Coexpression cluster:C2830

Full id: C2830_mature_Hepatocyte_mesenchymal_liver_pleomorphic_pancreas_chorionic

Phase1 CAGE Peaks

Hg19::chr5:78365455..78365489,+	p3@BHMT2
Hg19::chr5:78365536..78365543,+	p4@BHMT2
Hg19::chr5:78365545..78365572,+	p2@BHMT2
Hg19::chr7:150038704..150038758,-	p1@RARRES2

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:0047150	betaine-homocysteine S-methyltransferase activity	0.00185441379597977
GO:0008898	homocysteine S-methyltransferase activity	0.00185441379597977
GO:0008172	S-methyltransferase activity	0.00271948664090565
GO:0001523	retinoid metabolic process	0.00271948664090565
GO:0016101	diterpenoid metabolic process	0.00271948664090565
GO:0006721	terpenoid metabolic process	0.0028841766369992
GO:0006720	isoprenoid metabolic process	0.00794257461958667
GO:0019748	secondary metabolic process	0.00818429998071893
GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	0.0117988707879793
GO:0008168	methyltransferase activity	0.0311175964910053
GO:0016741	transferase activity, transferring one-carbon groups	0.0311175964910053

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
fat cell	4.73e-11	15
fibroblast	1.82e-07	76

Uber Anatomy

Ontology term	p-value	n
adult organism	6.77e-36	114
structure with developmental contribution from neural crest	6.42e-19	132
neural plate	1.57e-18	82
presumptive neural plate	1.57e-18	82
multi-tissue structure	1.95e-18	342
neurectoderm	1.78e-16	86
neural tube	2.06e-16	56
neural rod	2.06e-16	56
future spinal cord	2.06e-16	56
neural keel	2.06e-16	56
regional part of nervous system	2.54e-15	53
regional part of brain	2.54e-15	53
pre-chordal neural plate	4.79e-15	61
anatomical cluster	9.38e-14	373
regional part of forebrain	3.43e-13	41
forebrain	3.43e-13	41
anterior neural tube	3.43e-13	41
future forebrain	3.43e-13	41
cell layer	4.94e-13	309
epithelium	1.15e-12	306
brain	1.45e-12	68
future brain	1.45e-12	68
ecto-epithelium	2.52e-12	104
central nervous system	3.34e-12	81
multi-cellular organism	4.41e-12	656
nervous system	4.96e-12	89
tissue	8.85e-12	773
organ system subdivision	1.15e-11	223
anatomical system	1.59e-10	624
anatomical group	2.24e-10	625
brain grey matter	3.49e-10	34
gray matter	3.49e-10	34
organ	5.87e-10	503
telencephalon	6.28e-10	34
ectoderm-derived structure	7.07e-10	171
ectoderm	7.07e-10	171
presumptive ectoderm	7.07e-10	171
regional part of telencephalon	2.12e-09	32
cerebral hemisphere	2.30e-09	32
anatomical conduit	3.19e-09	240
organism subdivision	3.28e-09	264
tube	5.90e-09	192
mesenchyme	1.80e-08	160
entire embryonic mesenchyme	1.80e-08	160
liver	1.91e-07	19
digestive gland	1.91e-07	19
liver bud	1.91e-07	19
abdominal segment of trunk	3.12e-07	60
abdomen	3.12e-07	60
organ part	3.49e-07	218
trunk mesenchyme	7.23e-07	122
cerebral cortex	7.37e-07	25
pallium	7.37e-07	25

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
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323169309042788

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.