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Coexpression cluster:C2675: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.98e-33!112;UBERON:0003081!3.46e-32!216;UBERON:0002390!2.41e-30!102;UBERON:0003061!2.41e-30!102;UBERON:0002371!3.49e-30!80;UBERON:0002405!4.35e-25!115;UBERON:0001474!1.32e-24!86;UBERON:0004765!4.56e-19!101;UBERON:0001434!4.56e-19!101;UBERON:0002204!4.20e-12!167;UBERON:0000926!4.44e-09!448;UBERON:0004120!4.44e-09!448;UBERON:0006603!4.44e-09!448;UBERON:0007023!3.40e-07!115
|ontology_enrichment_uberon=UBERON:0002193!1.98e-33!112;UBERON:0003081!3.46e-32!216;UBERON:0002390!2.41e-30!102;UBERON:0003061!2.41e-30!102;UBERON:0002371!3.49e-30!80;UBERON:0002405!4.35e-25!115;UBERON:0001474!1.32e-24!86;UBERON:0004765!4.56e-19!101;UBERON:0001434!4.56e-19!101;UBERON:0002204!4.20e-12!167;UBERON:0000926!4.44e-09!448;UBERON:0004120!4.44e-09!448;UBERON:0006603!4.44e-09!448;UBERON:0007023!3.40e-07!115
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487323524058345!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.02405448902301!GATA1#2623;3:10.1702311078503:0.00151515816849827:0.00966597055523738!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283046043712913!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162839303490319
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}}
}}

Revision as of 13:58, 5 September 2012


Full id: C2675_Mast_CD14_immature_placenta_Basophils_Renal_chorionic



Phase1 CAGE Peaks

Hg19::chr2:182757484..182757503,-p@chr2:182757484..182757503
-
Hg19::chr3:119298314..119298392,+p2@ADPRH
Hg19::chr3:119298397..119298409,+p5@ADPRH
Hg19::chr3:119298429..119298454,+p3@ADPRH


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
granulocyte monocyte progenitor cell8.47e-3371
myeloid leukocyte5.95e-3176
macrophage dendritic cell progenitor8.01e-3065
myeloid lineage restricted progenitor cell3.23e-2970
monopoietic cell1.74e-2863
monocyte1.74e-2863
monoblast1.74e-2863
promonocyte1.74e-2863
CD14-positive, CD16-negative classical monocyte1.47e-2742
classical monocyte3.82e-2445
myeloid cell7.03e-24112
common myeloid progenitor7.03e-24112
leukocyte3.45e-15140
hematopoietic cell4.69e-13182
hematopoietic lineage restricted progenitor cell1.94e-12124
hematopoietic stem cell2.50e-12172
angioblastic mesenchymal cell2.50e-12172
hematopoietic oligopotent progenitor cell8.14e-12165
hematopoietic multipotent progenitor cell8.14e-12165
nongranular leukocyte1.16e-11119
endothelial cell5.41e-0935
meso-epithelial cell5.18e-0744
intermediate monocyte9.42e-079
CD14-positive, CD16-positive monocyte9.42e-079
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.98e-33112
lateral plate mesoderm3.46e-32216
hematopoietic system2.41e-30102
blood island2.41e-30102
bone marrow3.49e-3080
immune system4.35e-25115
bone element1.32e-2486
skeletal element4.56e-19101
skeletal system4.56e-19101
musculoskeletal system4.20e-12167
mesoderm4.44e-09448
mesoderm-derived structure4.44e-09448
presumptive mesoderm4.44e-09448
adult organism3.40e-07115


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
CCNT2#90534.752151182721970.01386206996689490.0487323524058345
EBF1#187936.679850134926750.005184294118278910.02405448902301
GATA1#2623310.17023110785030.001515158168498270.00966597055523738
HMGN3#932436.133910792512940.006640696683324720.0283046043712913
TCF12#693837.975848676639820.003090920396013070.0162839303490319



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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