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Coexpression cluster:C1996: Difference between revisions

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|tf_chipseq_enrich=CTCFL#140690;5:19.7464743589744:3.32745051287657e-07:1.66037077933262e-05!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0140052649631946
|tf_chipseq_enrich=CTCFL#140690;5:19.7464743589744:3.32745051287657e-07:1.66037077933262e-05!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0140052649631946
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}}
}}

Revision as of 15:14, 26 November 2012


Full id: C1996_Natural_CD8_NK_CD4_Peripheral_blood_Whole



Phase1 CAGE Peaks

Hg19::chr7:38357069..38357141,-p1@TARP
Hg19::chr7:38357145..38357165,-p6@TARP
Hg19::chr7:38357177..38357188,-p8@TARP
Hg19::chr7:38357258..38357299,-p2@TARP
Hg19::chr7:38375259..38375289,-p2@uc010kxk.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


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:0042605peptide antigen binding0.0050777110561639
GO:0042287MHC protein binding0.0050777110561639
GO:0003823antigen binding0.0229600847756976
GO:0042277peptide binding0.0229600847756976



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
CD8-positive, alpha-beta T cell1.31e-2011
mature alpha-beta T cell2.21e-1618
alpha-beta T cell2.21e-1618
immature T cell2.21e-1618
mature T cell2.21e-1618
immature alpha-beta T cell2.21e-1618
hematopoietic stem cell2.05e-14168
angioblastic mesenchymal cell2.05e-14168
T cell3.34e-1425
pro-T cell3.34e-1425
hematopoietic cell5.76e-13177
leukocyte1.36e-12136
nongranular leukocyte3.57e-12115
hematopoietic oligopotent progenitor cell3.89e-12161
hematopoietic multipotent progenitor cell3.89e-12161
hematopoietic lineage restricted progenitor cell2.39e-09120
lymphoid lineage restricted progenitor cell1.46e-0852
lymphocyte2.65e-0853
common lymphoid progenitor2.65e-0853
nucleate cell8.17e-0855
natural killer cell4.34e-073
pro-NK cell4.34e-073
single nucleate cell6.60e-073
mononuclear cell6.60e-073
basophil9.44e-073
Uber Anatomy
Ontology termp-valuen
adult organism1.12e-17114
blood2.08e-1715
haemolymphatic fluid2.08e-1715
organism substance2.08e-1715
hematopoietic system9.03e-1598
blood island9.03e-1598
hemolymphoid system2.26e-14108
hemopoietic organ1.03e-097
immune organ1.03e-097
thymus2.51e-084
hemolymphoid system gland2.51e-084
thymic region2.51e-084
pharyngeal gland2.51e-084
thymus primordium2.51e-084


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)

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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
CTCFL#140690519.74647435897443.32745051287657e-071.66037077933262e-05
MAX#414945.16204440720570.002526309009485180.0140052649631946



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.