Coexpression cluster:C921

Full id: C921_chronic_thymus_CD4_acute_CD8_Hodgkin_Peripheral

Phase1 CAGE Peaks

Hg19::chr17:80085772..80085810,-	p@chr17:80085772..80085810 -
Hg19::chr2:128399902..128399934,-	p11@LIMS2
Hg19::chr4:108991916..108991933,-	p36@LEF1
Hg19::chr4:109086281..109086319,-	p9@LEF1
Hg19::chr4:109087872..109087881,-	p28@LEF1
Hg19::chr4:109088772..109088783,-	p40@LEF1
Hg19::chr4:109088814..109088831,-	p18@LEF1
Hg19::chr4:109088863..109088887,-	p24@LEF1
Hg19::chr4:109089515..109089523,-	p31@LEF1

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:0021542	dentate gyrus development	0.00812350064703412
GO:0021766	hippocampus development	0.00812350064703412
GO:0048341	paraxial mesoderm formation	0.00812350064703412
GO:0048340	paraxial mesoderm morphogenesis	0.00812350064703412
GO:0048339	paraxial mesoderm development	0.00812350064703412
GO:0021543	pallium development	0.00812350064703412
GO:0021761	limbic system development	0.00812350064703412
GO:0045843	negative regulation of striated muscle development	0.00812350064703412
GO:0008301	DNA bending activity	0.00857341781035285
GO:0021537	telencephalon development	0.00857341781035285
GO:0016202	regulation of striated muscle development	0.00857341781035285
GO:0030879	mammary gland development	0.00857341781035285
GO:0001890	placenta development	0.00857341781035285
GO:0001707	mesoderm formation	0.00857341781035285
GO:0048332	mesoderm morphogenesis	0.00857341781035285
GO:0001704	formation of primary germ layer	0.00857341781035285
GO:0001756	somitogenesis	0.00857341781035285
GO:0042475	odontogenesis of dentine-containing teeth	0.00857341781035285
GO:0042476	odontogenesis	0.00953361626905974
GO:0007369	gastrulation	0.00953361626905974
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.00953361626905974
GO:0035282	segmentation	0.00953361626905974
GO:0030111	regulation of Wnt receptor signaling pathway	0.00953361626905974
GO:0030326	embryonic limb morphogenesis	0.0103600419735333
GO:0035113	embryonic appendage morphogenesis	0.0103600419735333
GO:0060173	limb development	0.0103600419735333
GO:0035107	appendage morphogenesis	0.0103600419735333
GO:0035108	limb morphogenesis	0.0103600419735333
GO:0048736	appendage development	0.0103600419735333
GO:0007498	mesoderm development	0.0116710002566134
GO:0030900	forebrain development	0.0116710002566134
GO:0048732	gland development	0.0116710002566134
GO:0009952	anterior/posterior pattern formation	0.0135298008372182
GO:0048729	tissue morphogenesis	0.0171865009779544
GO:0003002	regionalization	0.0197626731549567
GO:0014706	striated muscle development	0.0197626731549567
GO:0048598	embryonic morphogenesis	0.0197626731549567
GO:0009792	embryonic development ending in birth or egg hatching	0.0197626731549567
GO:0043009	chordate embryonic development	0.0197626731549567
GO:0003682	chromatin binding	0.0239255239947893
GO:0007389	pattern specification process	0.0245208906358903
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0245208906358903
GO:0007420	brain development	0.0256133909633335
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0256133909633335
GO:0016055	Wnt receptor signaling pathway	0.0261229374633611
GO:0048646	anatomical structure formation	0.0269617993721472
GO:0007517	muscle development	0.0296567886776082
GO:0045892	negative regulation of transcription, DNA-dependent	0.0342570240448924
GO:0005667	transcription factor complex	0.034711482782422
GO:0045893	positive regulation of transcription, DNA-dependent	0.0361161499760726
GO:0007417	central nervous system development	0.0365893036118252
GO:0009790	embryonic development	0.0365893036118252
GO:0003702	RNA polymerase II transcription factor activity	0.0418039915144584
GO:0045941	positive regulation of transcription	0.0418039915144584
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0420373414030184
GO:0016481	negative regulation of transcription	0.0420373414030184
GO:0009888	tissue development	0.0430868950323471
GO:0016563	transcription activator activity	0.0430868950323471
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0437209074162008
GO:0009887	organ morphogenesis	0.0483523964577336
GO:0031325	positive regulation of cellular metabolic process	0.0483523964577336
GO:0031324	negative regulation of cellular metabolic process	0.0496461326225933

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
lymphocyte	1.50e-14	53
common lymphoid progenitor	1.50e-14	53
lymphoid lineage restricted progenitor cell	4.94e-14	52
hematopoietic cell	1.45e-13	182
hematopoietic stem cell	1.77e-13	172
angioblastic mesenchymal cell	1.77e-13	172
leukocyte	2.40e-13	140
nongranular leukocyte	9.30e-13	119
mature alpha-beta T cell	3.25e-12	18
alpha-beta T cell	3.25e-12	18
immature T cell	3.25e-12	18
mature T cell	3.25e-12	18
immature alpha-beta T cell	3.25e-12	18
T cell	8.15e-12	25
pro-T cell	8.15e-12	25
hematopoietic oligopotent progenitor cell	2.99e-11	165
hematopoietic multipotent progenitor cell	2.99e-11	165
hematopoietic lineage restricted progenitor cell	3.65e-10	124
CD8-positive, alpha-beta T cell	3.47e-09	11

Uber Anatomy

Ontology term	p-value	n
blood	6.23e-10	15
haemolymphatic fluid	6.23e-10	15
organism substance	6.23e-10	15
adult organism	9.19e-10	115

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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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.