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|ontology_enrichment_uberon=UBERON:0002390!3.07e-34!102;UBERON:0003061!3.07e-34!102;UBERON:0002193!2.68e-30!112;UBERON:0007023!1.35e-28!115;UBERON:0002371!1.35e-25!80;UBERON:0001474!8.59e-22!86;UBERON:0002405!1.20e-19!115;UBERON:0004765!3.49e-15!101;UBERON:0001434!3.49e-15!101;UBERON:0001049!2.33e-11!57;UBERON:0005068!2.33e-11!57;UBERON:0006241!2.33e-11!57;UBERON:0007135!2.33e-11!57;UBERON:0002616!7.05e-09!59;UBERON:0003080!1.51e-08!42;UBERON:0002780!2.48e-08!41;UBERON:0001890!2.48e-08!41;UBERON:0006240!2.48e-08!41;UBERON:0003081!6.52e-08!216;UBERON:0000955!1.88e-07!69;UBERON:0006238!1.88e-07!69;UBERON:0000178!3.35e-07!15;UBERON:0000179!3.35e-07!15;UBERON:0000463!3.35e-07!15;UBERON:0001893!4.83e-07!34;UBERON:0002020!5.27e-07!34;UBERON:0003528!5.27e-07!34;UBERON:0002791!7.20e-07!33
|ontology_enrichment_uberon=UBERON:0002390!3.07e-34!102;UBERON:0003061!3.07e-34!102;UBERON:0002193!2.68e-30!112;UBERON:0007023!1.35e-28!115;UBERON:0002371!1.35e-25!80;UBERON:0001474!8.59e-22!86;UBERON:0002405!1.20e-19!115;UBERON:0004765!3.49e-15!101;UBERON:0001434!3.49e-15!101;UBERON:0001049!2.33e-11!57;UBERON:0005068!2.33e-11!57;UBERON:0006241!2.33e-11!57;UBERON:0007135!2.33e-11!57;UBERON:0002616!7.05e-09!59;UBERON:0003080!1.51e-08!42;UBERON:0002780!2.48e-08!41;UBERON:0001890!2.48e-08!41;UBERON:0006240!2.48e-08!41;UBERON:0003081!6.52e-08!216;UBERON:0000955!1.88e-07!69;UBERON:0006238!1.88e-07!69;UBERON:0000178!3.35e-07!15;UBERON:0000179!3.35e-07!15;UBERON:0000463!3.35e-07!15;UBERON:0001893!4.83e-07!34;UBERON:0002020!5.27e-07!34;UBERON:0003528!5.27e-07!34;UBERON:0002791!7.20e-07!33
|pathway_enrichment=5.55202746254732e-05;0.0175721669189623;3;511;Signaling in Immune system (Reactome):REACT_6900!3.63134547651233e-05;0.0175721669189623;2;55;{TRAF6,55} (Static Module):NA
|pathway_enrichment=5.55202746254732e-05;0.0175721669189623;3;511;Signaling in Immune system (Reactome):REACT_6900!3.63134547651233e-05;0.0175721669189623;2;55;{TRAF6,55} (Static Module):NA
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}}
}}

Revision as of 20:42, 8 August 2012


Full id: C691_Monocytederived_CD14_Macrophage_CD19_Dendritic_immature_Whole



Phase1 CAGE Peaks

Hg19::chr11:67771024..67771043,-p2@UNC93B1
Hg19::chr11:67771513..67771604,-p1@UNC93B1
Hg19::chr14:21249200..21249248,+p1@RNASE6
Hg19::chr14:21249254..21249267,+p3@RNASE6
Hg19::chr14:21249300..21249314,+p2@RNASE6
Hg19::chr14:21249998..21250018,+p5@RNASE6
Hg19::chr5:66492562..66492635,-p1@CD180
Hg19::chr6:32908739..32908746,-p3@HLA-DMB
Hg19::chr6:32908765..32908786,-p2@HLA-DMB
Hg19::chr6:32908792..32908830,-p1@HLA-DMB
Hg19::chr6:6588941..6588960,+p1@LY86
Hg19::chr6:6588974..6589011,+p2@LY86


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


p.valueFDRnGenesnPathwayName
5.55202746254732e-050.01757216691896233511Signaling in Immune system (Reactome):REACT_6900
3.63134547651233e-050.0175721669189623255{TRAF6,55} (Static Module):NA



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


GO IDGO nameFDR corrected p-value
GO:0006952defense response0.00398983501859937
GO:0006955immune response0.0145573104414221
GO:0002376immune system process0.0145573104414221
GO:0006954inflammatory response0.0145573104414221
GO:0009611response to wounding0.0244421873004799
GO:0009605response to external stimulus0.0357037352160071
GO:0004522pancreatic ribonuclease activity0.0357037352160071
GO:0016892endoribonuclease activity, producing 3'-phosphomonoesters0.0357037352160071
GO:0031902late endosome membrane0.0357037352160071
GO:0016894endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters0.0357037352160071
GO:0006401RNA catabolic process0.0466318094114567
GO:0005765lysosomal membrane0.0466318094114567
GO:0005770late endosome0.0466318094114567
GO:0005774vacuolar membrane0.0485780051467031
GO:0044437vacuolar part0.0485780051467031
GO:0004521endoribonuclease activity0.0485780051467031
GO:0006959humoral immune response0.0485780051467031
GO:0005886plasma membrane0.0485780051467031
GO:0006950response to stress0.0485780051467031
GO:0010008endosome membrane0.0485780051467031
GO:0044440endosomal part0.0485780051467031



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
leukocyte9.48e-49140
nongranular leukocyte6.82e-45119
hematopoietic stem cell4.10e-43172
angioblastic mesenchymal cell4.10e-43172
hematopoietic cell3.32e-41182
hematopoietic oligopotent progenitor cell1.77e-40165
hematopoietic multipotent progenitor cell1.77e-40165
hematopoietic lineage restricted progenitor cell1.12e-39124
macrophage dendritic cell progenitor1.33e-3065
myeloid leukocyte3.74e-3076
monopoietic cell1.52e-2963
monocyte1.52e-2963
monoblast1.52e-2963
promonocyte1.52e-2963
granulocyte monocyte progenitor cell2.04e-2871
myeloid cell3.83e-25112
common myeloid progenitor3.83e-25112
myeloid lineage restricted progenitor cell8.29e-2570
CD14-positive, CD16-negative classical monocyte2.56e-2442
classical monocyte3.00e-2245
lymphocyte9.33e-1453
common lymphoid progenitor9.33e-1453
lymphoid lineage restricted progenitor cell2.40e-1352
lymphocyte of B lineage3.15e-1324
pro-B cell3.15e-1324
B cell1.46e-0914
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.07e-34102
blood island3.07e-34102
hemolymphoid system2.68e-30112
adult organism1.35e-28115
bone marrow1.35e-2580
bone element8.59e-2286
immune system1.20e-19115
skeletal element3.49e-15101
skeletal system3.49e-15101
neural tube2.33e-1157
neural rod2.33e-1157
future spinal cord2.33e-1157
neural keel2.33e-1157
regional part of brain7.05e-0959
anterior neural tube1.51e-0842
regional part of forebrain2.48e-0841
forebrain2.48e-0841
future forebrain2.48e-0841
lateral plate mesoderm6.52e-08216
brain1.88e-0769
future brain1.88e-0769
blood3.35e-0715
haemolymphatic fluid3.35e-0715
organism substance3.35e-0715
telencephalon4.83e-0734
gray matter5.27e-0734
brain grey matter5.27e-0734
regional part of telencephalon7.20e-0733


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


No analysis results for this cluster

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.