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Coexpression cluster:C1812: Difference between revisions

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|ontology_enrichment_disease=DOID:8692!6.88e-15!31;DOID:1240!1.62e-12!39;DOID:2531!3.06e-09!51;DOID:0060083!3.06e-09!51
|ontology_enrichment_disease=DOID:8692!6.88e-15!31;DOID:1240!1.62e-12!39;DOID:2531!3.06e-09!51;DOID:0060083!3.06e-09!51
|ontology_enrichment_uberon=UBERON:0002390!2.34e-33!102;UBERON:0003061!2.34e-33!102;UBERON:0002193!1.27e-29!112;UBERON:0002371!3.18e-27!80;UBERON:0001474!1.97e-24!86;UBERON:0002405!4.65e-23!115;UBERON:0004765!1.96e-17!101;UBERON:0001434!1.96e-17!101;UBERON:0007023!6.46e-13!115;UBERON:0003081!7.60e-08!216;UBERON:0002384!1.06e-07!375;UBERON:0000178!1.75e-07!15;UBERON:0000179!1.75e-07!15;UBERON:0000463!1.75e-07!15
|ontology_enrichment_uberon=UBERON:0002390!2.34e-33!102;UBERON:0003061!2.34e-33!102;UBERON:0002193!1.27e-29!112;UBERON:0002371!3.18e-27!80;UBERON:0001474!1.97e-24!86;UBERON:0002405!4.65e-23!115;UBERON:0004765!1.96e-17!101;UBERON:0001434!1.96e-17!101;UBERON:0007023!6.46e-13!115;UBERON:0003081!7.60e-08!216;UBERON:0002384!1.06e-07!375;UBERON:0000178!1.75e-07!15;UBERON:0000179!1.75e-07!15;UBERON:0000463!1.75e-07!15
|tf_chipseq_enrich=MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256820993751589
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}}
}}

Revision as of 11:32, 5 September 2012


Full id: C1812_Mast_granulocyte_acute_Eosinophils_chronic_Basophils_CD133



Phase1 CAGE Peaks

Hg19::chr19:18391340..18391345,-p8@BC169275
Hg19::chr20:1448319..1448351,-p3@NSFL1C
Hg19::chr6:36665587..36665612,+p1@uc010jwl.1
Hg19::chr6:36665624..36665632,+p2@uc010jwl.1
Hg19::chr8:145516154..145516162,-p@chr8:145516154..145516162
-


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell3.10e-53172
angioblastic mesenchymal cell3.10e-53172
myeloid cell7.74e-53112
common myeloid progenitor7.74e-53112
hematopoietic oligopotent progenitor cell7.30e-50165
hematopoietic multipotent progenitor cell7.30e-50165
hematopoietic cell2.22e-47182
leukocyte1.30e-36140
myeloid leukocyte3.71e-3676
granulocyte monocyte progenitor cell8.77e-3271
myeloid lineage restricted progenitor cell2.47e-3170
hematopoietic lineage restricted progenitor cell4.28e-30124
macrophage dendritic cell progenitor4.12e-2765
CD14-positive, CD16-negative classical monocyte2.68e-2642
monopoietic cell2.91e-2663
monocyte2.91e-2663
monoblast2.91e-2663
promonocyte2.91e-2663
nongranular leukocyte6.50e-26119
classical monocyte4.24e-2345
mesenchymal cell7.77e-09358
connective tissue cell2.81e-08365
granulocyte1.70e-078
intermediate monocyte5.13e-079
CD14-positive, CD16-positive monocyte5.13e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.34e-33102
blood island2.34e-33102
hemolymphoid system1.27e-29112
bone marrow3.18e-2780
bone element1.97e-2486
immune system4.65e-23115
skeletal element1.96e-17101
skeletal system1.96e-17101
adult organism6.46e-13115
lateral plate mesoderm7.60e-08216
connective tissue1.06e-07375
blood1.75e-0715
haemolymphatic fluid1.75e-0715
organism substance1.75e-0715
Disease
Ontology termp-valuen
myeloid leukemia6.88e-1531
leukemia1.62e-1239
hematologic cancer3.06e-0951
immune system cancer3.06e-0951


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
MYC#460944.177825497287520.005691969036823440.0256820993751589



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1812&oldid=2130380"