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Coexpression cluster:C2860: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.0081966571094789
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.0081966571094789
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}}
}}

Revision as of 15:46, 26 November 2012


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
leukocyte1.22e-13136
myeloid leukocyte2.53e-1272
hematopoietic cell2.60e-11177
connective tissue cell6.56e-11361
mesenchymal cell9.76e-11354
hematopoietic stem cell1.35e-10168
angioblastic mesenchymal cell1.35e-10168
motile cell2.07e-09386
nongranular leukocyte3.15e-09115
hematopoietic oligopotent progenitor cell4.67e-09161
hematopoietic multipotent progenitor cell4.67e-09161
mature alpha-beta T cell5.34e-0918
alpha-beta T cell5.34e-0918
immature T cell5.34e-0918
mature T cell5.34e-0918
immature alpha-beta T cell5.34e-0918
granulocyte monocyte progenitor cell1.50e-0867
hematopoietic lineage restricted progenitor cell1.60e-08120
T cell1.80e-0825
pro-T cell1.80e-0825
classical monocyte4.56e-0842
CD14-positive, CD16-negative classical monocyte4.56e-0842
multi fate stem cell6.36e-08427
myeloid lineage restricted progenitor cell7.29e-0866
myeloid cell1.21e-07108
common myeloid progenitor1.21e-07108
monopoietic cell1.26e-0759
monocyte1.26e-0759
monoblast1.26e-0759
promonocyte1.26e-0759
CD8-positive, alpha-beta T cell3.24e-0711
somatic stem cell4.09e-07433
macrophage dendritic cell progenitor5.14e-0761
stem cell8.61e-07441
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.30e-1598
blood island5.30e-1598
hemolymphoid system1.97e-12108
connective tissue2.08e-10371
bone element6.19e-1082
skeletal system2.73e-09100
bone marrow3.39e-0976
skeletal element4.73e-0990
blood4.62e-0815
haemolymphatic fluid4.62e-0815
organism substance4.62e-0815
immune system1.20e-0793
musculoskeletal system2.94e-07167


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.

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