Coexpression cluster:C1213

Full id: C1213_thymus_Dendritic_CD4_non_chronic_vein_CD133

Phase1 CAGE Peaks

Hg19::chr15:78466862..78466878,-	p4@ACSBG1
Hg19::chr17:37322317..37322337,-	p2@ARL5C
Hg19::chr18:13218882..13218893,+	p8@C18orf1
Hg19::chr19:4302375..4302406,-	p1@TMIGD2
Hg19::chr3:35683620..35683628,+	p49@ARPP21
Hg19::chr6:138189241..138189298,-	p1@uc003qhq.1
Hg19::chr6:138189307..138189329,-	p3@uc003qhq.1

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:0031957	very-long-chain-fatty-acid-CoA ligase activity	0.00362062875309078
GO:0001676	long-chain fatty acid metabolic process	0.00723933921700654
GO:0000038	very-long-chain fatty acid metabolic process	0.00723933921700654
GO:0004467	long-chain-fatty-acid-CoA ligase activity	0.00723933921700654
GO:0015645	fatty-acid ligase activity	0.00723933921700654
GO:0042552	myelination	0.0128616026527903
GO:0016877	ligase activity, forming carbon-sulfur bonds	0.0128616026527903
GO:0008366	axon ensheathment	0.0128616026527903
GO:0007272	ensheathment of neurons	0.0128616026527903
GO:0001508	regulation of action potential	0.0144658947339719

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
mature alpha-beta T cell	4.07e-20	18
alpha-beta T cell	4.07e-20	18
immature T cell	4.07e-20	18
mature T cell	4.07e-20	18
immature alpha-beta T cell	4.07e-20	18
CD4-positive, alpha-beta T cell	8.00e-17	6
T cell	2.87e-16	25
pro-T cell	2.87e-16	25
lymphoid lineage restricted progenitor cell	3.39e-11	52
lymphocyte	6.63e-11	53
common lymphoid progenitor	6.63e-11	53
nucleate cell	2.35e-10	55
plasmacytoid dendritic cell	4.07e-10	3
single nucleate cell	1.66e-09	3
mononuclear cell	1.66e-09	3
naive T cell	3.08e-09	3
CD8-positive, alpha-beta T cell	1.13e-08	11
leukocyte	3.85e-07	136
nongranular leukocyte	7.91e-07	115

Uber Anatomy

Ontology term	p-value	n
adult organism	8.81e-08	114
thymus	1.69e-07	4
hemolymphoid system gland	1.69e-07	4
thymic region	1.69e-07	4
pharyngeal gland	1.69e-07	4
thymus primordium	1.69e-07	4
hemopoietic organ	4.53e-07	7
immune organ	4.53e-07	7

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
WRNIP1#56897	2	31.3771326712503	0.00168816337205727	0.0105492786701544

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.