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Coexpression cluster:C3227: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;2:23.0314018691589:0.00246467476084291:0.0138488280705693!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460374688485564!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127700983677403!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268744475496719!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027566669591456!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108838806324879
|tf_chipseq_enrich=BCL3#602;2:23.0314018691589:0.00246467476084291:0.0138488280705693!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460374688485564!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127700983677403!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268744475496719!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027566669591456!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108838806324879
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}}
}}

Revision as of 16:00, 26 November 2012


Full id: C3227_Neutrophils_Whole_Reticulocytes_blood_Eosinophils_CD4_CD19



Phase1 CAGE Peaks

Hg19::chr12:106696583..106696651,+p1@TCP11L2
Hg19::chr15:43477580..43477656,+p1@CCNDBP1
Hg19::chr16:15736897..15736928,-p2@KIAA0430


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:0005777peroxisome0.0440896712647909
GO:0042579microbody0.0440896712647909



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
leukocyte4.45e-19136
hematopoietic lineage restricted progenitor cell1.28e-16120
nongranular leukocyte1.33e-15115
hematopoietic stem cell1.32e-13168
angioblastic mesenchymal cell1.32e-13168
hematopoietic oligopotent progenitor cell6.66e-13161
hematopoietic multipotent progenitor cell6.66e-13161
hematopoietic cell9.44e-12177
myeloid leukocyte1.09e-1172
mature alpha-beta T cell4.06e-1018
alpha-beta T cell4.06e-1018
immature T cell4.06e-1018
mature T cell4.06e-1018
immature alpha-beta T cell4.06e-1018
classical monocyte1.06e-0942
CD14-positive, CD16-negative classical monocyte1.06e-0942
myeloid lineage restricted progenitor cell3.62e-0966
defensive cell1.13e-0848
phagocyte1.13e-0848
nucleate cell1.40e-0855
lymphoid lineage restricted progenitor cell4.43e-0852
granulocyte monocyte progenitor cell9.07e-0867
macrophage dendritic cell progenitor1.03e-0761
monopoietic cell1.19e-0759
monocyte1.19e-0759
monoblast1.19e-0759
promonocyte1.19e-0759
lymphocyte1.21e-0753
common lymphoid progenitor1.21e-0753
CD8-positive, alpha-beta T cell9.24e-0711
Uber Anatomy
Ontology termp-valuen
adult organism7.18e-25114
hematopoietic system6.13e-1298
blood island6.13e-1298
hemolymphoid system6.65e-12108
immune system1.38e-0793
blood3.59e-0715
haemolymphatic fluid3.59e-0715
organism substance3.59e-0715


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
BCL3#602223.03140186915890.002464674760842910.0138488280705693
ELF1#199734.258097958807540.01295179875054610.0460374688485564
IRF1#365937.63716375356390.002244692747297240.0127700983677403
NFKB1#479035.488063424193840.006049381815655430.0268744475496719
SIN3A#2594235.408884726815140.006318961977991520.027566669591456
SPI1#668838.204323508522730.001810593189410520.0108838806324879



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.