Coexpression cluster:C595

Full id: C595_teratocarcinoma_HES3GFP_H9_testicular_Wilms_hepatoblastoma_neuroblastoma

Phase1 CAGE Peaks

Hg19::chr12:75760714..75760729,+	p1@GLIPR1L1
Hg19::chr15:75052999..75053003,-	p@chr15:75052999..75053003 -
Hg19::chr18:11261018..11261023,-	p@chr18:11261018..11261023 -
Hg19::chr1:63220075..63220077,+	p@chr1:63220075..63220077 +
Hg19::chr22:35029651..35029657,-	p@chr22:35029651..35029657 -
Hg19::chr22:35029659..35029670,-	p@chr22:35029659..35029670 -
Hg19::chr6:10417399..10417415,-	p32@TFAP2A
Hg19::chr6:10417454..10417460,-	p40@TFAP2A
Hg19::chr6:3222149..3222154,+	p@chr6:3222149..3222154 +
Hg19::chr8:70963473..70963506,-	p@chr8:70963473..70963506 -
Hg19::chrX:136648643..136648711,+	p2@ZIC3
Hg19::chrX:136648735..136648747,+	p9@ZIC3
Hg19::chrX:136648753..136648767,+	p5@ZIC3
Hg19::chrX:136648768..136648781,+	p6@ZIC3
Hg19::chrX:136648807..136648822,+	p8@ZIC3

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:0009855	determination of bilateral symmetry	0.0312453970958568
GO:0009799	determination of symmetry	0.0312453970958568
GO:0007368	determination of left/right symmetry	0.0312453970958568
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0351417582722758

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
neurectodermal cell	2.11e-12	59
epithelial cell	2.72e-12	254
migratory neural crest cell	4.91e-11	41
ectodermal cell	1.79e-10	71
neural cell	1.81e-10	25
glial cell (sensu Vertebrata)	8.15e-08	15
glial cell	8.15e-08	15
glioblast	8.15e-08	15
glioblast (sensu Vertebrata)	8.15e-08	15
neuron associated cell	8.39e-08	17
neuron associated cell (sensu Vertebrata)	8.39e-08	17

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	2.82e-20	94
nervous system	2.82e-20	94
central nervous system	1.01e-16	82
ectoderm	3.45e-15	173
presumptive ectoderm	3.45e-15	173
ectoderm-derived structure	2.26e-14	169
brain	2.27e-12	69
future brain	2.27e-12	69
neurectoderm	5.55e-12	90
neural plate	3.57e-11	86
presumptive neural plate	3.57e-11	86
neural tube	1.55e-09	57
neural rod	1.55e-09	57
future spinal cord	1.55e-09	57
neural keel	1.55e-09	57
regional part of brain	7.53e-09	59
head	1.54e-08	123
anterior region of body	5.43e-08	129
craniocervical region	5.43e-08	129
posterior neural tube	5.87e-08	15
chordal neural plate	5.87e-08	15
segmental subdivision of nervous system	3.50e-07	13
pre-chordal neural plate	9.67e-07	61

Disease

Ontology term	p-value	n
cancer	3.43e-35	235
disease of cellular proliferation	1.40e-34	239
cell type cancer	4.83e-28	143
carcinoma	3.72e-19	106
organ system cancer	4.26e-12	137
germ cell and embryonal cancer	9.69e-10	22
germ cell cancer	9.69e-10	22

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
BCL3#602	3	6.90942056074766	0.00849511918490356	0.0324265104547401
POU5F1#5460	2	44.7252268602541	0.000907821130234052	0.00660848477176512

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.