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Coexpression cluster:C3584: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!4.67e-43!98;UBERON:0003061!4.67e-43!98;UBERON:0002193!1.02e-39!108;UBERON:0002371!1.89e-30!76;UBERON:0002405!4.20e-30!93;UBERON:0001474!5.52e-27!82;UBERON:0004765!4.13e-23!90;UBERON:0001434!3.94e-20!100;UBERON:0003081!7.78e-15!203;UBERON:0007023!7.98e-14!114;UBERON:0000178!8.86e-11!15;UBERON:0000179!8.86e-11!15;UBERON:0000463!8.86e-11!15;UBERON:0002204!1.31e-07!167
|ontology_enrichment_uberon=UBERON:0002390!4.67e-43!98;UBERON:0003061!4.67e-43!98;UBERON:0002193!1.02e-39!108;UBERON:0002371!1.89e-30!76;UBERON:0002405!4.20e-30!93;UBERON:0001474!5.52e-27!82;UBERON:0004765!4.13e-23!90;UBERON:0001434!3.94e-20!100;UBERON:0003081!7.78e-15!203;UBERON:0007023!7.98e-14!114;UBERON:0000178!8.86e-11!15;UBERON:0000179!8.86e-11!15;UBERON:0000463!8.86e-11!15;UBERON:0002204!1.31e-07!167
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}}
}}

Revision as of 16:13, 26 November 2012


Full id: C3584_Whole_CD14CD16_Neutrophils_Eosinophils_CD4_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr16:68034452..68034466,-p4@DPEP2
Hg19::chr16:68034470..68034496,-p2@DPEP2
Hg19::chr16:68034504..68034527,-p3@DPEP2


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
myeloid leukocyte1.97e-4572
leukocyte4.87e-44136
macrophage dendritic cell progenitor1.38e-4061
defensive cell5.12e-3948
phagocyte5.12e-3948
monopoietic cell8.64e-3959
monocyte8.64e-3959
monoblast8.64e-3959
promonocyte8.64e-3959
nongranular leukocyte1.26e-38115
granulocyte monocyte progenitor cell7.46e-3767
hematopoietic lineage restricted progenitor cell2.35e-35120
classical monocyte7.13e-3542
CD14-positive, CD16-negative classical monocyte7.13e-3542
myeloid lineage restricted progenitor cell2.53e-3466
hematopoietic stem cell1.78e-31168
angioblastic mesenchymal cell1.78e-31168
hematopoietic oligopotent progenitor cell2.40e-30161
hematopoietic multipotent progenitor cell2.40e-30161
hematopoietic cell1.55e-28177
myeloid cell4.05e-27108
common myeloid progenitor4.05e-27108
mature alpha-beta T cell1.80e-1618
alpha-beta T cell1.80e-1618
immature T cell1.80e-1618
mature T cell1.80e-1618
immature alpha-beta T cell1.80e-1618
stuff accumulating cell5.89e-1687
intermediate monocyte1.79e-129
CD14-positive, CD16-positive monocyte1.79e-129
T cell1.26e-1125
pro-T cell1.26e-1125
granulocyte1.53e-118
CD8-positive, alpha-beta T cell7.70e-1111
CD4-positive, alpha-beta T cell1.21e-086
blood cell8.39e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.67e-4398
blood island4.67e-4398
hemolymphoid system1.02e-39108
bone marrow1.89e-3076
immune system4.20e-3093
bone element5.52e-2782
skeletal element4.13e-2390
skeletal system3.94e-20100
lateral plate mesoderm7.78e-15203
adult organism7.98e-14114
blood8.86e-1115
haemolymphatic fluid8.86e-1115
organism substance8.86e-1115
musculoskeletal system1.31e-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)

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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.