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Difference between revisions of "Coexpression cluster:C3057"

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|full_id=C3057_Eosinophils_embryonic_CD14_gall_Smooth_Dendritic_chorionic
 
|full_id=C3057_Eosinophils_embryonic_CD14_gall_Smooth_Dendritic_chorionic
 
|id=C3057
 
|id=C3057
|ontology_enrichment_celltype=CL:0002057!1.30e-22!42;CL:0000860!1.79e-20!45;CL:0000766!1.21e-15!76;CL:0000839!6.27e-13!70;CL:0002194!6.63e-13!63;CL:0000576!6.63e-13!63;CL:0000040!6.63e-13!63;CL:0000559!6.63e-13!63;CL:0002009!3.01e-12!65;CL:0000557!1.64e-10!71;CL:0000763!1.73e-09!112;CL:0000049!1.73e-09!112;CL:0000738!7.45e-08!140;CL:0000094!3.64e-07!8;CL:0002031!8.50e-07!124
+
|ontology_enrichment_celltype=CL:0000860!2.58e-38!42;CL:0002057!2.58e-38!42;CL:0000473!3.06e-33!48;CL:0000234!3.06e-33!48;CL:0000766!8.71e-32!72;CL:0002194!4.13e-30!59;CL:0000576!4.13e-30!59;CL:0000040!4.13e-30!59;CL:0000559!4.13e-30!59;CL:0002009!4.64e-29!61;CL:0000839!1.05e-26!66;CL:0000557!2.82e-26!67;CL:0000763!2.33e-20!108;CL:0000049!2.33e-20!108;CL:0000771!4.10e-19!2;CL:0000325!2.73e-17!87;CL:0000738!1.31e-15!136;CL:0002087!2.38e-14!115;CL:0002031!1.19e-13!120;CL:0002032!9.43e-13!161;CL:0000837!9.43e-13!161;CL:0000037!4.21e-12!168;CL:0000566!4.21e-12!168;CL:0000988!2.42e-11!177
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001474!1.19e-08!86;UBERON:0002371!1.94e-08!80;UBERON:0004765!5.54e-08!101;UBERON:0001434!5.54e-08!101
+
|ontology_enrichment_uberon=UBERON:0002371!6.54e-23!76;UBERON:0001474!4.51e-21!82;UBERON:0004765!5.37e-19!90;UBERON:0002405!2.62e-18!93;UBERON:0002390!2.96e-17!98;UBERON:0003061!2.96e-17!98;UBERON:0001434!7.31e-17!100;UBERON:0002193!1.95e-15!108;UBERON:0002363!1.17e-09!1;UBERON:0007645!1.17e-09!1;UBERON:0007647!1.17e-09!1;UBERON:0010115!1.17e-09!1;UBERON:0002204!4.20e-09!167;UBERON:0003081!4.90e-07!203
 
|tf_chipseq_enrich=JUNB#3726;2:20.4070884398808:0.00313146219943874:0.0164444278281971
 
|tf_chipseq_enrich=JUNB#3726;2:20.4070884398808:0.00313146219943874:0.0164444278281971
 
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}}
 
}}

Revision as of 05:45, 19 October 2012


Full id: C3057_Eosinophils_embryonic_CD14_gall_Smooth_Dendritic_chorionic



Phase1 CAGE Peaks

Hg19::chr10:91174204..91174207,+p7@IFIT5
Hg19::chr17:76553904..76553912,+p@chr17:76553904..76553912
+
Hg19::chr17:76554780..76554789,+p@chr17:76554780..76554789
+


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
classical monocyte2.58e-3842
CD14-positive, CD16-negative classical monocyte2.58e-3842
defensive cell3.06e-3348
phagocyte3.06e-3348
myeloid leukocyte8.71e-3272
monopoietic cell4.13e-3059
monocyte4.13e-3059
monoblast4.13e-3059
promonocyte4.13e-3059
macrophage dendritic cell progenitor4.64e-2961
myeloid lineage restricted progenitor cell1.05e-2666
granulocyte monocyte progenitor cell2.82e-2667
myeloid cell2.33e-20108
common myeloid progenitor2.33e-20108
eosinophil4.10e-192
stuff accumulating cell2.73e-1787
leukocyte1.31e-15136
nongranular leukocyte2.38e-14115
hematopoietic lineage restricted progenitor cell1.19e-13120
hematopoietic oligopotent progenitor cell9.43e-13161
hematopoietic multipotent progenitor cell9.43e-13161
hematopoietic stem cell4.21e-12168
angioblastic mesenchymal cell4.21e-12168
hematopoietic cell2.42e-11177
Uber Anatomy
Ontology termp-valuen
bone marrow6.54e-2376
bone element4.51e-2182
skeletal element5.37e-1990
immune system2.62e-1893
hematopoietic system2.96e-1798
blood island2.96e-1798
skeletal system7.31e-17100
hemolymphoid system1.95e-15108
dura mater1.17e-091
future meninx1.17e-091
ectomeninx1.17e-091
future dura mater1.17e-091
musculoskeletal system4.20e-09167
lateral plate mesoderm4.90e-07203


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
JUNB#3726220.40708843988080.003131462199438740.0164444278281971



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.