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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2066_CD14_Eosinophils_Natural_CD14CD16_immature_CD4_Neutrophils
|full_id=C2066_CD14_Eosinophils_Natural_CD14CD16_immature_CD4_Neutrophils
|id=C2066
|id=C2066

Revision as of 14:44, 12 September 2012


Full id: C2066_CD14_Eosinophils_Natural_CD14CD16_immature_CD4_Neutrophils



Phase1 CAGE Peaks

Hg19::chr10:60027998..60028009,+p@chr10:60027998..60028009
+
Hg19::chr12:53894445..53894466,-p@chr12:53894445..53894466
-
Hg19::chr14:75593033..75593037,+p@chr14:75593033..75593037
+
Hg19::chr1:153917876..153917889,+p@chr1:153917876..153917889
+


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
leukocyte2.14e-49140
hematopoietic cell2.07e-47182
hematopoietic stem cell5.06e-47172
angioblastic mesenchymal cell5.06e-47172
hematopoietic oligopotent progenitor cell7.26e-43165
hematopoietic multipotent progenitor cell7.26e-43165
hematopoietic lineage restricted progenitor cell1.37e-38124
nongranular leukocyte5.32e-37119
myeloid leukocyte1.39e-2876
myeloid cell3.23e-27112
common myeloid progenitor3.23e-27112
granulocyte monocyte progenitor cell5.51e-2571
CD14-positive, CD16-negative classical monocyte6.33e-2542
myeloid lineage restricted progenitor cell3.49e-2370
classical monocyte1.54e-2245
connective tissue cell2.57e-22365
macrophage dendritic cell progenitor3.61e-2265
multi fate stem cell1.30e-21430
mesenchymal cell1.97e-21358
stem cell3.99e-21444
monopoietic cell5.38e-2163
monocyte5.38e-2163
monoblast5.38e-2163
promonocyte5.38e-2163
somatic stem cell3.33e-20436
motile cell2.59e-18390
lymphocyte7.20e-1453
common lymphoid progenitor7.20e-1453
lymphoid lineage restricted progenitor cell1.18e-1352
native cell6.17e-11722
mature alpha-beta T cell3.19e-1018
alpha-beta T cell3.19e-1018
immature T cell3.19e-1018
mature T cell3.19e-1018
immature alpha-beta T cell3.19e-1018
T cell4.51e-1025
pro-T cell4.51e-1025
intermediate monocyte1.51e-079
CD14-positive, CD16-positive monocyte1.51e-079
somatic cell2.31e-07591
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.05e-25102
blood island1.05e-25102
hemolymphoid system1.83e-24112
bone marrow1.27e-2280
connective tissue1.88e-21375
bone element2.62e-2186
immune system4.74e-19115
skeletal element8.51e-16101
skeletal system8.51e-16101
lateral plate mesoderm2.22e-10216
musculoskeletal system1.43e-09167


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
THAP1#55145215.68457230142570.005840469678357920.026241033028093
ZBTB7A#5134135.513931980906920.009038352821081090.034219921344241



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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