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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4578_CD14_CD19_CD4_CD14CD16_CD8_Natural_Peripheral
|full_id=C4578_CD14_CD19_CD4_CD14CD16_CD8_Natural_Peripheral
|id=C4578
|id=C4578

Revision as of 17:40, 12 September 2012


Full id: C4578_CD14_CD19_CD4_CD14CD16_CD8_Natural_Peripheral



Phase1 CAGE Peaks

Hg19::chr6:158248908..158248912,+p@chr6:158248908..158248912
+
Hg19::chr6:158255218..158255219,+p@chr6:158255218..158255219
+
Hg19::chr6:158255392..158255396,+p@chr6:158255392..158255396
+


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
CD14-positive, CD16-negative classical monocyte5.08e-2042
classical monocyte5.56e-1745
macrophage dendritic cell progenitor3.00e-1665
myeloid lineage restricted progenitor cell1.18e-1570
granulocyte monocyte progenitor cell1.38e-1571
monopoietic cell2.59e-1563
monocyte2.59e-1563
monoblast2.59e-1563
promonocyte2.59e-1563
leukocyte3.34e-15140
myeloid leukocyte2.56e-1476
hematopoietic lineage restricted progenitor cell5.61e-14124
nongranular leukocyte1.70e-13119
hematopoietic stem cell2.95e-10172
angioblastic mesenchymal cell2.95e-10172
hematopoietic cell3.95e-09182
myeloid cell6.34e-09112
common myeloid progenitor6.34e-09112
hematopoietic oligopotent progenitor cell9.01e-09165
hematopoietic multipotent progenitor cell9.01e-09165
intermediate monocyte3.91e-079
CD14-positive, CD16-positive monocyte3.91e-079
Uber Anatomy
Ontology termp-valuen
bone element7.74e-1486
hematopoietic system1.12e-13102
blood island1.12e-13102
bone marrow1.18e-1380
hemolymphoid system9.01e-13112
skeletal element4.25e-11101
skeletal system4.25e-11101
immune system1.02e-09115


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
NFYB#4801211.17319550235760.01025467135054530.0381555317674159
TRIM28#10155212.39368336350830.008368344129438470.0329418978754824



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.