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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3030_cord_CD4_mycosis_adult_anaplastic_hairy_Neutrophils
|full_id=C3030_cord_CD4_mycosis_adult_anaplastic_hairy_Neutrophils
|id=C3030
|id=C3030

Revision as of 15:53, 12 September 2012


Full id: C3030_cord_CD4_mycosis_adult_anaplastic_hairy_Neutrophils



Phase1 CAGE Peaks

Hg19::chr10:6054574..6054588,-p@chr10:6054574..6054588
-
Hg19::chr10:6054812..6054831,+p@chr10:6054812..6054831
+
Hg19::chr10:6066253..6066277,+p@chr10:6066253..6066277
+


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 cell1.41e-24182
hematopoietic stem cell1.21e-22172
angioblastic mesenchymal cell1.21e-22172
leukocyte2.64e-22140
hematopoietic oligopotent progenitor cell1.14e-21165
hematopoietic multipotent progenitor cell1.14e-21165
nongranular leukocyte7.42e-20119
hematopoietic lineage restricted progenitor cell1.19e-19124
lymphocyte1.66e-1453
common lymphoid progenitor1.66e-1453
lymphoid lineage restricted progenitor cell2.87e-1352
T cell1.19e-1125
pro-T cell1.19e-1125
circulating cell4.12e-116
myeloid cell5.59e-09112
common myeloid progenitor5.59e-09112
myeloid leukocyte3.19e-0776
myeloid lineage restricted progenitor cell3.22e-0770
mature alpha-beta T cell4.47e-0718
alpha-beta T cell4.47e-0718
immature T cell4.47e-0718
mature T cell4.47e-0718
immature alpha-beta T cell4.47e-0718
granulocyte monocyte progenitor cell5.09e-0771
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.44e-13112
hematopoietic system7.35e-13102
blood island7.35e-13102
blood1.12e-0715
haemolymphatic fluid1.12e-0715
organism substance1.12e-0715
immune system7.41e-07115


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.