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Difference between revisions of "Coexpression cluster:C1199"

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|tf_chipseq_enrich=BATF#10538;4:13.9187438813164:8.99003089381936e-05:0.00131242638596533!NR3C1#2908;4:8.55601333209888:0.000590591852092926:0.00494435450426718!PAX5#5079;4:3.81118030353019:0.0120826168155519:0.0438280222839477!POU2F2#5452;4:5.20349946156716:0.00386671431017981:0.0190650446530483!TRIM28#10155;4:10.6231571687214:0.000256730100512827:0.00276248042112705
 
|tf_chipseq_enrich=BATF#10538;4:13.9187438813164:8.99003089381936e-05:0.00131242638596533!NR3C1#2908;4:8.55601333209888:0.000590591852092926:0.00494435450426718!PAX5#5079;4:3.81118030353019:0.0120826168155519:0.0438280222839477!POU2F2#5452;4:5.20349946156716:0.00386671431017981:0.0190650446530483!TRIM28#10155;4:10.6231571687214:0.000256730100512827:0.00276248042112705
 
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 +
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}}
 
}}

Revision as of 05:44, 26 November 2012


Full id: C1199_CD4_Natural_CD8_Basophils_Peripheral_mycosis_cord



Phase1 CAGE Peaks

Hg19::chr14:53619091..53619109,-p2@DDHD1
Hg19::chr1:108329128..108329139,-p@chr1:108329128..108329139
-
Hg19::chr1:25255763..25255774,-p10@RUNX3
Hg19::chr6:106546731..106546755,+p5@PRDM1
Hg19::chr6:106546786..106546802,+p6@PRDM1
Hg19::chr6:106546808..106546833,+p3@PRDM1
Hg19::chr6:106546871..106546878,+p17@PRDM1


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:0006366transcription from RNA polymerase II promoter0.0450225075370137
GO:0050680negative regulation of epithelial cell proliferation0.0450225075370137



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
nongranular leukocyte6.00e-23115
leukocyte1.32e-21136
mature alpha-beta T cell3.40e-2118
alpha-beta T cell3.40e-2118
immature T cell3.40e-2118
mature T cell3.40e-2118
immature alpha-beta T cell3.40e-2118
T cell1.08e-2025
pro-T cell1.08e-2025
lymphoid lineage restricted progenitor cell4.31e-2052
lymphocyte1.81e-1953
common lymphoid progenitor1.81e-1953
nucleate cell2.71e-1855
hematopoietic lineage restricted progenitor cell6.09e-18120
CD8-positive, alpha-beta T cell6.22e-1411
hematopoietic cell9.87e-14177
hematopoietic stem cell2.17e-13168
angioblastic mesenchymal cell2.17e-13168
hematopoietic oligopotent progenitor cell1.52e-12161
hematopoietic multipotent progenitor cell1.52e-12161
CD4-positive, alpha-beta T cell1.81e-086
circulating cell7.92e-086
classical monocyte3.95e-0742
CD14-positive, CD16-negative classical monocyte3.95e-0742
Uber Anatomy
Ontology termp-valuen
blood5.90e-1415
haemolymphatic fluid5.90e-1415
organism substance5.90e-1415
adult organism8.64e-13114
hematopoietic system1.20e-1198
blood island1.20e-1198
hemolymphoid system1.01e-10108


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#10538413.91874388131648.99003089381936e-050.00131242638596533
NR3C1#290848.556013332098880.0005905918520929260.00494435450426718
PAX5#507943.811180303530190.01208261681555190.0438280222839477
POU2F2#545245.203499461567160.003866714310179810.0190650446530483
TRIM28#10155410.62315716872140.0002567301005128270.00276248042112705



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.