Personal tools

Coexpression cluster:C2860

From FANTOM5_SSTAR

Revision as of 15:39, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2860_Dendritic_Mast_granulocyte_Neutrophils_gall_anaplastic_pagetoid



Phase1 CAGE Peaks

Hg19::chr6:45390269..45390298,+p5@RUNX2
Hg19::chr6:45390343..45390388,+p10@RUNX2
Hg19::chr6:45390399..45390418,+p15@RUNX2
Hg19::chr6:45390442..45390479,+p8@RUNX2


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
leukocyte1.83e-12140
hematopoietic cell1.65e-10182
myeloid leukocyte2.05e-1076
connective tissue cell3.03e-10365
hematopoietic stem cell3.51e-10172
angioblastic mesenchymal cell3.51e-10172
mesenchymal cell3.82e-10358
mature alpha-beta T cell2.53e-0918
alpha-beta T cell2.53e-0918
immature T cell2.53e-0918
mature T cell2.53e-0918
immature alpha-beta T cell2.53e-0918
T cell9.08e-0925
pro-T cell9.08e-0925
motile cell1.07e-08390
hematopoietic oligopotent progenitor cell1.15e-08165
hematopoietic multipotent progenitor cell1.15e-08165
CD14-positive, CD16-negative classical monocyte2.52e-0842
nongranular leukocyte2.78e-08119
hematopoietic lineage restricted progenitor cell1.29e-07124
CD8-positive, alpha-beta T cell3.10e-0711
multi fate stem cell5.05e-07430
granulocyte monocyte progenitor cell5.54e-0771
myeloid cell6.07e-07112
common myeloid progenitor6.07e-07112
classical monocyte7.97e-0745
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.76e-13102
blood island1.76e-13102
hemolymphoid system4.18e-11112
connective tissue9.35e-10375
blood1.18e-0815
haemolymphatic fluid1.18e-0815
organism substance1.18e-0815
bone element1.82e-0886
bone marrow1.02e-0780
skeletal element1.07e-07101
skeletal system1.07e-07101


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
CTCF#1066445.360256373075030.001211145381643620.0081966571094789



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.