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Coexpression cluster:C3828: Difference between revisions

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|tf_chipseq_enrich=NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324777693990716
|tf_chipseq_enrich=NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324777693990716
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}}
}}

Revision as of 16:22, 26 November 2012


Full id: C3828_Neutrophils_Whole_Eosinophils_CD8_CD4_Natural_small



Phase1 CAGE Peaks

Hg19::chr19:58326267..58326292,-p1@ZNF552
Hg19::chr3:36949995..36950042,-p1@TRANK1
Hg19::chr6:26402517..26402535,+p2@BTN3A1


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


No GOStat results

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
leukocyte4.77e-26136
hematopoietic lineage restricted progenitor cell1.52e-19120
nongranular leukocyte3.07e-19115
hematopoietic stem cell1.45e-16168
angioblastic mesenchymal cell1.45e-16168
nucleate cell5.75e-1655
lymphocyte1.10e-1553
common lymphoid progenitor1.10e-1553
lymphoid lineage restricted progenitor cell1.92e-1552
hematopoietic cell1.12e-14177
hematopoietic oligopotent progenitor cell1.56e-14161
hematopoietic multipotent progenitor cell1.56e-14161
mature alpha-beta T cell2.29e-1118
alpha-beta T cell2.29e-1118
immature T cell2.29e-1118
mature T cell2.29e-1118
immature alpha-beta T cell2.29e-1118
myeloid leukocyte8.35e-0972
T cell1.91e-0825
pro-T cell1.91e-0825
CD8-positive, alpha-beta T cell2.62e-0811
B cell4.03e-0714
lymphocyte of B lineage7.75e-0724
pro-B cell7.75e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.27e-1198
blood island6.27e-1198
hemolymphoid system1.17e-10108
blood1.19e-0715
haemolymphatic fluid1.19e-0715
organism substance1.19e-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
NFYA#4800212.28372046655370.008516011403724430.0324777693990716



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.