Coexpression cluster:C4090

Full id: C4090_salivary_Hepatocyte_liver_parotid_submaxillary_tongue_lung

Phase1 CAGE Peaks

Hg19::chr22:25507144..25507210,+	p@chr22:25507144..25507210 +
Hg19::chr22:25507901..25507915,+	p@chr22:25507901..25507915 +
Hg19::chr22:25507920..25507932,+	p@chr22:25507920..25507932 +

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><br>

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Cell Type

Ontology term	p-value	n
endothelial cell of vascular tree	2.76e-12	24
endothelial cell	1.42e-10	35
blood vessel endothelial cell	1.02e-09	18
embryonic blood vessel endothelial progenitor cell	1.02e-09	18
meso-epithelial cell	3.87e-08	44

Uber Anatomy

Ontology term	p-value	n
adult organism	2.56e-38	115
anatomical conduit	6.69e-23	241
anatomical cluster	6.88e-19	286
tube	2.66e-16	194
anterior region of body	2.72e-15	129
craniocervical region	2.72e-15	129
neural tube	3.02e-15	57
neural rod	3.02e-15	57
future spinal cord	3.02e-15	57
neural keel	3.02e-15	57
anterior neural tube	7.98e-15	42
neural plate	8.95e-15	86
presumptive neural plate	8.95e-15	86
epithelium	1.65e-14	309
regional part of forebrain	3.32e-14	41
forebrain	3.32e-14	41
future forebrain	3.32e-14	41
pre-chordal neural plate	4.39e-14	61
head	6.39e-14	123
cell layer	7.78e-14	312
regional part of nervous system	1.31e-13	94
nervous system	1.31e-13	94
neurectoderm	2.24e-13	90
central nervous system	4.85e-13	82
brain	1.05e-12	69
future brain	1.05e-12	69
regional part of brain	2.28e-12	59
multi-tissue structure	3.05e-12	347
multi-cellular organism	4.98e-12	659
ectoderm-derived structure	1.05e-11	169
cerebral hemisphere	1.57e-11	32
organism subdivision	2.18e-11	365
telencephalon	3.90e-11	34
gray matter	3.93e-11	34
brain grey matter	3.93e-11	34
embryo	5.53e-11	612
anatomical group	5.58e-11	626
ectoderm	6.25e-11	173
presumptive ectoderm	6.25e-11	173
anatomical system	6.86e-11	625
regional part of telencephalon	1.24e-10	33
regional part of cerebral cortex	2.71e-10	22
embryonic structure	9.23e-10	605
developing anatomical structure	9.23e-10	605
neocortex	1.01e-09	20
endothelium	1.02e-09	18
blood vessel endothelium	1.02e-09	18
cardiovascular system endothelium	1.02e-09	18
germ layer	1.26e-09	604
embryonic tissue	1.26e-09	604
presumptive structure	1.26e-09	604
epiblast (generic)	1.26e-09	604
cerebral cortex	1.58e-08	25
pallium	1.58e-08	25
organ part	2.68e-08	219
simple squamous epithelium	2.80e-08	22
subdivision of digestive tract	5.61e-08	129
endodermal part of digestive tract	5.61e-08	129
squamous epithelium	7.83e-08	25
digestive system	1.93e-07	155
digestive tract	1.93e-07	155
primitive gut	1.93e-07	155
gland	6.80e-07	59
foregut	7.25e-07	98
subdivision of trunk	7.94e-07	113
endoderm-derived structure	8.37e-07	169
endoderm	8.37e-07	169
presumptive endoderm	8.37e-07	169

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279986445556914
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00582179699861113
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107357106622587
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190667597364836

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.