Coexpression cluster:C3157

Full id: C3157_cerebellum_smooth_ductus_occipital_bladder_brain_heart

Phase1 CAGE Peaks

Hg19::chr11:47546146..47546156,-	p34@CELF1
Hg19::chr11:47546176..47546188,-	p10@CELF1
Hg19::chr22:41763408..41763417,+	p5@TEF

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:0003690	double-stranded DNA binding	0.0487681031437654
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0487681031437654
GO:0043566	structure-specific DNA binding	0.0487681031437654
GO:0045893	positive regulation of transcription, DNA-dependent	0.0487681031437654
GO:0003702	RNA polymerase II transcription factor activity	0.0487681031437654
GO:0045941	positive regulation of transcription	0.0487681031437654
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0487681031437654
GO:0016563	transcription activator activity	0.0487681031437654
GO:0031325	positive regulation of cellular metabolic process	0.0487681031437654
GO:0046983	protein dimerization activity	0.0487681031437654
GO:0009893	positive regulation of metabolic process	0.0487681031437654
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0487681031437654

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	7.79e-65	114
neural tube	5.46e-30	56
neural rod	5.46e-30	56
future spinal cord	5.46e-30	56
neural keel	5.46e-30	56
regional part of nervous system	1.01e-29	53
regional part of brain	1.01e-29	53
brain	5.96e-25	68
future brain	5.96e-25	68
central nervous system	8.97e-25	81
telencephalon	1.45e-24	34
cerebral hemisphere	8.06e-24	32
regional part of forebrain	9.55e-24	41
forebrain	9.55e-24	41
anterior neural tube	9.55e-24	41
future forebrain	9.55e-24	41
regional part of cerebral cortex	1.59e-22	22
neocortex	5.08e-22	20
nervous system	2.04e-21	89
regional part of telencephalon	3.60e-21	32
neural plate	6.47e-21	82
presumptive neural plate	6.47e-21	82
brain grey matter	1.15e-19	34
gray matter	1.15e-19	34
neurectoderm	1.51e-19	86
cerebral cortex	1.94e-19	25
pallium	1.94e-19	25
structure with developmental contribution from neural crest	6.76e-16	132
pre-chordal neural plate	1.53e-15	61
ecto-epithelium	1.01e-14	104
organ system subdivision	2.29e-11	223
gyrus	2.86e-11	6
ectoderm-derived structure	5.10e-10	171
ectoderm	5.10e-10	171
presumptive ectoderm	5.10e-10	171
temporal lobe	2.98e-09	6
male genital duct	1.28e-08	3
internal male genitalia	1.28e-08	3
anatomical cluster	2.35e-08	373
anatomical conduit	5.12e-08	240
posterior neural tube	1.83e-07	15
chordal neural plate	1.83e-07	15
tube	2.28e-07	192
segmental subdivision of hindbrain	3.41e-07	12
hindbrain	3.41e-07	12
presumptive hindbrain	3.41e-07	12
organ	7.13e-07	503
multi-tissue structure	7.42e-07	342

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
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108966159335484

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.