Personal tools

Coexpression cluster:C3942: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C3942_Mast_CD14_CD4_CD8_Natural_Eosinophils_Basophils |id=C3942 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C3942_Mast_CD14_CD4_CD8_Natural_Eosinophils_Basophils
|full_id=C3942_Mast_CD14_CD4_CD8_Natural_Eosinophils_Basophils
|id=C3942
|id=C3942
|ontology_enrichment_celltype=CL:0000738!3.42e-34!140;CL:0000988!4.32e-31!182;CL:0000037!8.77e-31!172;CL:0000566!8.77e-31!172;CL:0000766!8.79e-29!76;CL:0002032!4.85e-27!165;CL:0000837!4.85e-27!165;CL:0002031!3.77e-25!124;CL:0002057!4.64e-25!42;CL:0000557!1.28e-24!71;CL:0000763!2.38e-24!112;CL:0000049!2.38e-24!112;CL:0002087!1.61e-22!119;CL:0000839!1.87e-22!70;CL:0000860!2.19e-22!45;CL:0002009!5.80e-21!65;CL:0002194!1.89e-19!63;CL:0000576!1.89e-19!63;CL:0000040!1.89e-19!63;CL:0000559!1.89e-19!63;CL:0002393!1.03e-10!9;CL:0002397!1.03e-10!9;CL:0000134!4.92e-09!358;CL:0002320!1.49e-08!365;CL:0000451!1.63e-07!10;CL:0000081!4.90e-07!11;CL:0000080!6.60e-07!6;CL:0000624!7.38e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.16e-22!102;UBERON:0003061!2.16e-22!102;UBERON:0002371!7.86e-21!80;UBERON:0002193!6.89e-20!112;UBERON:0001474!9.71e-20!86;UBERON:0004765!1.67e-15!101;UBERON:0001434!1.67e-15!101;UBERON:0002405!9.17e-14!115;UBERON:0002384!4.00e-08!375;UBERON:0003081!1.21e-07!216
}}
}}

Revision as of 14:42, 21 May 2012


Full id: C3942_Mast_CD14_CD4_CD8_Natural_Eosinophils_Basophils



Phase1 CAGE Peaks

Hg19::chr1:224033095..224033112,-p@chr1:224033095..224033112
-
Hg19::chr1:224033119..224033129,-p@chr1:224033119..224033129
-
Hg19::chr2:197127963..197127981,-p@chr2:197127963..197127981
-


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
leukocyte3.42e-34140
hematopoietic cell4.32e-31182
hematopoietic stem cell8.77e-31172
angioblastic mesenchymal cell8.77e-31172
myeloid leukocyte8.79e-2976
hematopoietic oligopotent progenitor cell4.85e-27165
hematopoietic multipotent progenitor cell4.85e-27165
hematopoietic lineage restricted progenitor cell3.77e-25124
CD14-positive, CD16-negative classical monocyte4.64e-2542
granulocyte monocyte progenitor cell1.28e-2471
myeloid cell2.38e-24112
common myeloid progenitor2.38e-24112
nongranular leukocyte1.61e-22119
myeloid lineage restricted progenitor cell1.87e-2270
classical monocyte2.19e-2245
macrophage dendritic cell progenitor5.80e-2165
monopoietic cell1.89e-1963
monocyte1.89e-1963
monoblast1.89e-1963
promonocyte1.89e-1963
intermediate monocyte1.03e-109
CD14-positive, CD16-positive monocyte1.03e-109
mesenchymal cell4.92e-09358
connective tissue cell1.49e-08365
dendritic cell1.63e-0710
blood cell4.90e-0711
circulating cell6.60e-076
CD4-positive, alpha-beta T cell7.38e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.16e-22102
blood island2.16e-22102
bone marrow7.86e-2180
hemolymphoid system6.89e-20112
bone element9.71e-2086
skeletal element1.67e-15101
skeletal system1.67e-15101
immune system9.17e-14115
connective tissue4.00e-08375
lateral plate mesoderm1.21e-07216


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.