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Coexpression cluster:C3787: Difference between revisions

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|full_id=C3787_CD14_Eosinophils_Neutrophils_Peripheral_aorta_Natural_CD4
|full_id=C3787_CD14_Eosinophils_Neutrophils_Peripheral_aorta_Natural_CD4
|id=C3787
|id=C3787
|ontology_enrichment_celltype=CL:0000738!1.08e-28!140;CL:0002057!3.79e-23!42;CL:0002087!9.06e-23!119;CL:0000037!1.88e-22!172;CL:0000566!1.88e-22!172;CL:0000860!2.24e-22!45;CL:0002031!1.28e-21!124;CL:0002032!2.25e-21!165;CL:0000837!2.25e-21!165;CL:0000988!1.87e-20!182;CL:0000766!2.34e-18!76;CL:0000557!1.70e-14!71;CL:0002009!3.27e-14!65;CL:0002194!2.79e-13!63;CL:0000576!2.79e-13!63;CL:0000040!2.79e-13!63;CL:0000559!2.79e-13!63;CL:0000763!4.95e-13!112;CL:0000049!4.95e-13!112;CL:0000839!5.33e-13!70;CL:0000542!2.24e-08!53;CL:0000051!2.24e-08!53;CL:0000838!3.70e-08!52;CL:0002320!9.94e-08!365;CL:0000134!1.38e-07!358;CL:0002393!7.53e-07!9;CL:0002397!7.53e-07!9
|ontology_enrichment_celltype=CL:0000738!3.80e-29!136;CL:0000860!9.58e-25!42;CL:0002057!9.58e-25!42;CL:0002087!2.01e-21!115;CL:0002031!6.63e-21!120;CL:0000037!7.68e-21!168;CL:0000566!7.68e-21!168;CL:0002032!7.85e-20!161;CL:0000837!7.85e-20!161;CL:0000988!8.01e-20!177;CL:0000473!3.14e-19!48;CL:0000234!3.14e-19!48;CL:0000766!7.11e-19!72;CL:0000557!1.12e-14!67;CL:0002009!7.14e-14!61;CL:0000839!3.83e-13!66;CL:0002194!8.20e-13!59;CL:0000576!8.20e-13!59;CL:0000040!8.20e-13!59;CL:0000559!8.20e-13!59;CL:0000763!2.06e-12!108;CL:0000049!2.06e-12!108;CL:0002393!8.12e-08!9;CL:0002397!8.12e-08!9;CL:0000542!1.42e-07!53;CL:0000051!1.42e-07!53;CL:0000838!2.09e-07!52;CL:0000094!3.12e-07!8;CL:0000134!6.62e-07!354;CL:0002242!6.84e-07!55;CL:0000081!8.45e-07!11
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.10e-17!102;UBERON:0003061!1.10e-17!102;UBERON:0002193!1.33e-14!112;UBERON:0002371!4.86e-13!80;UBERON:0001474!1.37e-11!86;UBERON:0002405!9.14e-11!115;UBERON:0004765!2.63e-09!101;UBERON:0001434!2.63e-09!101;UBERON:0002384!3.39e-07!375
|ontology_enrichment_uberon=UBERON:0002390!4.08e-16!98;UBERON:0003061!4.08e-16!98;UBERON:0002193!1.52e-13!108;UBERON:0002371!2.66e-12!76;UBERON:0001474!8.32e-11!82;UBERON:0002405!2.11e-10!93;UBERON:0004765!2.97e-09!90;UBERON:0001434!2.74e-08!100
|tf_chipseq_enrich=BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183878839521322!BCL3#602;2:23.0314018691589:0.00246467476084291:0.0138533000025656!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401949161775988!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.0268347634696819!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.046040682825896!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00882092668443226
|tf_chipseq_enrich=BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183878839521322!BCL3#602;2:23.0314018691589:0.00246467476084291:0.0138533000025656!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401949161775988!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.0268347634696819!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.046040682825896!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00882092668443226
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}}
}}

Revision as of 15:24, 19 October 2012


Full id: C3787_CD14_Eosinophils_Neutrophils_Peripheral_aorta_Natural_CD4



Phase1 CAGE Peaks

Hg19::chr19:39900896..39900918,+p@chr19:39900896..39900918
+
Hg19::chr19:39900924..39900973,+p@chr19:39900924..39900973
+
Hg19::chr19:39901623..39901638,+p@chr19:39901623..39901638
+


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
leukocyte3.80e-29136
classical monocyte9.58e-2542
CD14-positive, CD16-negative classical monocyte9.58e-2542
nongranular leukocyte2.01e-21115
hematopoietic lineage restricted progenitor cell6.63e-21120
hematopoietic stem cell7.68e-21168
angioblastic mesenchymal cell7.68e-21168
hematopoietic oligopotent progenitor cell7.85e-20161
hematopoietic multipotent progenitor cell7.85e-20161
hematopoietic cell8.01e-20177
defensive cell3.14e-1948
phagocyte3.14e-1948
myeloid leukocyte7.11e-1972
granulocyte monocyte progenitor cell1.12e-1467
macrophage dendritic cell progenitor7.14e-1461
myeloid lineage restricted progenitor cell3.83e-1366
monopoietic cell8.20e-1359
monocyte8.20e-1359
monoblast8.20e-1359
promonocyte8.20e-1359
myeloid cell2.06e-12108
common myeloid progenitor2.06e-12108
intermediate monocyte8.12e-089
CD14-positive, CD16-positive monocyte8.12e-089
lymphocyte1.42e-0753
common lymphoid progenitor1.42e-0753
lymphoid lineage restricted progenitor cell2.09e-0752
granulocyte3.12e-078
mesenchymal cell6.62e-07354
nucleate cell6.84e-0755
blood cell8.45e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.08e-1698
blood island4.08e-1698
hemolymphoid system1.52e-13108
bone marrow2.66e-1276
bone element8.32e-1182
immune system2.11e-1093
skeletal element2.97e-0990
skeletal system2.74e-08100


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
BCL11A#53335218.91297006907140.003639406248379680.0183878839521322
BCL3#602223.03140186915890.002464674760842910.0138533000025656
ELK4#2005210.8237877723120.01091284719516480.0401949161775988
IRF4#3662214.60967512449610.006056122473217890.0268347634696819
NR3C1#290829.982015554115360.01278474365547170.046040682825896
POU2F2#545239.106124057742520.001324165192682130.00882092668443226



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.