Personal tools

Coexpression cluster:C2680: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C2680_Neutrophils_Eosinophils_CD14_Whole_migratory_CD8_immature |id=C2680 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C2680_Neutrophils_Eosinophils_CD14_Whole_migratory_CD8_immature
|full_id=C2680_Neutrophils_Eosinophils_CD14_Whole_migratory_CD8_immature
|id=C2680
|id=C2680
|ontology_enrichment_celltype=CL:0000037!7.67e-47!172;CL:0000566!7.67e-47!172;CL:0002032!8.36e-46!165;CL:0000837!8.36e-46!165;CL:0000988!1.25e-45!182;CL:0000738!6.34e-43!140;CL:0002031!4.33e-35!124;CL:0002087!1.29e-33!119;CL:0000763!2.16e-29!112;CL:0000049!2.16e-29!112;CL:0000766!1.16e-23!76;CL:0002057!2.01e-21!42;CL:0000557!1.40e-20!71;CL:0000839!3.45e-19!70;CL:0002009!9.88e-19!65;CL:0000860!3.18e-18!45;CL:0002194!1.30e-17!63;CL:0000576!1.30e-17!63;CL:0000040!1.30e-17!63;CL:0000559!1.30e-17!63;CL:0000542!2.14e-14!53;CL:0000051!2.14e-14!53;CL:0000838!3.00e-14!52;CL:0000791!1.61e-10!18;CL:0000789!1.61e-10!18;CL:0002420!1.61e-10!18;CL:0002419!1.61e-10!18;CL:0000790!1.61e-10!18;CL:0000134!3.30e-10!358;CL:0000084!3.48e-09!25;CL:0000827!3.48e-09!25;CL:0002320!8.02e-09!365;CL:0000625!1.46e-07!11;CL:0000048!3.86e-07!430
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.34e-28!112;UBERON:0002390!3.88e-26!102;UBERON:0003061!3.88e-26!102;UBERON:0003081!1.09e-24!216;UBERON:0002405!3.69e-16!115;UBERON:0002371!3.81e-16!80;UBERON:0001474!1.30e-12!86;UBERON:0000178!6.24e-10!15;UBERON:0000179!6.24e-10!15;UBERON:0000463!6.24e-10!15;UBERON:0001009!4.70e-09!113;UBERON:0004535!1.76e-08!110;UBERON:0004765!2.96e-08!101;UBERON:0001434!2.96e-08!101;UBERON:0002384!3.69e-08!375
}}
}}

Revision as of 14:27, 21 May 2012


Full id: C2680_Neutrophils_Eosinophils_CD14_Whole_migratory_CD8_immature



Phase1 CAGE Peaks

Hg19::chr2:201983381..201983425,+p2@CFLAR
Hg19::chr2:201983432..201983453,+p5@CFLAR
Hg19::chr2:201983467..201983478,+p19@CFLAR
Hg19::chr2:201983487..201983498,+p23@CFLAR


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
hematopoietic stem cell7.67e-47172
angioblastic mesenchymal cell7.67e-47172
hematopoietic oligopotent progenitor cell8.36e-46165
hematopoietic multipotent progenitor cell8.36e-46165
hematopoietic cell1.25e-45182
leukocyte6.34e-43140
hematopoietic lineage restricted progenitor cell4.33e-35124
nongranular leukocyte1.29e-33119
myeloid cell2.16e-29112
common myeloid progenitor2.16e-29112
myeloid leukocyte1.16e-2376
CD14-positive, CD16-negative classical monocyte2.01e-2142
granulocyte monocyte progenitor cell1.40e-2071
myeloid lineage restricted progenitor cell3.45e-1970
macrophage dendritic cell progenitor9.88e-1965
classical monocyte3.18e-1845
monopoietic cell1.30e-1763
monocyte1.30e-1763
monoblast1.30e-1763
promonocyte1.30e-1763
lymphocyte2.14e-1453
common lymphoid progenitor2.14e-1453
lymphoid lineage restricted progenitor cell3.00e-1452
mature alpha-beta T cell1.61e-1018
alpha-beta T cell1.61e-1018
immature T cell1.61e-1018
mature T cell1.61e-1018
immature alpha-beta T cell1.61e-1018
mesenchymal cell3.30e-10358
T cell3.48e-0925
pro-T cell3.48e-0925
connective tissue cell8.02e-09365
CD8-positive, alpha-beta T cell1.46e-0711
multi fate stem cell3.86e-07430
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.34e-28112
hematopoietic system3.88e-26102
blood island3.88e-26102
lateral plate mesoderm1.09e-24216
immune system3.69e-16115
bone marrow3.81e-1680
bone element1.30e-1286
blood6.24e-1015
haemolymphatic fluid6.24e-1015
organism substance6.24e-1015
circulatory system4.70e-09113
cardiovascular system1.76e-08110
skeletal element2.96e-08101
skeletal system2.96e-08101
connective tissue3.69e-08375


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


No analysis results for this cluster

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.