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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1928_CD4_adult_NK_Dendritic_acute_mycosis_CD14
|full_id=C1928_CD4_adult_NK_Dendritic_acute_mycosis_CD14
|gostat_on_coexpression_clusters=GO:0004708!MAP kinase kinase activity!0.02589987277053!7867$GO:0004712!protein serine/threonine/tyrosine kinase activity!0.02589987277053!7867
|gostat_on_coexpression_clusters=GO:0004708!MAP kinase kinase activity!0.02589987277053!7867$GO:0004712!protein serine/threonine/tyrosine kinase activity!0.02589987277053!7867

Revision as of 14:34, 12 September 2012


Full id: C1928_CD4_adult_NK_Dendritic_acute_mycosis_CD14



Phase1 CAGE Peaks

Hg19::chr3:50644501..50644509,-p@chr3:50644501..50644509
-
Hg19::chr3:50645235..50645254,+p1@CU689193
Hg19::chr3:50645893..50645912,-p@chr3:50645893..50645912
-
Hg19::chr3:50649192..50649212,-p1@CISH
Hg19::chr3:50649746..50649765,+p6@MAPKAPK3


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


GO IDGO nameFDR corrected p-value
GO:0004708MAP kinase kinase activity0.02589987277053
GO:0004712protein serine/threonine/tyrosine kinase activity0.02589987277053



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>disease_data<br>


Cell Type
Ontology termp-valuen
myeloid cell4.42e-26112
common myeloid progenitor4.42e-26112
hematopoietic stem cell2.61e-25172
angioblastic mesenchymal cell2.61e-25172
hematopoietic cell2.93e-25182
hematopoietic oligopotent progenitor cell4.84e-24165
hematopoietic multipotent progenitor cell4.84e-24165
myeloid leukocyte4.36e-1576
myeloid lineage restricted progenitor cell8.23e-1570
leukocyte3.51e-14140
granulocyte monocyte progenitor cell2.41e-1371
hematopoietic lineage restricted progenitor cell2.79e-13124
monopoietic cell3.04e-1263
monocyte3.04e-1263
monoblast3.04e-1263
promonocyte3.04e-1263
nongranular leukocyte7.38e-12119
CD14-positive, CD16-negative classical monocyte1.03e-1142
macrophage dendritic cell progenitor1.42e-1165
classical monocyte9.05e-1045
mature alpha-beta T cell7.82e-0918
alpha-beta T cell7.82e-0918
immature T cell7.82e-0918
mature T cell7.82e-0918
immature alpha-beta T cell7.82e-0918
T cell3.57e-0825
pro-T cell3.57e-0825
CD8-positive, alpha-beta T cell7.28e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.77e-17102
blood island1.77e-17102
hemolymphoid system4.09e-15112
immune system7.04e-11115
bone marrow1.80e-1080
adult organism6.63e-10115
bone element1.66e-0986
blood3.50e-0815
haemolymphatic fluid3.50e-0815
organism substance3.50e-0815
skeletal element9.40e-07101
skeletal system9.40e-07101
Disease
Ontology termp-valuen
myeloid leukemia2.63e-1231
leukemia1.84e-1039


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
EP300#203345.419153380978560.00209386927943890.0121240568650729
PRDM1#639252.73238231098430.0005663251415203910.00482985721502925



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.