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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3493_Eosinophils_CD14_Neutrophils_Mast_CD14CD16_CD34_Peripheral
|full_id=C3493_Eosinophils_CD14_Neutrophils_Mast_CD14CD16_CD34_Peripheral
|id=C3493
|id=C3493

Revision as of 16:25, 12 September 2012


Full id: C3493_Eosinophils_CD14_Neutrophils_Mast_CD14CD16_CD34_Peripheral



Phase1 CAGE Peaks

Hg19::chr15:45879256..45879273,-p@chr15:45879256..45879273
-
Hg19::chr19:54713776..54713805,-p1@ENST00000413723
Hg19::chr3:44482076..44482098,+p1@ENST00000500374


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
hematopoietic stem cell1.81e-39172
angioblastic mesenchymal cell1.81e-39172
leukocyte2.35e-38140
classical monocyte1.42e-3745
hematopoietic cell7.78e-37182
CD14-positive, CD16-negative classical monocyte1.11e-3642
hematopoietic oligopotent progenitor cell1.58e-36165
hematopoietic multipotent progenitor cell1.58e-36165
myeloid leukocyte2.64e-3676
myeloid cell1.52e-35112
common myeloid progenitor1.52e-35112
granulocyte monocyte progenitor cell2.96e-3171
hematopoietic lineage restricted progenitor cell6.67e-30124
myeloid lineage restricted progenitor cell5.45e-2970
macrophage dendritic cell progenitor3.43e-2865
nongranular leukocyte7.28e-28119
monopoietic cell1.09e-2663
monocyte1.09e-2663
monoblast1.09e-2663
promonocyte1.09e-2663
intermediate monocyte2.30e-109
CD14-positive, CD16-positive monocyte2.30e-109
mesenchymal cell2.88e-09358
connective tissue cell8.76e-09365
granulocyte3.49e-078
stem cell3.85e-07444
motile cell5.17e-07390
multi fate stem cell7.91e-07430
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.23e-35102
blood island3.23e-35102
hemolymphoid system1.97e-32112
bone marrow1.29e-2780
bone element4.55e-2586
immune system1.57e-22115
skeletal element1.76e-19101
skeletal system1.76e-19101
lateral plate mesoderm1.04e-09216
musculoskeletal system5.91e-08167
connective tissue1.09e-07375
blood1.59e-0715
haemolymphatic fluid1.59e-0715
organism substance1.59e-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
BRF2#552901358.1918604651160.002789217733358720.0152778680890676
GATA1#2623313.56030814380040.0004009615963782630.00387346481954948
SREBF1#6720231.33723296032550.00133816265136180.00887454718983841



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.