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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.25e-14!102;UBERON:0003061!2.25e-14!102;UBERON:0002193!1.69e-13!112;UBERON:0000178!6.46e-10!15;UBERON:0000179!6.46e-10!15;UBERON:0000463!6.46e-10!15;UBERON:0002371!8.24e-07!80
|ontology_enrichment_uberon=UBERON:0002390!2.25e-14!102;UBERON:0003061!2.25e-14!102;UBERON:0002193!1.69e-13!112;UBERON:0000178!6.46e-10!15;UBERON:0000179!6.46e-10!15;UBERON:0000463!6.46e-10!15;UBERON:0002371!8.24e-07!80
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}}
}}

Revision as of 16:55, 8 August 2012


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

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

GO IDGO nameFDR corrected p-value
GO:0021542dentate gyrus development0.00376780878370423
GO:0021766hippocampus development0.00376780878370423
GO:0048341paraxial mesoderm formation0.00376780878370423
GO:0048340paraxial mesoderm morphogenesis0.00376780878370423
GO:0048339paraxial mesoderm development0.00376780878370423
GO:0021543pallium development0.00376780878370423
GO:0021761limbic system development0.00376780878370423
GO:0045843negative regulation of striated muscle development0.00376780878370423
GO:0008301DNA bending activity0.00397713149391001
GO:0021537telencephalon development0.00397713149391001
GO:0016202regulation of striated muscle development0.00397713149391001
GO:0030879mammary gland development0.00397713149391001
GO:0001890placenta development0.00397713149391001
GO:0001707mesoderm formation0.00397713149391001
GO:0048332mesoderm morphogenesis0.00397713149391001
GO:0001704formation of primary germ layer0.00397713149391001
GO:0001756somitogenesis0.00397713149391001
GO:0042475odontogenesis of dentine-containing teeth0.00397713149391001
GO:0042476odontogenesis0.00442307987652235
GO:0007369gastrulation0.00442307987652235
GO:0035282segmentation0.00442307987652235
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.00442307987652235
GO:0030111regulation of Wnt receptor signaling pathway0.00442307987652235
GO:0030326embryonic limb morphogenesis0.00480720431024332
GO:0035113embryonic appendage morphogenesis0.00480720431024332
GO:0060173limb development0.00480720431024332
GO:0035107appendage morphogenesis0.00480720431024332
GO:0035108limb morphogenesis0.00480720431024332
GO:0048736appendage development0.00480720431024332
GO:0007498mesoderm development0.00541622512657482
GO:0030900forebrain development0.00541622512657482
GO:0048732gland development0.00541622512657482
GO:0009952anterior/posterior pattern formation0.00627968130617371
GO:0048729tissue morphogenesis0.00797888918902071
GO:0003002regionalization0.00917799575517696
GO:0014706striated muscle development0.00917799575517696
GO:0048598embryonic morphogenesis0.00917799575517696
GO:0009792embryonic development ending in birth or egg hatching0.00917799575517696
GO:0043009chordate embryonic development0.00917799575517696
GO:0003682chromatin binding0.0111150359119275
GO:0007389pattern specification process0.011393136084058
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.011393136084058
GO:0007420brain development0.0119028504757929
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0119028504757929
GO:0016055Wnt receptor signaling pathway0.0121407171919358
GO:0048646anatomical structure formation0.0125320596501467
GO:0007517muscle development0.0137885768254708
GO:0045892negative regulation of transcription, DNA-dependent0.0159346913144158
GO:0005667transcription factor complex0.016147751930161
GO:0045893positive regulation of transcription, DNA-dependent0.0168044271753208
GO:0007417central nervous system development0.0170275973878941
GO:0009790embryonic development0.0170275973878941
GO:0003702RNA polymerase II transcription factor activity0.0194670120491385
GO:0045941positive regulation of transcription0.0194670120491385
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0195791492153202
GO:0016481negative regulation of transcription0.0195791492153202
GO:0009888tissue development0.0200733261062863
GO:0016563transcription activator activity0.0200733261062863
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.020371711898333
GO:0009887organ morphogenesis0.0225450853451154
GO:0031325positive regulation of cellular metabolic process0.0225450853451154
GO:0031324negative regulation of cellular metabolic process0.0231537926869566
GO:0009893positive regulation of metabolic process0.0233843370544183
GO:0006357regulation of transcription from RNA polymerase II promoter0.0249028611797951
GO:0009892negative regulation of metabolic process0.0252733019953083
GO:0044451nucleoplasm part0.0258037813671865
GO:0005654nucleoplasm0.0291864590857088
GO:0006366transcription from RNA polymerase II promoter0.0354617297289809
GO:0031981nuclear lumen0.0376780878370422
GO:0007399nervous system development0.0385393012733175
GO:0009966regulation of signal transduction0.0424541834783575
GO:0043565sequence-specific DNA binding0.0456323508248623
GO:0048522positive regulation of cellular process0.0487805643863574
GO:0031974membrane-enclosed lumen0.0487805643863574
GO:0043233organelle lumen0.0487805643863574



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>

Cell Type
Ontology termp-valuen
leukocyte1.23e-35140
nongranular leukocyte1.84e-33119
hematopoietic stem cell6.28e-30172
angioblastic mesenchymal cell6.28e-30172
hematopoietic lineage restricted progenitor cell5.09e-28124
hematopoietic cell9.22e-28182
hematopoietic oligopotent progenitor cell2.00e-26165
hematopoietic multipotent progenitor cell2.00e-26165
lymphocyte1.43e-2253
common lymphoid progenitor1.43e-2253
lymphoid lineage restricted progenitor cell5.03e-2252
T cell4.25e-1725
pro-T cell4.25e-1725
mature alpha-beta T cell8.30e-1718
alpha-beta T cell8.30e-1718
immature T cell8.30e-1718
mature T cell8.30e-1718
immature alpha-beta T cell8.30e-1718
CD14-positive, CD16-negative classical monocyte6.19e-1342
myeloid leukocyte1.54e-1276
classical monocyte2.72e-1245
CD8-positive, alpha-beta T cell4.11e-1211
monopoietic cell2.89e-1063
monocyte2.89e-1063
monoblast2.89e-1063
promonocyte2.89e-1063
macrophage dendritic cell progenitor1.34e-0965
myeloid lineage restricted progenitor cell2.39e-0970
granulocyte monocyte progenitor cell4.69e-0971
myeloid cell2.26e-08112
common myeloid progenitor2.26e-08112
CD4-positive, alpha-beta T cell9.56e-086
B cell1.40e-0714
intermediate monocyte1.45e-079
CD14-positive, CD16-positive monocyte1.45e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.25e-14102
blood island2.25e-14102
hemolymphoid system1.69e-13112
blood6.46e-1015
haemolymphatic fluid6.46e-1015
organism substance6.46e-1015
bone marrow8.24e-0780


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

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

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

This analysis result is provided for C0 - C305 clusters.

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