Coexpression cluster:C2400

Full id: C2400_Alveolar_embryonic_Mesenchymal_Renal_Smooth_acute_granulocyte

Phase1 CAGE Peaks

Hg19::chr17:33469299..33469328,-	p1@NLE1
Hg19::chr19:13044513..13044543,-	p1@FARSA
Hg19::chr19:48949218..48949267,+	p1@GRWD1
Hg19::chr19:56166360..56166452,+	p1@U2AF2

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:0001826	inner cell mass cell differentiation	0.00977232251375934
GO:0001825	blastocyst formation	0.00977232251375934
GO:0006432	phenylalanyl-tRNA aminoacylation	0.0146558949108512
GO:0004826	phenylalanine-tRNA ligase activity	0.0146558949108512
GO:0001824	blastocyst development	0.0273480076998137

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
animal cell	1.08e-26	679
eukaryotic cell	1.08e-26	679
epithelial cell	5.76e-24	254
embryonic cell	4.33e-21	248
native cell	2.29e-16	722
mesodermal cell	2.24e-12	119
somatic cell	7.22e-10	591
non-terminally differentiated cell	1.37e-09	180
squamous epithelial cell	7.26e-09	62
contractile cell	1.40e-08	59
electrically responsive cell	1.37e-07	60
electrically active cell	1.37e-07	60
muscle cell	6.10e-07	54
muscle precursor cell	9.37e-07	57
myoblast	9.37e-07	57
multi-potent skeletal muscle stem cell	9.37e-07	57

Uber Anatomy

Ontology term	p-value	n
mesenchyme	4.53e-12	238
entire embryonic mesenchyme	4.53e-12	238
epithelial tube	4.32e-10	118
unilaminar epithelium	3.03e-09	138
multilaminar epithelium	1.82e-08	82
trunk	3.58e-08	216
vessel	5.02e-08	69
vasculature	7.51e-08	79
vascular system	7.51e-08	79
dermomyotome	8.61e-08	70
blood vessel	9.03e-08	60
epithelial tube open at both ends	9.03e-08	60
blood vasculature	9.03e-08	60
vascular cord	9.03e-08	60
trunk mesenchyme	1.16e-07	143
artery	1.49e-07	42
arterial blood vessel	1.49e-07	42
arterial system	1.49e-07	42
segment of respiratory tract	1.54e-07	46
splanchnic layer of lateral plate mesoderm	2.14e-07	84
primordium	4.16e-07	168
respiratory primordium	5.61e-07	38
endoderm of foregut	5.61e-07	38
simple squamous epithelium	8.87e-07	22

Disease

Ontology term	p-value	n
cancer	2.88e-21	235
disease of cellular proliferation	9.39e-21	239
hematologic cancer	1.00e-15	51
immune system cancer	1.00e-15	51
leukemia	9.78e-14	39
myeloid leukemia	2.64e-12	31
organ system cancer	1.18e-11	137
cell type cancer	5.00e-09	143
carcinoma	4.53e-08	106

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
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00511888133871851
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160804843861814
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0192024326437538
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378550283561341
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185897277567356
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.028291903439249
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466142918479397
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186323575403902
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227572411283288
POU5F1#5460	1	83.8598003629764	0.0118715423909156	0.0432395904221536
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321949802216212
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243978653227886
USF1#7391	3	4.77112445790597	0.0137046588718802	0.048294391062533
USF2#7392	3	9.7441480388022	0.00171834184841007	0.01071798281809
XRCC4#7518	1	1074.57558139535	0.000930282808003446	0.00674379164191518
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106769705535761

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.