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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2526_acute_CD14_CD14CD16_Whole_CD4_biphenotypic_Dendritic
|full_id=C2526_acute_CD14_CD14CD16_Whole_CD4_biphenotypic_Dendritic
|id=C2526
|id=C2526

Revision as of 15:16, 12 September 2012


Full id: C2526_acute_CD14_CD14CD16_Whole_CD4_biphenotypic_Dendritic



Phase1 CAGE Peaks

Hg19::chr1:151129103..151129130,+p2@TNFAIP8L2
Hg19::chr1:151129135..151129165,+p1@TNFAIP8L2
Hg19::chr8:22437965..22438000,+p3@PDLIM2
Hg19::chr8:22438009..22438035,+p4@PDLIM2


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell1.56e-78172
angioblastic mesenchymal cell1.56e-78172
hematopoietic oligopotent progenitor cell9.60e-75165
hematopoietic multipotent progenitor cell9.60e-75165
hematopoietic cell3.45e-73182
leukocyte1.60e-62140
hematopoietic lineage restricted progenitor cell5.86e-54124
nongranular leukocyte7.19e-53119
myeloid cell2.28e-50112
common myeloid progenitor2.28e-50112
myeloid leukocyte1.08e-3576
granulocyte monocyte progenitor cell2.03e-3271
myeloid lineage restricted progenitor cell1.04e-3170
macrophage dendritic cell progenitor1.85e-3065
monopoietic cell1.09e-2963
monocyte1.09e-2963
monoblast1.09e-2963
promonocyte1.09e-2963
CD14-positive, CD16-negative classical monocyte1.66e-2542
classical monocyte3.18e-2245
lymphocyte4.04e-2053
common lymphoid progenitor4.04e-2053
lymphoid lineage restricted progenitor cell8.89e-2052
T cell2.10e-1125
pro-T cell2.10e-1125
mesenchymal cell9.93e-10358
mature alpha-beta T cell1.22e-0918
alpha-beta T cell1.22e-0918
immature T cell1.22e-0918
mature T cell1.22e-0918
immature alpha-beta T cell1.22e-0918
lymphocyte of B lineage1.08e-0824
pro-B cell1.08e-0824
connective tissue cell1.43e-08365
intermediate monocyte9.99e-089
CD14-positive, CD16-positive monocyte9.99e-089
CD8-positive, alpha-beta T cell4.87e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.75e-39102
blood island5.75e-39102
hemolymphoid system3.52e-36112
bone marrow5.66e-2880
bone element4.28e-2686
immune system6.44e-22115
adult organism1.50e-20115
skeletal element5.71e-20101
skeletal system5.71e-20101
blood1.03e-0815
haemolymphatic fluid1.03e-0815
organism substance1.03e-0815
lateral plate mesoderm8.04e-08216
connective tissue1.49e-07375
Disease
Ontology termp-valuen
leukemia9.80e-1739
hematologic cancer1.02e-1651
immune system cancer1.02e-1651
myeloid leukemia2.63e-1431


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
CTCF#1066445.360256373075030.001211145381643620.00817546616555573



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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