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Coexpression cluster:C712: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;7:3.1268162176271:0.00257034513840731:0.0142199531682446
|tf_chipseq_enrich=CTCF#10664;7:3.1268162176271:0.00257034513840731:0.0142199531682446
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}}
}}

Revision as of 14:25, 26 November 2012


Full id: C712_thymus_biphenotypic_CD4_non_granulocyte_merkel_acute



Phase1 CAGE Peaks

Hg19::chr3:18480105..18480108,-p48@SATB1
Hg19::chr3:18480151..18480162,-p18@SATB1
Hg19::chr3:18480173..18480189,-p6@SATB1
Hg19::chr3:18486202..18486209,-p5@TBC1D5
Hg19::chr3:18486296..18486319,-p3@TBC1D5
Hg19::chr3:18486324..18486338,-p4@TBC1D5
Hg19::chr3:18486354..18486377,-p2@SATB1
Hg19::chr3:18486459..18486481,+p2@ENST00000414198
Hg19::chr3:18486486..18486500,+p1@ENST00000414198
Hg19::chr3:18487033..18487044,-p23@SATB1
Hg19::chr3:18487057..18487105,-p4@SATB1
Hg19::chr8:66754259..66754276,-p2@PDE7A


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:00041153',5'-cyclic-AMP phosphodiesterase activity0.0284167707669588
GO:0016571histone methylation0.0284167707669588
GO:0005720nuclear heterochromatin0.0284167707669588
GO:0000792heterochromatin0.0284167707669588
GO:0008213protein amino acid alkylation0.0284167707669588
GO:0006479protein amino acid methylation0.0284167707669588
GO:0000790nuclear chromatin0.0284167707669588
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0360071200977271
GO:0043414biopolymer methylation0.0360071200977271
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0360071200977271
GO:0016570histone modification0.0360071200977271
GO:0016569covalent chromatin modification0.0360071200977271
GO:0044454nuclear chromosome part0.0444142842183568
GO:0032259methylation0.0444142842183568



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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell8.80e-36168
angioblastic mesenchymal cell8.80e-36168
hematopoietic cell2.16e-34177
hematopoietic oligopotent progenitor cell6.27e-31161
hematopoietic multipotent progenitor cell6.27e-31161
leukocyte5.82e-28136
nongranular leukocyte1.66e-26115
lymphoid lineage restricted progenitor cell4.62e-2552
lymphocyte2.86e-2453
common lymphoid progenitor2.86e-2453
hematopoietic lineage restricted progenitor cell3.02e-23120
nucleate cell8.87e-2355
T cell4.51e-2125
pro-T cell4.51e-2125
mature alpha-beta T cell1.77e-1818
alpha-beta T cell1.77e-1818
immature T cell1.77e-1818
mature T cell1.77e-1818
immature alpha-beta T cell1.77e-1818
CD8-positive, alpha-beta T cell4.57e-1211
myeloid cell2.04e-10108
common myeloid progenitor2.04e-10108
B cell1.42e-0914
CD4-positive, alpha-beta T cell2.41e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.04e-1398
blood island6.04e-1398
blood2.29e-1215
haemolymphatic fluid2.29e-1215
organism substance2.29e-1215
hemolymphoid system9.84e-12108
neocortex4.60e-0920
adult organism6.34e-09114
regional part of cerebral cortex8.11e-0922
cerebral cortex3.55e-0725
pallium3.55e-0725
Disease
Ontology termp-valuen
hematologic cancer2.29e-1151
immune system cancer2.29e-1151
leukemia1.62e-1039
myeloid leukemia3.30e-0931


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
CTCF#1066473.12681621762710.002570345138407310.0142199531682446



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.