Coexpression cluster:C3230

Full id: C3230_skeletal_Whole_blood_tongue_heart_penis_left

Phase1 CAGE Peaks

Hg19::chr12:10865870..10865888,-	p6@CSDA
Hg19::chr12:10865922..10865934,-	p15@CSDA
Hg19::chr16:31581029..31581037,-	p1@CSDAP1

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:0009409	response to cold	0.0124808665960203
GO:0009266	response to temperature stimulus	0.0226215707052867
GO:0003714	transcription corepressor activity	0.0367739819347025
GO:0003690	double-stranded DNA binding	0.0367739819347025
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0367739819347025
GO:0043566	structure-specific DNA binding	0.0367739819347025
GO:0009628	response to abiotic stimulus	0.0367739819347025
GO:0045892	negative regulation of transcription, DNA-dependent	0.0370959090492824
GO:0016564	transcription repressor activity	0.0370959090492824
GO:0003702	RNA polymerase II transcription factor activity	0.038282658116639
GO:0016481	negative regulation of transcription	0.038282658116639
GO:0003712	transcription cofactor activity	0.038282658116639
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.038282658116639
GO:0031324	negative regulation of cellular metabolic process	0.0400121899695943
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0400121899695943
GO:0008134	transcription factor binding	0.0400121899695943
GO:0009892	negative regulation of metabolic process	0.0400121899695943

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
classical monocyte	5.80e-14	45
CD14-positive, CD16-negative classical monocyte	3.22e-13	42
epithelial cell	1.08e-09	254
squamous epithelial cell	1.63e-07	62
endothelial cell of vascular tree	3.85e-07	24
granulocyte monocyte progenitor cell	4.19e-07	71
macrophage dendritic cell progenitor	4.22e-07	65
myeloid lineage restricted progenitor cell	7.23e-07	70

Uber Anatomy

Ontology term	p-value	n
mesoderm	1.34e-21	448
mesoderm-derived structure	1.34e-21	448
presumptive mesoderm	1.34e-21	448
lateral plate mesoderm	1.24e-15	216
multi-cellular organism	2.92e-15	659
anatomical system	7.10e-13	625
anatomical group	1.04e-12	626
embryo	1.09e-11	612
circulatory system	4.56e-11	113
embryonic structure	9.13e-11	605
developing anatomical structure	9.13e-11	605
germ layer	9.40e-11	604
embryonic tissue	9.40e-11	604
presumptive structure	9.40e-11	604
epiblast (generic)	9.40e-11	604
cardiovascular system	7.73e-10	110
hemolymphoid system	4.19e-08	112
splanchnic layer of lateral plate mesoderm	7.64e-08	84
vessel	1.10e-07	69
musculoskeletal system	1.90e-07	167
hematopoietic system	3.77e-07	102
blood island	3.77e-07	102
blood vessel	6.69e-07	60
epithelial tube open at both ends	6.69e-07	60
blood vasculature	6.69e-07	60
vascular cord	6.69e-07	60

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)
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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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No analysis results for this cluster

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.