Coexpression cluster:C2686

Full id: C2686_Neural_Ciliary_Astrocyte_neuroblastoma_Lens_teratocarcinoma_Neurons

Phase1 CAGE Peaks

Hg19::chr2:210798655..210798664,+	p@chr2:210798655..210798664 +
Hg19::chr3:147657737..147657747,+	p2@ENST00000467198
Hg19::chr9:117880804..117880815,-	p4@TNC
Hg19::chr9:117880865..117880885,-	p3@TNC

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:0007528	neuromuscular junction development	0.00824208171435299
GO:0050808	synapse organization and biogenesis	0.00865418580007064
GO:0048741	skeletal muscle fiber development	0.00865418580007064
GO:0048747	muscle fiber development	0.00865418580007064
GO:0007519	skeletal muscle development	0.0090662898857883
GO:0005604	basement membrane	0.0090662898857883
GO:0043062	extracellular structure organization and biogenesis	0.0090662898857883
GO:0014706	striated muscle development	0.0090662898857883
GO:0044420	extracellular matrix part	0.0119968078286694
GO:0007517	muscle development	0.0141763805486871
GO:0005578	proteinaceous extracellular matrix	0.0315446945612964

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
neural cell	7.08e-09	25
non-terminally differentiated cell	4.91e-08	180
oligodendrocyte	1.45e-07	7
macroglial cell	1.45e-07	7
astrocyte	1.45e-07	7
oligodendrocyte precursor cell	1.45e-07	7
neurectodermal cell	6.37e-07	59

Uber Anatomy

Ontology term	p-value	n
central nervous system	5.95e-16	82
regional part of nervous system	1.24e-14	94
nervous system	1.24e-14	94
ectoderm	1.16e-12	173
presumptive ectoderm	1.16e-12	173
ectoderm-derived structure	6.94e-12	169
neurectoderm	3.36e-10	90
neural tube	5.55e-10	57
neural rod	5.55e-10	57
future spinal cord	5.55e-10	57
neural keel	5.55e-10	57
brain	7.66e-10	69
future brain	7.66e-10	69
neural plate	2.09e-09	86
presumptive neural plate	2.09e-09	86
regional part of brain	3.77e-09	59
head	1.10e-08	123
anterior region of body	1.72e-08	129
craniocervical region	1.72e-08	129
organism subdivision	7.52e-08	365

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
CTBP2#1488	2	31.3585001696641	0.00149267688204723	0.00954178485029567
ESR1#2099	2	15.3843016480772	0.00606557262969351	0.0268413346838083
NANOG#79923	2	14.6223892405063	0.00669875771536376	0.0284927733581036

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.