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Coexpression cluster:C3514: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!4.62e-19!98;UBERON:0003061!4.62e-19!98;UBERON:0002193!1.51e-16!108;UBERON:0002371!9.20e-11!76;UBERON:0002405!1.66e-10!93;UBERON:0001474!6.71e-10!82;UBERON:0000178!3.10e-09!15;UBERON:0000179!3.10e-09!15;UBERON:0000463!3.10e-09!15;UBERON:0004765!1.34e-08!90;UBERON:0001434!3.46e-07!100
|ontology_enrichment_uberon=UBERON:0002390!4.62e-19!98;UBERON:0003061!4.62e-19!98;UBERON:0002193!1.51e-16!108;UBERON:0002371!9.20e-11!76;UBERON:0002405!1.66e-10!93;UBERON:0001474!6.71e-10!82;UBERON:0000178!3.10e-09!15;UBERON:0000179!3.10e-09!15;UBERON:0000463!3.10e-09!15;UBERON:0004765!1.34e-08!90;UBERON:0001434!3.46e-07!100
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}}
}}

Revision as of 16:10, 26 November 2012


Full id: C3514_Eosinophils_CD4_Neutrophils_CD8_Whole_CD14_blood



Phase1 CAGE Peaks

Hg19::chr15:74908120..74908140,-p@chr15:74908120..74908140
-
Hg19::chr19:1028295..1028312,+p@chr19:1028295..1028312
+
Hg19::chr1:150550293..150550307,-p@chr1:150550293..150550307
-


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
leukocyte3.45e-38136
hematopoietic lineage restricted progenitor cell1.64e-27120
nongranular leukocyte2.43e-27115
hematopoietic stem cell2.93e-27168
angioblastic mesenchymal cell2.93e-27168
hematopoietic cell6.44e-26177
hematopoietic oligopotent progenitor cell9.23e-24161
hematopoietic multipotent progenitor cell9.23e-24161
mature alpha-beta T cell1.21e-1918
alpha-beta T cell1.21e-1918
immature T cell1.21e-1918
mature T cell1.21e-1918
immature alpha-beta T cell1.21e-1918
T cell1.23e-1825
pro-T cell1.23e-1825
myeloid leukocyte3.44e-1872
classical monocyte2.54e-1742
CD14-positive, CD16-negative classical monocyte2.54e-1742
lymphoid lineage restricted progenitor cell1.65e-1652
lymphocyte5.59e-1653
common lymphoid progenitor5.59e-1653
nucleate cell5.56e-1555
CD8-positive, alpha-beta T cell4.45e-1411
defensive cell7.21e-1448
phagocyte7.21e-1448
granulocyte monocyte progenitor cell5.20e-1267
myeloid lineage restricted progenitor cell2.20e-1166
granulocyte2.09e-108
macrophage dendritic cell progenitor2.61e-1061
monopoietic cell5.01e-1059
monocyte5.01e-1059
monoblast5.01e-1059
promonocyte5.01e-1059
myeloid cell1.24e-09108
common myeloid progenitor1.24e-09108
intermediate monocyte1.43e-099
CD14-positive, CD16-positive monocyte1.43e-099
CD4-positive, alpha-beta T cell9.49e-096
blood cell6.27e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.62e-1998
blood island4.62e-1998
hemolymphoid system1.51e-16108
bone marrow9.20e-1176
immune system1.66e-1093
bone element6.71e-1082
blood3.10e-0915
haemolymphatic fluid3.10e-0915
organism substance3.10e-0915
skeletal element1.34e-0890
skeletal system3.46e-07100


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.

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