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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1776_embryonic_CD8_Natural_Whole_NK_blood_Basophils
|full_id=C1776_embryonic_CD8_Natural_Whole_NK_blood_Basophils
|id=C1776
|id=C1776

Revision as of 14:23, 12 September 2012


Full id: C1776_embryonic_CD8_Natural_Whole_NK_blood_Basophils



Phase1 CAGE Peaks

Hg19::chr17:34199262..34199274,-p@chr17:34199262..34199274
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Hg19::chr17:34199297..34199315,-p@chr17:34199297..34199315
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Hg19::chr17:34205568..34205579,-p@chr17:34205568..34205579
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Hg19::chr17:34205625..34205636,-p@chr17:34205625..34205636
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Hg19::chr17:34207354..34207372,-p1@CCL5


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 cell2.18e-32172
angioblastic mesenchymal cell2.18e-32172
hematopoietic oligopotent progenitor cell2.59e-31165
hematopoietic multipotent progenitor cell2.59e-31165
hematopoietic cell5.45e-31182
leukocyte1.09e-30140
nongranular leukocyte1.52e-29119
hematopoietic lineage restricted progenitor cell3.43e-25124
myeloid cell5.69e-19112
common myeloid progenitor5.69e-19112
myeloid leukocyte3.42e-1876
monopoietic cell2.17e-1663
monocyte2.17e-1663
monoblast2.17e-1663
promonocyte2.17e-1663
macrophage dendritic cell progenitor1.36e-1565
myeloid lineage restricted progenitor cell1.70e-1470
granulocyte monocyte progenitor cell2.98e-1371
CD14-positive, CD16-negative classical monocyte2.68e-1242
classical monocyte6.46e-1245
lymphocyte1.47e-1153
common lymphoid progenitor1.47e-1153
lymphoid lineage restricted progenitor cell1.73e-1152
mature alpha-beta T cell2.08e-1018
alpha-beta T cell2.08e-1018
immature T cell2.08e-1018
mature T cell2.08e-1018
immature alpha-beta T cell2.08e-1018
CD8-positive, alpha-beta T cell1.22e-0811
T cell2.92e-0725
pro-T cell2.92e-0725
Uber Anatomy
Ontology termp-valuen
hemolymphoid system8.12e-22112
hematopoietic system1.88e-21102
blood island1.88e-21102
adult organism1.89e-13115
bone marrow1.41e-1180
immune system1.11e-10115
blood1.50e-1015
haemolymphatic fluid1.50e-1015
organism substance1.50e-1015
bone element1.22e-0986


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

No analysis results for this cluster

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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