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Coexpression cluster:C3788: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!1.95e-32!98;UBERON:0003061!1.95e-32!98;UBERON:0002193!4.67e-28!108;UBERON:0000178!5.78e-18!15;UBERON:0000179!5.78e-18!15;UBERON:0000463!5.78e-18!15;UBERON:0002371!1.47e-16!76;UBERON:0002405!3.75e-16!93;UBERON:0001474!1.13e-14!82;UBERON:0004765!1.45e-12!90;UBERON:0003081!1.50e-11!203;UBERON:0001434!1.95e-10!100
|ontology_enrichment_uberon=UBERON:0002390!1.95e-32!98;UBERON:0003061!1.95e-32!98;UBERON:0002193!4.67e-28!108;UBERON:0000178!5.78e-18!15;UBERON:0000179!5.78e-18!15;UBERON:0000463!5.78e-18!15;UBERON:0002371!1.47e-16!76;UBERON:0002405!3.75e-16!93;UBERON:0001474!1.13e-14!82;UBERON:0004765!1.45e-12!90;UBERON:0003081!1.50e-11!203;UBERON:0001434!1.95e-10!100
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}}
}}

Revision as of 16:21, 26 November 2012


Full id: C3788_Reticulocytes_Neutrophils_Basophils_Whole_CD34_Eosinophils_chronic



Phase1 CAGE Peaks

Hg19::chr19:40228629..40228645,-p1@CLC
Hg19::chr19:40228657..40228674,-p2@CLC
Hg19::chr8:23424897..23424916,+p20@SLC25A37


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

GO IDGO nameFDR corrected p-value
GO:0048250mitochondrial iron ion transport0.00441540091840339
GO:0005381iron ion transmembrane transporter activity0.0132446430480771
GO:0004622lysophospholipase activity0.0132446430480771
GO:0046915transition metal ion transmembrane transporter activity0.0331013720421312
GO:0006839mitochondrial transport0.0359243444714689
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0359243444714689
GO:0006826iron ion transport0.0359243444714689
GO:0007005mitochondrion organization and biogenesis0.049057712163764
GO:0000041transition metal ion transport0.0499668210433594



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 leukocyte4.08e-3072
hematopoietic stem cell3.58e-29168
angioblastic mesenchymal cell3.58e-29168
myeloid cell6.77e-28108
common myeloid progenitor6.77e-28108
hematopoietic cell9.81e-27177
leukocyte1.01e-25136
hematopoietic oligopotent progenitor cell7.51e-25161
hematopoietic multipotent progenitor cell7.51e-25161
classical monocyte1.10e-2242
CD14-positive, CD16-negative classical monocyte1.10e-2242
myeloid lineage restricted progenitor cell2.35e-2266
monopoietic cell2.81e-2259
monocyte2.81e-2259
monoblast2.81e-2259
promonocyte2.81e-2259
macrophage dendritic cell progenitor3.04e-2161
nongranular leukocyte3.70e-20115
defensive cell7.52e-1948
phagocyte7.52e-1948
granulocyte monocyte progenitor cell1.62e-1867
hematopoietic lineage restricted progenitor cell9.83e-18120
granulocyte3.71e-168
blood cell3.21e-1111
intermediate monocyte9.22e-099
CD14-positive, CD16-positive monocyte9.22e-099
neutrophil3.01e-073
stuff accumulating cell3.35e-0787
basophil5.63e-073
single nucleate cell8.75e-073
mononuclear cell8.75e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.95e-3298
blood island1.95e-3298
hemolymphoid system4.67e-28108
blood5.78e-1815
haemolymphatic fluid5.78e-1815
organism substance5.78e-1815
bone marrow1.47e-1676
immune system3.75e-1693
bone element1.13e-1482
skeletal element1.45e-1290
lateral plate mesoderm1.50e-11203
skeletal system1.95e-10100


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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