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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3940_CD14_Natural_CD8_Basophils_CD19_CD4_Neutrophils
|full_id=C3940_CD14_Natural_CD8_Basophils_CD19_CD4_Neutrophils
|id=C3940
|id=C3940

Revision as of 16:56, 12 September 2012


Full id: C3940_CD14_Natural_CD8_Basophils_CD19_CD4_Neutrophils



Phase1 CAGE Peaks

Hg19::chr1:222817465..222817510,-p@chr1:222817465..222817510
-
Hg19::chr6:20319928..20319935,+p@chr6:20319928..20319935
+
Hg19::chrX:24498109..24498113,-p@chrX:24498109..24498113
-


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
leukocyte7.86e-53140
hematopoietic stem cell2.20e-51172
angioblastic mesenchymal cell2.20e-51172
hematopoietic cell8.98e-51182
hematopoietic oligopotent progenitor cell1.32e-47165
hematopoietic multipotent progenitor cell1.32e-47165
hematopoietic lineage restricted progenitor cell6.00e-44124
nongranular leukocyte4.14e-43119
mesenchymal cell3.14e-26358
CD14-positive, CD16-negative classical monocyte8.79e-2642
myeloid leukocyte1.75e-2576
myeloid cell4.66e-25112
common myeloid progenitor4.66e-25112
connective tissue cell7.58e-25365
classical monocyte1.16e-2345
motile cell1.93e-23390
stem cell1.40e-22444
multi fate stem cell1.84e-22430
granulocyte monocyte progenitor cell1.90e-2271
somatic stem cell8.00e-22436
myeloid lineage restricted progenitor cell2.65e-2170
lymphocyte5.60e-2153
common lymphoid progenitor5.60e-2153
lymphoid lineage restricted progenitor cell6.07e-2152
native cell1.72e-20722
macrophage dendritic cell progenitor2.21e-2065
monopoietic cell1.18e-1963
monocyte1.18e-1963
monoblast1.18e-1963
promonocyte1.18e-1963
somatic cell4.29e-14591
mature alpha-beta T cell2.83e-1118
alpha-beta T cell2.83e-1118
immature T cell2.83e-1118
mature T cell2.83e-1118
immature alpha-beta T cell2.83e-1118
T cell3.16e-1125
pro-T cell3.16e-1125
lymphocyte of B lineage4.32e-0924
pro-B cell4.32e-0924
animal cell6.80e-09679
eukaryotic cell6.80e-09679
B cell2.89e-0814
CD8-positive, alpha-beta T cell2.38e-0711
intermediate monocyte7.19e-079
CD14-positive, CD16-positive monocyte7.19e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.43e-26102
blood island1.43e-26102
connective tissue1.12e-23375
hemolymphoid system1.69e-23112
bone marrow2.75e-2280
bone element4.22e-2186
skeletal element4.26e-16101
skeletal system4.26e-16101
immune system7.16e-15115
lateral plate mesoderm1.96e-10216
musculoskeletal system8.15e-08167


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
NFYA#4800212.28372046655370.008516011403724430.0324801415109219
NFYB#4801211.17319550235760.01025467135054530.0381378684274481
TRIM28#10155212.39368336350830.008368344129438470.0329146044716011



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.