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Coexpression cluster:C2312: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!4.36e-25!80;UBERON:0001474!9.29e-24!86;UBERON:0002390!9.84e-24!102;UBERON:0003061!9.84e-24!102;UBERON:0002193!1.71e-20!112;UBERON:0004765!1.41e-19!101;UBERON:0001434!1.41e-19!101;UBERON:0002405!2.16e-17!115;UBERON:0003081!2.38e-08!216;UBERON:0002204!5.81e-07!167
|ontology_enrichment_uberon=UBERON:0002371!4.36e-25!80;UBERON:0001474!9.29e-24!86;UBERON:0002390!9.84e-24!102;UBERON:0003061!9.84e-24!102;UBERON:0002193!1.71e-20!112;UBERON:0004765!1.41e-19!101;UBERON:0001434!1.41e-19!101;UBERON:0002405!2.16e-17!115;UBERON:0003081!2.38e-08!216;UBERON:0002204!5.81e-07!167
|tf_chipseq_enrich=ESRRA#2101;1:120.960078534031:0.00824166246177904:0.0324823950279536!JUNB#3726;2:15.3053163299106:0.00612694714847562:0.0270957077083183
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}}
}}

Revision as of 12:40, 5 September 2012


Full id: C2312_testis_Eosinophils_CD14_Neutrophils_Basophils_immature_cord



Phase1 CAGE Peaks

Hg19::chr14:77292773..77292782,+p1@C14orf166B
Hg19::chr1:155960989..155961011,-p@chr1:155960989..155961011
-
Hg19::chr20:44600983..44600997,-p8@ZNF335
Hg19::chr2:69064331..69064344,-p1@ENST00000415448


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
classical monocyte7.99e-3345
CD14-positive, CD16-negative classical monocyte9.14e-3342
myeloid leukocyte1.19e-3276
leukocyte2.31e-31140
macrophage dendritic cell progenitor1.03e-2865
monopoietic cell3.22e-2763
monocyte3.22e-2763
monoblast3.22e-2763
promonocyte3.22e-2763
granulocyte monocyte progenitor cell3.60e-2771
myeloid lineage restricted progenitor cell5.41e-2570
nongranular leukocyte8.68e-25119
hematopoietic stem cell4.11e-23172
angioblastic mesenchymal cell4.11e-23172
hematopoietic lineage restricted progenitor cell4.48e-23124
hematopoietic cell1.24e-22182
hematopoietic oligopotent progenitor cell1.20e-20165
hematopoietic multipotent progenitor cell1.20e-20165
myeloid cell2.18e-20112
common myeloid progenitor2.18e-20112
granulocyte6.27e-088
intermediate monocyte2.33e-079
CD14-positive, CD16-positive monocyte2.33e-079
Uber Anatomy
Ontology termp-valuen
bone marrow4.36e-2580
bone element9.29e-2486
hematopoietic system9.84e-24102
blood island9.84e-24102
hemolymphoid system1.71e-20112
skeletal element1.41e-19101
skeletal system1.41e-19101
immune system2.16e-17115
lateral plate mesoderm2.38e-08216
musculoskeletal system5.81e-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)

{{{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
ESRRA#21011120.9600785340310.008241662461779040.0324823950279536
JUNB#3726215.30531632991060.006126947148475620.0270957077083183



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.