Coexpression cluster:C1435

Full id: C1435_Renal_lung_retina_Mesenchymal_placenta_Hepatic_uterus

Phase1 CAGE Peaks

Hg19::chr17:40913145..40913205,+	p2@RAMP2
Hg19::chr17:40913210..40913221,+	p3@RAMP2
Hg19::chr17:40913222..40913233,+	p4@RAMP2
Hg19::chr17:40913236..40913252,+	p1@RAMP2
Hg19::chr17:40913264..40913273,+	p6@RAMP2
Hg19::chr17:72966776..72966789,+	p@chr17:72966776..72966789 +

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	6.63e-12	24
endothelial cell	1.02e-11	35
meso-epithelial cell	9.37e-11	44
lining cell	9.01e-10	57
barrier cell	9.01e-10	57
blood vessel endothelial cell	1.04e-08	18
embryonic blood vessel endothelial progenitor cell	1.04e-08	18

Uber Anatomy

Ontology term	p-value	n
adult organism	3.32e-31	115
anatomical conduit	3.00e-24	241
tube	1.16e-23	194
cell layer	2.80e-21	312
epithelium	4.81e-21	309
anatomical cluster	6.72e-21	286
regional part of nervous system	5.06e-17	94
nervous system	5.06e-17	94
neurectoderm	2.60e-15	90
central nervous system	3.47e-15	82
multi-cellular organism	2.22e-14	659
neural tube	2.62e-14	57
neural rod	2.62e-14	57
future spinal cord	2.62e-14	57
neural keel	2.62e-14	57
neural plate	4.15e-14	86
presumptive neural plate	4.15e-14	86
brain	5.83e-12	69
future brain	5.83e-12	69
regional part of brain	6.53e-12	59
epithelial tube	6.97e-12	118
anterior neural tube	1.90e-11	42
organism subdivision	3.87e-11	365
regional part of forebrain	6.65e-11	41
forebrain	6.65e-11	41
future forebrain	6.65e-11	41
anatomical system	7.99e-11	625
anatomical group	1.02e-10	626
multi-tissue structure	1.85e-10	347
pre-chordal neural plate	6.13e-10	61
embryo	8.01e-10	612
telencephalon	1.17e-09	34
splanchnic layer of lateral plate mesoderm	1.86e-09	84
gray matter	2.32e-09	34
brain grey matter	2.32e-09	34
regional part of telencephalon	2.67e-09	33
ectoderm	4.66e-09	173
presumptive ectoderm	4.66e-09	173
cerebral hemisphere	5.50e-09	32
organ part	8.65e-09	219
vessel	9.21e-09	69
endothelium	1.04e-08	18
blood vessel endothelium	1.04e-08	18
cardiovascular system endothelium	1.04e-08	18
embryonic structure	2.52e-08	605
developing anatomical structure	2.52e-08	605
ectoderm-derived structure	3.22e-08	169
vasculature	4.58e-08	79
vascular system	4.58e-08	79
germ layer	5.03e-08	604
embryonic tissue	5.03e-08	604
presumptive structure	5.03e-08	604
epiblast (generic)	5.03e-08	604
compound organ	7.49e-08	69
regional part of cerebral cortex	8.30e-08	22
neocortex	2.67e-07	20
cerebral cortex	3.71e-07	25
pallium	3.71e-07	25
blood vessel	3.82e-07	60
epithelial tube open at both ends	3.82e-07	60
blood vasculature	3.82e-07	60
vascular cord	3.82e-07	60
anterior region of body	4.57e-07	129
craniocervical region	4.57e-07	129

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	4	3.57350424871668	0.0131663500723851	0.0466065765730013
REST#5978	5	8.04169059677335	6.54774545315482e-05	0.00106186333444416
USF1#7391	5	5.3012493976733	0.000500332754985889	0.00441224796064944

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.