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Coexpression cluster:C1886: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!8.48e-30!112;UBERON:0002390!1.47e-27!102;UBERON:0003061!1.47e-27!102;UBERON:0002371!2.09e-22!80;UBERON:0002405!3.10e-21!115;UBERON:0001474!2.75e-18!86;UBERON:0004765!9.88e-14!101;UBERON:0001434!9.88e-14!101;UBERON:0003081!1.30e-11!216;UBERON:0002204!2.73e-07!167
|ontology_enrichment_uberon=UBERON:0002193!8.48e-30!112;UBERON:0002390!1.47e-27!102;UBERON:0003061!1.47e-27!102;UBERON:0002371!2.09e-22!80;UBERON:0002405!3.10e-21!115;UBERON:0001474!2.75e-18!86;UBERON:0004765!9.88e-14!101;UBERON:0001434!9.88e-14!101;UBERON:0003081!1.30e-11!216;UBERON:0002204!2.73e-07!167
|tf_chipseq_enrich=CTBP2#1488;2:25.0868001357313:0.00246143859967838:0.0138522570272557
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}}
}}

Revision as of 11:50, 5 September 2012


Full id: C1886_CD14CD16_CD14_CD19_Basophils_CD133_renal_blood



Phase1 CAGE Peaks

Hg19::chr2:182174024..182174027,-p@chr2:182174024..182174027
-
Hg19::chr3:56789155..56789207,-p6@ARHGEF3
Hg19::chr5:56112749..56112774,+p@chr5:56112749..56112774
+
Hg19::chr5:56112822..56112834,+p@chr5:56112822..56112834
+
Hg19::chr6:116783272..116783399,+p1@FAM26F


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
leukocyte3.67e-37140
hematopoietic stem cell2.98e-35172
angioblastic mesenchymal cell2.98e-35172
nongranular leukocyte1.89e-33119
hematopoietic oligopotent progenitor cell7.94e-33165
hematopoietic multipotent progenitor cell7.94e-33165
hematopoietic cell2.71e-31182
hematopoietic lineage restricted progenitor cell2.89e-30124
myeloid leukocyte4.91e-2776
CD14-positive, CD16-negative classical monocyte1.95e-2642
macrophage dendritic cell progenitor6.92e-2665
monopoietic cell3.91e-2563
monocyte3.91e-2563
monoblast3.91e-2563
promonocyte3.91e-2563
granulocyte monocyte progenitor cell1.73e-2471
myeloid cell5.08e-24112
common myeloid progenitor5.08e-24112
myeloid lineage restricted progenitor cell1.39e-2270
classical monocyte2.35e-2245
B cell2.80e-0914
lymphocyte2.97e-0853
common lymphoid progenitor2.97e-0853
lymphoid lineage restricted progenitor cell6.36e-0852
intermediate monocyte3.19e-079
CD14-positive, CD16-positive monocyte3.19e-079
lymphocyte of B lineage5.81e-0724
pro-B cell5.81e-0724
Uber Anatomy
Ontology termp-valuen
hemolymphoid system8.48e-30112
hematopoietic system1.47e-27102
blood island1.47e-27102
bone marrow2.09e-2280
immune system3.10e-21115
bone element2.75e-1886
skeletal element9.88e-14101
skeletal system9.88e-14101
lateral plate mesoderm1.30e-11216
musculoskeletal system2.73e-07167


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
CTBP2#1488225.08680013573130.002461438599678380.0138522570272557



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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