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Coexpression cluster:C2404: Difference between revisions

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|full_id=C2404_CD14_Mast_Eosinophils_Neutrophils_Mesenchymal_Basophils_CD19
|full_id=C2404_CD14_Mast_Eosinophils_Neutrophils_Mesenchymal_Basophils_CD19
|id=C2404
|id=C2404
|ontology_enrichment_celltype=CL:0000766!1.55e-32!76;CL:0000557!1.47e-28!71;CL:0002057!3.79e-27!42;CL:0000738!1.55e-26!140;CL:0002009!1.02e-25!65;CL:0000839!2.61e-25!70;CL:0000860!6.32e-25!45;CL:0000763!7.52e-25!112;CL:0000049!7.52e-25!112;CL:0002194!1.19e-24!63;CL:0000576!1.19e-24!63;CL:0000040!1.19e-24!63;CL:0000559!1.19e-24!63;CL:0000988!1.75e-24!182;CL:0000037!1.75e-24!172;CL:0000566!1.75e-24!172;CL:0002032!9.06e-23!165;CL:0000837!9.06e-23!165;CL:0002031!5.15e-22!124;CL:0002087!8.24e-21!119;CL:0002320!1.16e-16!365;CL:0000134!3.83e-15!358;CL:0000219!3.67e-13!390;CL:0000048!9.77e-08!430;CL:0002371!1.69e-07!591;CL:0000063!3.48e-07!578;CL:0000723!3.57e-07!436
|ontology_enrichment_celltype=CL:0000766!2.26e-34!72;CL:0000557!1.07e-29!67;CL:0000839!5.07e-28!66;CL:0000860!2.06e-27!42;CL:0002057!2.06e-27!42;CL:0002009!2.19e-27!61;CL:0000738!2.22e-27!136;CL:0002194!2.28e-26!59;CL:0000576!2.28e-26!59;CL:0000040!2.28e-26!59;CL:0000559!2.28e-26!59;CL:0000763!2.57e-26!108;CL:0000049!2.57e-26!108;CL:0000037!5.74e-25!168;CL:0000566!5.74e-25!168;CL:0000473!1.40e-24!48;CL:0000234!1.40e-24!48;CL:0000988!1.60e-24!177;CL:0002032!2.43e-23!161;CL:0000837!2.43e-23!161;CL:0002031!3.88e-23!120;CL:0002087!3.94e-21!115;CL:0002320!1.20e-12!361;CL:0000134!1.48e-11!354;CL:0000325!2.87e-10!87;CL:0000219!4.14e-10!386
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.43e-31!102;UBERON:0003061!1.43e-31!102;UBERON:0002193!2.79e-29!112;UBERON:0002371!4.43e-28!80;UBERON:0001474!5.12e-27!86;UBERON:0002405!2.03e-26!115;UBERON:0004765!5.29e-22!101;UBERON:0001434!5.29e-22!101;UBERON:0002384!4.72e-16!375;UBERON:0003081!4.00e-14!216;UBERON:0002204!1.22e-09!167
|ontology_enrichment_uberon=UBERON:0002390!1.08e-30!98;UBERON:0003061!1.08e-30!98;UBERON:0002193!5.26e-29!108;UBERON:0002371!3.01e-27!76;UBERON:0001474!1.92e-25!82;UBERON:0002405!2.65e-25!93;UBERON:0004765!7.53e-24!90;UBERON:0001434!2.39e-21!100;UBERON:0002384!6.87e-12!371;UBERON:0003081!1.39e-11!203;UBERON:0002204!3.13e-08!167
|tf_chipseq_enrich=BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296220065884612!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428365545260782
|tf_chipseq_enrich=BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296220065884612!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428365545260782
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}}
}}

Revision as of 13:59, 19 October 2012


Full id: C2404_CD14_Mast_Eosinophils_Neutrophils_Mesenchymal_Basophils_CD19



Phase1 CAGE Peaks

Hg19::chr17:38474489..38474548,+p1@RARA
Hg19::chr17:38487563..38487578,+p10@RARA
Hg19::chr6:130005257..130005290,-p@chr6:130005257..130005290
-
Hg19::chr9:137217884..137217916,-p@chr9:137217884..137217916
-


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
myeloid leukocyte2.26e-3472
granulocyte monocyte progenitor cell1.07e-2967
myeloid lineage restricted progenitor cell5.07e-2866
classical monocyte2.06e-2742
CD14-positive, CD16-negative classical monocyte2.06e-2742
macrophage dendritic cell progenitor2.19e-2761
leukocyte2.22e-27136
monopoietic cell2.28e-2659
monocyte2.28e-2659
monoblast2.28e-2659
promonocyte2.28e-2659
myeloid cell2.57e-26108
common myeloid progenitor2.57e-26108
hematopoietic stem cell5.74e-25168
angioblastic mesenchymal cell5.74e-25168
defensive cell1.40e-2448
phagocyte1.40e-2448
hematopoietic cell1.60e-24177
hematopoietic oligopotent progenitor cell2.43e-23161
hematopoietic multipotent progenitor cell2.43e-23161
hematopoietic lineage restricted progenitor cell3.88e-23120
nongranular leukocyte3.94e-21115
connective tissue cell1.20e-12361
mesenchymal cell1.48e-11354
stuff accumulating cell2.87e-1087
motile cell4.14e-10386
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.08e-3098
blood island1.08e-3098
hemolymphoid system5.26e-29108
bone marrow3.01e-2776
bone element1.92e-2582
immune system2.65e-2593
skeletal element7.53e-2490
skeletal system2.39e-21100
connective tissue6.87e-12371
lateral plate mesoderm1.39e-11203
musculoskeletal system3.13e-08167


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#53335214.18472755180350.007108328585298740.0296220065884612
PBX3#5090210.95725634337210.01174530180688030.0428365545260782



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.