Coexpression cluster:C19

Full id: C19_embryonic_testis_cord_chronic_CD14_NK_mesothelioma

Phase1 CAGE Peaks

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Hg19::chr10:112092238..112092244,+	p@chr10:112092238..112092244 +
Hg19::chr10:120518956..120518964,-	p@chr10:120518956..120518964 -
Hg19::chr10:120543321..120543328,+	p@chr10:120543321..120543328 +
Hg19::chr10:122794003..122794008,-	p@chr10:122794003..122794008 -
Hg19::chr10:123737306..123737313,-	p@chr10:123737306..123737313 -
Hg19::chr10:124639597..124639599,-	p3@CUZD1 p3@FAM24B
Hg19::chr10:124768217..124768228,-	p2@IKZF5
Hg19::chr10:27195771..27195778,+	p@chr10:27195771..27195778 +
Hg19::chr10:31191066..31191082,-	p@chr10:31191066..31191082 -
Hg19::chr10:31218537..31218558,-	p@chr10:31218537..31218558 -
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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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p.value	FDR	nGenes	nPathway	Name
0.000108536357284342	0.0238823869374849	4	92	Ribosome (KEGG):03010
0.000113186667950165	0.0238823869374849	4	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
0.00037879664527403	0.0479556552916922	2	11	Signaling by VEGF (Reactome):REACT_12529
0.000247996709377488	0.0392454792589875	4	114	Regulation of beta-cell development (Reactome):REACT_13698
4.08210231317272e-05	0.0238823869374849	5	143	Influenza Infection (Reactome):REACT_6167

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:0044424	intracellular part	0.000118251118478727
GO:0044237	cellular metabolic process	0.000118251118478727
GO:0043229	intracellular organelle	0.000118251118478727
GO:0043226	organelle	0.000118251118478727
GO:0043231	intracellular membrane-bound organelle	0.000264921640815833
GO:0043227	membrane-bound organelle	0.000264921640815833
GO:0005634	nucleus	0.000264921640815833
GO:0043283	biopolymer metabolic process	0.000436316018510323
GO:0005622	intracellular	0.000454795999831926
GO:0003677	DNA binding	0.000638329673173698
GO:0003676	nucleic acid binding	0.000680990050141197
GO:0050789	regulation of biological process	0.000959069478515697
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00169134958778105
GO:0050794	regulation of cellular process	0.00222394499945679
GO:0044238	primary metabolic process	0.00261868380308172
GO:0019222	regulation of metabolic process	0.00261868380308172
GO:0010467	gene expression	0.00261868380308172
GO:0043170	macromolecule metabolic process	0.00288656026368036
GO:0031323	regulation of cellular metabolic process	0.00368743257469057
GO:0050930	induction of positive chemotaxis	0.00385761371356052
GO:0045449	regulation of transcription	0.00385761371356052
GO:0006355	regulation of transcription, DNA-dependent	0.00385761371356052
GO:0065007	biological regulation	0.00450793968205722
GO:0003723	RNA binding	0.00461241352901987
GO:0050926	regulation of positive chemotaxis	0.00461241352901987
GO:0050927	positive regulation of positive chemotaxis	0.00461241352901987
GO:0050918	positive chemotaxis	0.00461241352901987
GO:0006351	transcription, DNA-dependent	0.00461241352901987
GO:0032774	RNA biosynthetic process	0.00461241352901987
GO:0050921	positive regulation of chemotaxis	0.00507701195539429
GO:0048010	vascular endothelial growth factor receptor signaling pathway	0.00507701195539429
GO:0006350	transcription	0.00530438430267921
GO:0050920	regulation of chemotaxis	0.00532145601135416
GO:0004386	helicase activity	0.00532145601135416
GO:0010468	regulation of gene expression	0.00532145601135416
GO:0016070	RNA metabolic process	0.00532145601135416
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00532145601135416
GO:0005515	protein binding	0.00818749528637169
GO:0005830	cytosolic ribosome (sensu Eukaryota)	0.00902551579835063
GO:0044464	cell part	0.0111103756860159
GO:0048522	positive regulation of cellular process	0.0128505742145479
GO:0006512	ubiquitin cycle	0.0156105322851209
GO:0048518	positive regulation of biological process	0.024311547562387
GO:0032003	interleukin-28 receptor binding	0.0297058361788139
GO:0032023	trypsinogen activation	0.0297058361788139
GO:0045345	positive regulation of MHC class I biosynthetic process	0.0297058361788139
GO:0004595	pantetheine-phosphate adenylyltransferase activity	0.0297058361788139
GO:0004140	dephospho-CoA kinase activity	0.0297058361788139
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	0.0317741409504344
GO:0045941	positive regulation of transcription	0.0369311487256354
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0410791181765393
GO:0046475	glycerophospholipid catabolic process	0.0499800720172071
GO:0008106	alcohol dehydrogenase (NADP+) activity	0.0499800720172071
GO:0045343	regulation of MHC class I biosynthetic process	0.0499800720172071
GO:0045341	MHC class I biosynthetic process	0.0499800720172071
GO:0000281	cytokinesis after mitosis	0.0499800720172071
GO:0006931	substrate-bound cell migration, cell attachment to substrate	0.0499800720172071

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
antibody secreting cell	4.22e-21	1
plasma cell	4.22e-21	1
plasmablast	4.22e-21	1
mature B cell	3.02e-11	2
pre-B-II cell	3.02e-11	2
transitional stage B cell	3.02e-11	2
small pre-B-II cell	3.02e-11	2
immature B cell	3.02e-11	2
precursor B cell	6.34e-08	3

Uber Anatomy

Ontology term	p-value	n
testis	5.15e-11	8
male reproductive organ	2.92e-08	11

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
MA0004.1	0.127521
MA0006.1	8.3523e-06
MA0007.1	10.3159
MA0009.1	0.000686214
MA0014.1	0
MA0017.1	3.46048e-06
MA0019.1	0.00246484
MA0024.1	0.0173789
MA0025.1	0.10017
MA0027.1	0.60469
MA0028.1	1.43198e-06
MA0029.1	80.4385
MA0030.1	0.000190256
MA0031.1	59.1855
MA0038.1	45.5705
MA0040.1	0.00291099
MA0041.1	0.0300519
MA0042.1	2.42939e-07
MA0043.1	0.889988
MA0046.1	1.62374e-05
MA0048.1	0
MA0050.1	0.0691598
MA0051.1	13.0291
MA0052.1	0.00760578
MA0055.1	6.01039e-05
MA0056.1	0
MA0057.1	1.44649e-16
MA0058.1	0.0865594
MA0059.1	1.0318
MA0060.1	1476.51
MA0061.1	0.310524
MA0063.1	0
MA0066.1	2.88559e-05
MA0067.1	0.0811869
MA0068.1	2.35335e-06
MA0069.1	0.011781
MA0070.1	15.7119
MA0071.1	0.00326992
MA0072.1	44.0103
MA0073.1	0
MA0074.1	0.00233749
MA0076.1	7.29868e-06
MA0077.1	0.0572633
MA0078.1	0.190838
MA0081.1	6.94207e-07
MA0083.1	63.7714
MA0084.1	0.0106307
MA0087.1	0.00110151
MA0088.1	9.16111e-16
MA0089.1	0
MA0090.1	9.2671e-05
MA0091.1	7.01603e-05
MA0092.1	0.000367467
MA0093.1	0.184846
MA0095.1	0
MA0098.1	0
MA0100.1	5.84978e-05
MA0101.1	0.815305
MA0103.1	0.00537382
MA0105.1	6.51334e-08
MA0106.1	0.00402017
MA0107.1	3.07048
MA0108.2	3.25785
MA0109.1	0
MA0111.1	0.00074789
MA0113.1	0.0120547
MA0114.1	1.06074e-09
MA0115.1	0.0135419
MA0116.1	7.32323e-07
MA0117.1	0.0557349
MA0119.1	0.00132538
MA0122.1	0.721572
MA0124.1	0.00772192
MA0125.1	0.622919
MA0130.1	0
MA0131.1	0.000282118
MA0132.1	0
MA0133.1	0
MA0135.1	0.000323111
MA0136.1	0.00375107
MA0139.1	4.29318e-09
MA0140.1	225.777
MA0141.1	6.26178e-06
MA0142.1	0.00184801
MA0143.1	0.000979281
MA0144.1	2.34683e-08
MA0145.1	4.04058
MA0146.1	0
MA0147.1	0.0651727
MA0148.1	0.0017164
MA0149.1	1.58969e-09
MA0062.2	3.21941e-10
MA0035.2	135.401
MA0039.2	2.03873
MA0138.2	4.21981e-06
MA0002.2	3.744e-13
MA0137.2	2.81354e-06
MA0104.2	0.00803413
MA0047.2	0.00822449
MA0112.2	4.60225e-13
MA0065.2	0
MA0150.1	0.554303
MA0151.1	0
MA0152.1	0.0104269
MA0153.1	0.00141735
MA0154.1	0
MA0155.1	9.64327e-16
MA0156.1	5.13133
MA0157.1	84.4114
MA0158.1	0
MA0159.1	1.58877e-09
MA0160.1	0.00200503
MA0161.1	0
MA0162.1	0
MA0163.1	0
MA0164.1	0.00155934
MA0080.2	6.87016e-05
MA0018.2	0.414774
MA0099.2	2.46056
MA0079.2	0
MA0102.2	0.0683544
MA0258.1	4.04543e-08
MA0259.1	3.07338
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
JUNB#3726	41	1.61523286879365	0.00219104073600709	0.0126327759427981
MAFF#23764	29	2.10186015213438	0.000196675016207157	0.00236342676535028
MAFK#7975	47	1.63929788607208	0.000800752302881657	0.00611552246878664
NFYA#4800	424	10.0546283355575	3.10234688467927e-318	2.94550914803707e-314
NFYB#4801	358	7.72201542440933	6.4969602989265e-221	3.57124229820834e-217

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
embryonic kidney cell line: HEK293/SLAM infection, 24hr CNhs11047	1.06
cord blood derived cell line:COBL-a 24h infection(-C) CNhs11049	0.11
testis, adult, pool1 CNhs10632	0.11
testis, adult, pool2 CNhs12998	0.10
Clontech Human Universal Reference Total RNA, pool1 CNhs10608	0.05
plasma cell leukemia cell line:ARH-77 CNhs12807	0.05
embryonic kidney cell line: HEK293/SLAM untreated CNhs11046	0.04
epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep1 CNhs12325	0.04
epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep2 CNhs12326	0.03
epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep3 CNhs12327	0.03

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