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Coexpression cluster:C2584: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!2.01e-38!80;UBERON:0002390!1.21e-35!102;UBERON:0003061!1.21e-35!102;UBERON:0002193!8.82e-35!112;UBERON:0001474!3.90e-34!86;UBERON:0002405!3.84e-28!115;UBERON:0004765!6.21e-27!101;UBERON:0001434!6.21e-27!101;UBERON:0003081!2.74e-12!216;UBERON:0002204!2.57e-10!167;UBERON:0002384!3.65e-10!375
|ontology_enrichment_uberon=UBERON:0002371!2.01e-38!80;UBERON:0002390!1.21e-35!102;UBERON:0003061!1.21e-35!102;UBERON:0002193!8.82e-35!112;UBERON:0001474!3.90e-34!86;UBERON:0002405!3.84e-28!115;UBERON:0004765!6.21e-27!101;UBERON:0001434!6.21e-27!101;UBERON:0003081!2.74e-12!216;UBERON:0002204!2.57e-10!167;UBERON:0002384!3.65e-10!375
|tf_chipseq_enrich=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360220183451847!BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296267351392775!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172999384507345!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240512834674365!IRF4#3662;2:10.9572563433721:0.0117453018068803:0.042848525059689!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.00488827414814061!MEF2C#4208;2:20.655677246312:0.00340257057944504:0.0173583953080627!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435023074014891!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281025986383469!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162798242593781
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}}
}}

Revision as of 12:01, 5 September 2012


Full id: C2584_Dendritic_CD14_Basophils_CD14CD16_Peripheral_CD34_granulocyte



Phase1 CAGE Peaks

Hg19::chr1:42194773..42194782,+p@chr1:42194773..42194782
+
Hg19::chr22:44422556..44422575,-p@chr22:44422556..44422575
-
Hg19::chr2:128321442..128321453,+p@chr2:128321442..128321453
+
Hg19::chr8:11724934..11724951,+p@chr8:11724934..11724951
+


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
leukocyte3.31e-61140
hematopoietic stem cell2.17e-55172
angioblastic mesenchymal cell2.17e-55172
nongranular leukocyte1.65e-53119
hematopoietic lineage restricted progenitor cell3.16e-51124
hematopoietic cell3.85e-51182
hematopoietic oligopotent progenitor cell7.29e-50165
hematopoietic multipotent progenitor cell7.29e-50165
CD14-positive, CD16-negative classical monocyte2.08e-4642
granulocyte monocyte progenitor cell7.86e-4371
classical monocyte4.52e-4245
macrophage dendritic cell progenitor2.79e-4165
myeloid leukocyte1.42e-4076
monopoietic cell2.07e-3963
monocyte2.07e-3963
monoblast2.07e-3963
promonocyte2.07e-3963
myeloid lineage restricted progenitor cell3.38e-3870
myeloid cell1.86e-35112
common myeloid progenitor1.86e-35112
lymphocyte1.77e-1253
common lymphoid progenitor1.77e-1253
lymphoid lineage restricted progenitor cell5.18e-1252
intermediate monocyte9.32e-129
CD14-positive, CD16-positive monocyte9.32e-129
mesenchymal cell9.36e-12358
connective tissue cell6.40e-11365
motile cell4.37e-09390
dendritic cell3.16e-0810
lymphocyte of B lineage4.24e-0724
pro-B cell4.24e-0724
stem cell5.90e-07444
Uber Anatomy
Ontology termp-valuen
bone marrow2.01e-3880
hematopoietic system1.21e-35102
blood island1.21e-35102
hemolymphoid system8.82e-35112
bone element3.90e-3486
immune system3.84e-28115
skeletal element6.21e-27101
skeletal system6.21e-27101
lateral plate mesoderm2.74e-12216
musculoskeletal system2.57e-10167
connective tissue3.65e-10375


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
BATF#10538212.17890089615180.009566758805047810.0360220183451847
BCL11A#53335214.18472755180350.007108328585298740.0296267351392775
CHD2#110637.758017125587640.003351522464536340.0172999384507345
EBF1#187936.679850134926750.005184294118278910.0240512834674365
IRF4#3662210.95725634337210.01174530180688030.042848525059689
MEF2A#4205314.0574231822330.0005830038854186610.00488827414814061
MEF2C#4208220.6556772463120.003402570579445040.0173583953080627
PAX5#507935.002174148383370.01196533174786410.0435023074014891
SPI1#668836.153242631392040.006580387113059030.0281025986383469
TCF12#693837.975848676639820.003090920396013070.0162798242593781



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.