0297645329767371
GO:0030948	negative regulation of vascular endothelial growth factor receptor signaling pathway	0.0297645329767371
GO:0015181	arginine transmembrane transporter activity	0.0297645329767371
GO:0015189	L-lysine transmembrane transporter activity	0.0297645329767371
GO:0003682	chromatin binding	0.0304552529509428
GO:0007276	gamete generation	0.0366063061321303
GO:0019783	small conjugating protein-specific protease activity	0.046711025402069
GO:0048856	anatomical structure development	0.0475713832166307
GO:0016264	gap junction assembly	0.0475713832166307
GO:0042149	cellular response to glucose starvation	0.0475713832166307
GO:0015867	ATP transport	0.0475713832166307
GO:0051503	adenine nucleotide transport	0.0475713832166307
GO:0003691	double-stranded telomeric DNA binding	0.0475713832166307
GO:0015809	arginine transport	0.0475713832166307
GO:0015865	purine nucleotide transport	0.0475713832166307
GO:0045844	positive regulation of striated muscle development	0.0475713832166307
GO:0035065	regulation of histone acetylation	0.0475713832166307
GO:0000739	DNA strand annealing activity	0.0475713832166307

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
embryonic stem cell	4.19e-67	5
germ line cell	4.81e-30	7
germ cell	4.81e-30	7
neuron	1.09e-20	6
neuroblast	1.09e-20	6
electrically signaling cell	1.09e-20	6
neuronal stem cell	1.10e-15	8
melanocyte	9.65e-13	10
melanoblast	9.65e-13	10
pigment cell	2.91e-09	14
neurectodermal cell	1.28e-07	59

Uber Anatomy

Ontology term	p-value	n
testis	2.40e-26	8
male reproductive organ	2.85e-19	11
gonad	1.71e-15	21
indifferent external genitalia	1.71e-15	21
indifferent gonad	1.71e-15	21
gonad primordium	1.71e-15	21
external genitalia	8.64e-15	22
male organism	8.69e-10	22
male reproductive system	8.69e-10	22
body cavity	4.72e-07	46
reproductive organ	9.37e-07	48

Disease

Ontology term	p-value	n
germ cell and embryonal cancer	5.51e-21	22
germ cell cancer	5.51e-21	22

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	0.800809
MA0004.1	0.0771229
MA0006.1	0.10408
MA0007.1	0.550234
MA0009.1	0.837723
MA0014.1	1.31198
MA0017.1	0.203291
MA0019.1	0.248072
MA0024.1	1.29973
MA0025.1	0.0330094
MA0027.1	0.896654
MA0028.1	0.00252954
MA0029.1	0.689488
MA0030.1	0.463521
MA0031.1	0.17933
MA0038.1	0.368225
MA0040.1	0.522298
MA0041.1	0.109867
MA0042.1	1.70116
MA0043.1	0.00116511
MA0046.1	0.138702
MA0048.1	0.0202017
MA0050.1	0.00339647
MA0051.1	0.0294325
MA0052.1	0.372495
MA0055.1	2.99722e-08
MA0056.1	0
MA0057.1	4.20171
MA0058.1	0.0163497
MA0059.1	0.321565
MA0060.1	0.613184
MA0061.1	1.23003
MA0063.1	0
MA0066.1	0.0170395
MA0067.1	0.284846
MA0068.1	1.08773
MA0069.1	1.62701
MA0070.1	0.0218839
MA0071.1	0.397132
MA0072.1	0.117016
MA0073.1	4.48549
MA0074.1	1.04479
MA0076.1	0.00133405
MA0077.1	1.46421
MA0078.1	0.419086
MA0081.1	0.00524314
MA0083.1	0.079975
MA0084.1	0.277796
MA0087.1	0.499039
MA0088.1	0.331573
MA0089.1	0
MA0090.1	0.278446
MA0091.1	0.00544509
MA0092.1	0.0213306
MA0093.1	0.0612765
MA0095.1	0
MA0098.1	0
MA0100.1	0.0110454
MA0101.1	0.0332303
MA0103.1	1.4114
MA0105.1	2.85393
MA0106.1	2.83741
MA0107.1	0.282091
MA0108.2	2.64195
MA0109.1	0
MA0111.1	0.347045
MA0113.1	0.0265107
MA0114.1	0.650424
MA0115.1	0.376626
MA0116.1	1.48343
MA0117.1	1.31058
MA0119.1	0.539458
MA0122.1	0.054912
MA0124.1	0.305514
MA0125.1	2.19786
MA0130.1	0
MA0131.1	0.110455
MA0132.1	0
MA0133.1	0
MA0135.1	0.503105
MA0136.1	0.036603
MA0139.1	0.0161207
MA0140.1	3.22756
MA0141.1	0.108906
MA0142.1	17.2677
MA0143.1	11.6533
MA0144.1	0.201561
MA0145.1	0.070685
MA0146.1	0.0876199
MA0147.1	0.39746
MA0148.1	0.17347
MA0149.1	0.0350261
MA0062.2	0.00169708
MA0035.2	2.92124
MA0039.2	11.4989
MA0138.2	0.0502373
MA0002.2	0.0689023
MA0137.2	0.230987
MA0104.2	0.682583
MA0047.2	0.139088
MA0112.2	0.0502628
MA0065.2	5.64287
MA0150.1	0.0212582
MA0151.1	0
MA0152.1	0.415986
MA0153.1	0.303662
MA0154.1	1.50426
MA0155.1	2.36161
MA0156.1	0.00657359
MA0157.1	0.0508382
MA0158.1	0
MA0159.1	0.727413
MA0160.1	0.0273165
MA0161.1	0
MA0162.1	0.0958032
MA0163.1	1.80063
MA0164.1	0.158603
MA0080.2	0.0045609
MA0018.2	0.00126724
MA0099.2	0.00130439
MA0079.2	29.772
MA0102.2	0.0957963
MA0258.1	0.149814
MA0259.1	0.340788
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
BCL11A#53335	25	1.92204980376742	0.00162439411405001	0.0101678212093059
CTBP2#1488	17	2.88940109964384	0.000116215029985314	0.0015793599891524
NANOG#79923	78	6.18182309354739	3.33551519093832e-38	1.7956591290021e-35
POLR2A#5430	230	1.33852095015815	8.1705249827463e-10	7.68758070876613e-08
POU5F1#5460	34	30.9076770985496	2.57280266612752e-39	1.45243750079833e-36
SP1#6667	90	1.38984911661973	0.0005596376442309	0.00477633373586916
TAF1#6872	183	1.6579335238249	1.89067109621869e-15	3.47640490524619e-13
TAF7#6879	95	2.94347315302919	5.55656838565741e-22	1.54341075965339e-19
TBP#6908	148	1.48672645444516	3.06564915825508e-08	2.07231930381231e-06

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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FF samples	Score

FF samples	Score
H9 Embryonic Stem cells, biol_rep2 (H9ES-2) CNhs12824	0.82
H9 Embryoid body cells, melanocytic induction, day00, biol_rep3 (H9EB-3 d0) CNhs12908	0.78
H9 Embryoid body cells, melanocytic induction, day00, biol_rep1 (H9EB-1 d0) CNhs12822	0.76
H9 Embryonic Stem cells, biol_rep3 (H9ES-3) CNhs12837	0.75
iPS differentiation to neuron, control donor C32-CRL1502, day00, rep2 CNhs13839	0.75
iPS differentiation to neuron, control donor C32-CRL1502, day00, rep1 CNhs13826	0.72
iPS differentiation to neuron, control donor C11-CRL2429, day00, rep2 CNhs13822	0.71
HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep3 (UH-3) CNhs13738	0.63
H9 Embryoid body cells, melanocytic induction, day00, biol_rep2 (H9EB-2 d0) CNhs12825	0.60
testicular germ cell embryonal carcinoma cell line:ITO-II CNhs11876	0.45

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