Coexpression cluster:C3629

Full id: C3629_clear_serous_papillotubular_testicular_signet_breast_esophagus

Phase1 CAGE Peaks

Hg19::chr17:37894179..37894202,+	p3@GRB7
Hg19::chr17:37894206..37894222,+	p2@GRB7
Hg19::chr17:37894570..37894614,+	p1@GRB7

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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No GOStat results

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
epithelial cell	1.42e-40	253
endodermal cell	6.14e-20	58
endo-epithelial cell	1.39e-18	42
epithelial cell of alimentary canal	1.99e-09	20
kidney tubule cell	1.98e-08	10
nephron tubule epithelial cell	1.98e-08	10
kidney cell	2.83e-07	17
kidney epithelial cell	2.83e-07	17

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	4.77e-25	160
endoderm	4.77e-25	160
presumptive endoderm	4.77e-25	160
digestive system	1.77e-21	145
digestive tract	1.77e-21	145
primitive gut	1.77e-21	145
subdivision of digestive tract	1.86e-20	118
trunk region element	6.41e-18	101
immaterial anatomical entity	9.54e-15	117
foregut	9.87e-15	87
respiratory system	1.95e-13	74
organ	2.97e-13	503
anatomical space	4.11e-13	95
renal system	6.73e-13	48
urinary system structure	2.27e-12	47
organ part	2.97e-12	218
endo-epithelium	2.42e-11	82
subdivision of trunk	3.68e-11	112
respiratory tract	7.29e-11	54
respiratory primordium	3.80e-10	38
endoderm of foregut	3.80e-10	38
organ system subdivision	1.10e-09	223
multi-tissue structure	1.36e-09	342
organism subdivision	3.00e-09	264
epithelial bud	7.15e-09	37
nephron tubule epithelium	1.98e-08	10
primordium	2.00e-08	160
reproductive structure	3.16e-08	59
reproductive system	3.16e-08	59
kidney	3.40e-08	26
kidney mesenchyme	3.40e-08	26
upper urinary tract	3.40e-08	26
kidney rudiment	3.40e-08	26
kidney field	3.40e-08	26
segment of respiratory tract	5.97e-08	47
abdomen element	7.19e-08	54
abdominal segment element	7.19e-08	54
thoracic cavity element	8.86e-08	34
thoracic cavity	8.86e-08	34
reproductive organ	1.02e-07	48
internal genitalia	1.26e-07	25
cavitated compound organ	1.37e-07	31
epithelial fold	1.38e-07	47
orifice	1.40e-07	36
thoracic segment organ	2.55e-07	35
organ segment	2.98e-07	98
lung	4.37e-07	22
respiratory tube	4.37e-07	22
respiration organ	4.37e-07	22
pair of lungs	4.37e-07	22
lung primordium	4.37e-07	22
lung bud	4.37e-07	22
anatomical cluster	4.77e-07	373
embryo	5.27e-07	592
multi-cellular organism	6.72e-07	656
anatomical cavity	8.55e-07	61
excretory tube	9.50e-07	16
kidney epithelium	9.50e-07	16

Disease

Ontology term	p-value	n
carcinoma	3.67e-34	106
cell type cancer	2.99e-24	143
adenocarcinoma	9.56e-12	25
cancer	2.31e-09	235
squamous cell carcinoma	4.89e-09	14
disease of cellular proliferation	1.49e-08	239

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
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000850644836088615
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246740105458715

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.