Coexpression cluster:C1137

Full id: C1137_CD4_CD8_thymus_Natural_blood_Whole_Peripheral

Phase1 CAGE Peaks

Hg19::chr11:14671615..14671618,+	p@chr11:14671615..14671618 +
Hg19::chr14:105944163..105944184,+	p@chr14:105944163..105944184 +
Hg19::chr14:22265481..22265487,+	p5@TRAV8-1
Hg19::chr4:109088233..109088240,-	p62@LEF1
Hg19::chr5:133449741..133449744,-	p@chr5:133449741..133449744 -
Hg19::chr7:142021271..142021284,+	p1@AF020656 p1@AF325867 p1@AF395795 p1@AY611551 p1@AY751843 p1@AY751887 p1@AY751915 p1@EF592002 p1@GQ502881 p1@GQ502883 p1@HM236508 p1@HM236510 p1@HM236512 p1@HM236514 p1@HM236515 p1@HM236544 p1@HM236615 p1@HM236635 p1@HM236642 p1@HM236659 p1@HM236662 p1@HM236673 p1@HM236674 p1@HM236676 p1@HM236718 p1@HM236776 p1@HM236777 p1@HM236807 p1@HM467843 p1@HM467856 p1@HM467875 p1@HM467876 p1@HM467877 p1@HM467878 p1@JF731146 p1@JF731148 p1@JF731150
Hg19::chrX:11776810..11776821,+	p17@MSL3

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	0.00376780878370423
GO:0021766	hippocampus development	0.00376780878370423
GO:0048341	paraxial mesoderm formation	0.00376780878370423
GO:0048340	paraxial mesoderm morphogenesis	0.00376780878370423
GO:0048339	paraxial mesoderm development	0.00376780878370423
GO:0021543	pallium development	0.00376780878370423
GO:0021761	limbic system development	0.00376780878370423
GO:0045843	negative regulation of striated muscle development	0.00376780878370423
GO:0008301	DNA bending activity	0.00397713149391001
GO:0021537	telencephalon development	0.00397713149391001
GO:0016202	regulation of striated muscle development	0.00397713149391001
GO:0030879	mammary gland development	0.00397713149391001
GO:0001890	placenta development	0.00397713149391001
GO:0001707	mesoderm formation	0.00397713149391001
GO:0048332	mesoderm morphogenesis	0.00397713149391001
GO:0001704	formation of primary germ layer	0.00397713149391001
GO:0001756	somitogenesis	0.00397713149391001
GO:0042475	odontogenesis of dentine-containing teeth	0.00397713149391001
GO:0042476	odontogenesis	0.00442307987652235
GO:0007369	gastrulation	0.00442307987652235
GO:0035282	segmentation	0.00442307987652235
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.00442307987652235
GO:0030111	regulation of Wnt receptor signaling pathway	0.00442307987652235
GO:0030326	embryonic limb morphogenesis	0.00480720431024332
GO:0035113	embryonic appendage morphogenesis	0.00480720431024332
GO:0060173	limb development	0.00480720431024332
GO:0035107	appendage morphogenesis	0.00480720431024332
GO:0035108	limb morphogenesis	0.00480720431024332
GO:0048736	appendage development	0.00480720431024332
GO:0007498	mesoderm development	0.00541622512657482
GO:0030900	forebrain development	0.00541622512657482
GO:0048732	gland development	0.00541622512657482
GO:0009952	anterior/posterior pattern formation	0.00627968130617371
GO:0048729	tissue morphogenesis	0.00797888918902071
GO:0003002	regionalization	0.00917799575517696
GO:0014706	striated muscle development	0.00917799575517696
GO:0048598	embryonic morphogenesis	0.00917799575517696
GO:0009792	embryonic development ending in birth or egg hatching	0.00917799575517696
GO:0043009	chordate embryonic development	0.00917799575517696
GO:0003682	chromatin binding	0.0111150359119275
GO:0007389	pattern specification process	0.011393136084058
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.011393136084058
GO:0007420	brain development	0.0119028504757929
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0119028504757929
GO:0016055	Wnt receptor signaling pathway	0.0121407171919358
GO:0048646	anatomical structure formation	0.0125320596501467
GO:0007517	muscle development	0.0137885768254708
GO:0045892	negative regulation of transcription, DNA-dependent	0.0159346913144158
GO:0005667	transcription factor complex	0.016147751930161
GO:0045893	positive regulation of transcription, DNA-dependent	0.0168044271753208
GO:0007417	central nervous system development	0.0170275973878941
GO:0009790	embryonic development	0.0170275973878941
GO:0003702	RNA polymerase II transcription factor activity	0.0194670120491385
GO:0045941	positive regulation of transcription	0.0194670120491385
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0195791492153202
GO:0016481	negative regulation of transcription	0.0195791492153202
GO:0009888	tissue development	0.0200733261062863
GO:0016563	transcription activator activity	0.0200733261062863
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.020371711898333
GO:0009887	organ morphogenesis	0.0225450853451154
GO:0031325	positive regulation of cellular metabolic process	0.0225450853451154
GO:0031324	negative regulation of cellular metabolic process	0.0231537926869566
GO:0009893	positive regulation of metabolic process	0.0233843370544183
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0249028611797951
GO:0009892	negative regulation of metabolic process	0.0252733019953083
GO:0044451	nucleoplasm part	0.0258037813671865
GO:0005654	nucleoplasm	0.0291864590857088
GO:0006366	transcription from RNA polymerase II promoter	0.0354617297289809
GO:0031981	nuclear lumen	0.0376780878370422
GO:0007399	nervous system development	0.0385393012733175
GO:0009966	regulation of signal transduction	0.0424541834783575
GO:0043565	sequence-specific DNA binding	0.0456323508248623
GO:0048522	positive regulation of cellular process	0.0487805643863574
GO:0031974	membrane-enclosed lumen	0.0487805643863574
GO:0043233	organelle lumen	0.0487805643863574

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	3.14e-46	18
alpha-beta T cell	3.14e-46	18
immature T cell	3.14e-46	18
mature T cell	3.14e-46	18
immature alpha-beta T cell	3.14e-46	18
T cell	4.82e-37	25
pro-T cell	4.82e-37	25
CD4-positive, alpha-beta T cell	4.46e-27	6
CD8-positive, alpha-beta T cell	5.27e-25	11
lymphoid lineage restricted progenitor cell	8.81e-24	52
lymphocyte	2.99e-23	53
common lymphoid progenitor	2.99e-23	53
nucleate cell	3.00e-22	55
natural killer cell	2.20e-14	3
pro-NK cell	2.20e-14	3
naive T cell	3.60e-14	3
single nucleate cell	2.00e-13	3
mononuclear cell	2.00e-13	3
nongranular leukocyte	2.47e-13	115
leukocyte	5.98e-13	136
regulatory T cell	6.88e-10	2
CD4-positive, CD25-positive, alpha-beta regulatory T cell	6.88e-10	2
naive regulatory T cell	6.88e-10	2
hematopoietic stem cell	1.82e-09	168
angioblastic mesenchymal cell	1.82e-09	168
hematopoietic lineage restricted progenitor cell	6.40e-09	120
hematopoietic cell	1.02e-08	177
hematopoietic oligopotent progenitor cell	3.05e-07	161
hematopoietic multipotent progenitor cell	3.05e-07	161
circulating cell	6.10e-07	6

Uber Anatomy

Ontology term	p-value	n
thymus	5.61e-11	4
hemolymphoid system gland	5.61e-11	4
thymic region	5.61e-11	4
pharyngeal gland	5.61e-11	4
thymus primordium	5.61e-11	4
pharyngeal epithelium	1.88e-07	6
chordate pharynx	2.69e-07	10
pharyngeal region of foregut	2.69e-07	10
blood	5.79e-07	15
haemolymphatic fluid	5.79e-07	15
organism substance	5.79e-07	15

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.