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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.86e-11!115;UBERON:0000178!1.23e-08!15;UBERON:0000179!1.23e-08!15;UBERON:0000463!1.23e-08!15;UBERON:0002370!2.16e-07!4;UBERON:0005058!2.16e-07!4;UBERON:0009113!2.16e-07!4;UBERON:0003295!2.16e-07!4;UBERON:0005562!2.16e-07!4;UBERON:0004177!4.00e-07!7
|ontology_enrichment_uberon=UBERON:0007023!4.86e-11!115;UBERON:0000178!1.23e-08!15;UBERON:0000179!1.23e-08!15;UBERON:0000463!1.23e-08!15;UBERON:0002370!2.16e-07!4;UBERON:0005058!2.16e-07!4;UBERON:0009113!2.16e-07!4;UBERON:0003295!2.16e-07!4;UBERON:0005562!2.16e-07!4;UBERON:0004177!4.00e-07!7
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}}
}}

Revision as of 17:11, 8 August 2012


Full id: C1355_Natural_NK_CD8_CD14_Eosinophils_Peripheral_spleen



Phase1 CAGE Peaks

Hg19::chr12:10425198..10425201,-p@chr12:10425198..10425201
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Hg19::chr12:10425221..10425239,-p@chr12:10425221..10425239
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Hg19::chr12:10425243..10425252,-p@chr12:10425243..10425252
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Hg19::chr12:10425255..10425266,-p@chr12:10425255..10425266
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Hg19::chr20:37493438..37493456,-p@chr20:37493438..37493456
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Hg19::chr2:85912270..85912280,+p12@GNLY


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
mature alpha-beta T cell9.94e-3518
alpha-beta T cell9.94e-3518
immature T cell9.94e-3518
mature T cell9.94e-3518
immature alpha-beta T cell9.94e-3518
CD8-positive, alpha-beta T cell3.06e-3211
T cell7.55e-2425
pro-T cell7.55e-2425
lymphoid lineage restricted progenitor cell6.23e-2252
lymphocyte2.11e-2153
common lymphoid progenitor2.11e-2153
leukocyte4.78e-20140
nongranular leukocyte2.61e-15119
hematopoietic stem cell1.70e-14172
angioblastic mesenchymal cell1.70e-14172
hematopoietic cell3.58e-13182
hematopoietic oligopotent progenitor cell2.33e-12165
hematopoietic multipotent progenitor cell2.33e-12165
hematopoietic lineage restricted progenitor cell5.22e-11124
natural killer cell3.39e-103
pro-NK cell3.39e-103
mononuclear cell1.14e-093
basophil2.08e-093
naive T cell5.42e-093
thymocyte3.04e-072
double negative thymocyte3.04e-072
double-positive, alpha-beta thymocyte3.04e-072
DN4 thymocyte3.04e-072
DN1 thymic pro-T cell3.04e-072
DN2 thymocyte3.04e-072
DN3 thymocyte3.04e-072
immature single positive thymocyte3.04e-072
early T lineage precursor3.04e-072
Uber Anatomy
Ontology termp-valuen
adult organism4.86e-11115
blood1.23e-0815
haemolymphatic fluid1.23e-0815
organism substance1.23e-0815
thymus2.16e-074
hemolymphoid system gland2.16e-074
thymic region2.16e-074
pharyngeal gland2.16e-074
thymus primordium2.16e-074
hemopoietic organ4.00e-077


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.