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Coexpression cluster:C3131: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!1.62e-19!216;UBERON:0002384!2.43e-15!375;UBERON:0002390!3.75e-15!102;UBERON:0003061!3.75e-15!102;UBERON:0001474!9.56e-15!86;UBERON:0002193!1.30e-14!112;UBERON:0002371!1.44e-14!80;UBERON:0002204!7.16e-13!167;UBERON:0004765!5.68e-12!101;UBERON:0001434!5.68e-12!101;UBERON:0002405!1.99e-11!115;UBERON:0001637!2.53e-09!42;UBERON:0003509!2.53e-09!42;UBERON:0004572!2.53e-09!42;UBERON:0004535!6.56e-09!110;UBERON:0001009!4.64e-08!113;UBERON:0002049!5.61e-08!79;UBERON:0007798!5.61e-08!79;UBERON:0004573!5.18e-07!33;UBERON:0004571!5.18e-07!33;UBERON:0000055!6.58e-07!69
|ontology_enrichment_uberon=UBERON:0003081!1.62e-19!216;UBERON:0002384!2.43e-15!375;UBERON:0002390!3.75e-15!102;UBERON:0003061!3.75e-15!102;UBERON:0001474!9.56e-15!86;UBERON:0002193!1.30e-14!112;UBERON:0002371!1.44e-14!80;UBERON:0002204!7.16e-13!167;UBERON:0004765!5.68e-12!101;UBERON:0001434!5.68e-12!101;UBERON:0002405!1.99e-11!115;UBERON:0001637!2.53e-09!42;UBERON:0003509!2.53e-09!42;UBERON:0004572!2.53e-09!42;UBERON:0004535!6.56e-09!110;UBERON:0001009!4.64e-08!113;UBERON:0002049!5.61e-08!79;UBERON:0007798!5.61e-08!79;UBERON:0004573!5.18e-07!33;UBERON:0004571!5.18e-07!33;UBERON:0000055!6.58e-07!69
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189190102302064!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319115395979895!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108318760524705!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017232440111392!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027548258057249!YY1#7528;3:4.91117074985386:0.00844145534180826:0.032800697761854
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}}
}}

Revision as of 14:21, 5 September 2012


Full id: C3131_CD8_Natural_Peripheral_CD4_Eosinophils_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr11:207734..207745,+p7@RIC8A
Hg19::chr11:208610..208627,-p@chr11:208610..208627
-
Hg19::chr11:236025..236096,+p3@PSMD13


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:0001965G-protein alpha-subunit binding0.00188387666372531
GO:0005838proteasome regulatory particle (sensu Eukaryota)0.00565079814737156
GO:0000502proteasome complex (sensu Eukaryota)0.0232098562760032



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
somatic cell2.68e-23591
multi fate stem cell6.38e-23430
stem cell2.73e-22444
somatic stem cell4.25e-22436
leukocyte8.78e-22140
native cell1.28e-21722
myeloid leukocyte2.43e-1976
mesenchymal cell3.28e-17358
animal cell5.20e-17679
eukaryotic cell5.20e-17679
connective tissue cell1.16e-16365
CD14-positive, CD16-negative classical monocyte3.06e-1642
hematopoietic cell3.80e-16182
hematopoietic lineage restricted progenitor cell6.99e-16124
nongranular leukocyte1.05e-15119
granulocyte monocyte progenitor cell2.74e-1571
hematopoietic stem cell3.62e-15172
angioblastic mesenchymal cell3.62e-15172
classical monocyte1.15e-1445
macrophage dendritic cell progenitor2.47e-1465
motile cell4.05e-14390
myeloid lineage restricted progenitor cell4.62e-1470
monopoietic cell2.48e-1363
monocyte2.48e-1363
monoblast2.48e-1363
promonocyte2.48e-1363
hematopoietic oligopotent progenitor cell9.28e-13165
hematopoietic multipotent progenitor cell9.28e-13165
myeloid cell2.48e-10112
common myeloid progenitor2.48e-10112
blood cell3.72e-0711
intermediate monocyte7.12e-079
CD14-positive, CD16-positive monocyte7.12e-079
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.62e-19216
connective tissue2.43e-15375
hematopoietic system3.75e-15102
blood island3.75e-15102
bone element9.56e-1586
hemolymphoid system1.30e-14112
bone marrow1.44e-1480
musculoskeletal system7.16e-13167
skeletal element5.68e-12101
skeletal system5.68e-12101
immune system1.99e-11115
artery2.53e-0942
arterial blood vessel2.53e-0942
arterial system2.53e-0942
cardiovascular system6.56e-09110
circulatory system4.64e-08113
vasculature5.61e-0879
vascular system5.61e-0879
systemic artery5.18e-0733
systemic arterial system5.18e-0733
vessel6.58e-0769


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#90536.336201576962630.003930750035764890.0189190102302064
EGR1#195834.988179094810140.008056488137383440.0319115395979895
HMGN3#932438.178547723350590.001827766942164210.0108318760524705
PAX5#507936.669565531177830.003370290999677260.017232440111392
SIN3A#2594235.408884726815140.006318961977991520.027548258057249
YY1#752834.911170749853860.008441455341808260.032800697761854



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.