Personal tools

Coexpression cluster:C1588: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0050516!inositol polyphosphate multikinase activity!0.0044742070763476!253430$GO:0046853!inositol and derivative phosphorylation!0.0044742070763476!253430$GO:0046835!carbohydrate phosphorylation!0.00760447274511088!253430$GO:0008440!inositol trisphosphate 3-kinase activity!0.00760447274511088!253430$GO:0006020!inositol metabolic process!0.00760447274511088!253430$GO:0051766!inositol trisphosphate kinase activity!0.00760447274511088!253430$GO:0001839!neural plate morphogenesis!0.00760447274511088!253430$GO:0001841!neural tube formation!0.00760447274511088!253430$GO:0001840!neural plate development!0.00760447274511088!253430$GO:0001838!embryonic epithelial tube formation!0.00760447274511088!253430$GO:0021915!neural tube development!0.00772624213739308!253430$GO:0016331!morphogenesis of embryonic epithelium!0.00820029831559406!253430$GO:0006914!autophagy!0.00894525314623864!53917$GO:0005793!ER-Golgi intermediate compartment!0.0137339145107121!53917$GO:0005770!late endosome!0.0152013327330055!53917$GO:0002009!morphogenesis of an epithelium!0.0173540881453391!253430$GO:0004428!inositol or phosphatidylinositol kinase activity!0.0173540881453391!253430$GO:0035239!tube morphogenesis!0.0202127547381958!253430$GO:0048598!embryonic morphogenesis!0.0202127547381958!253430$GO:0009792!embryonic development ending in birth or egg hatching!0.0202127547381958!253430$GO:0043009!chordate embryonic development!0.0202127547381958!253430$GO:0035295!tube development!0.0237543708322871!253430$GO:0005768!endosome!0.0374388860274241!53917$GO:0009790!embryonic development!0.0436597004450281!253430$GO:0019318!hexose metabolic process!0.046962490367732!253430$GO:0005996!monosaccharide metabolic process!0.046962490367732!253430
|gostat_on_coexpression_clusters=GO:0050516!inositol polyphosphate multikinase activity!0.0044742070763476!253430$GO:0046853!inositol and derivative phosphorylation!0.0044742070763476!253430$GO:0046835!carbohydrate phosphorylation!0.00760447274511088!253430$GO:0008440!inositol trisphosphate 3-kinase activity!0.00760447274511088!253430$GO:0006020!inositol metabolic process!0.00760447274511088!253430$GO:0051766!inositol trisphosphate kinase activity!0.00760447274511088!253430$GO:0001839!neural plate morphogenesis!0.00760447274511088!253430$GO:0001841!neural tube formation!0.00760447274511088!253430$GO:0001840!neural plate development!0.00760447274511088!253430$GO:0001838!embryonic epithelial tube formation!0.00760447274511088!253430$GO:0021915!neural tube development!0.00772624213739308!253430$GO:0016331!morphogenesis of embryonic epithelium!0.00820029831559406!253430$GO:0006914!autophagy!0.00894525314623864!53917$GO:0005793!ER-Golgi intermediate compartment!0.0137339145107121!53917$GO:0005770!late endosome!0.0152013327330055!53917$GO:0002009!morphogenesis of an epithelium!0.0173540881453391!253430$GO:0004428!inositol or phosphatidylinositol kinase activity!0.0173540881453391!253430$GO:0035239!tube morphogenesis!0.0202127547381958!253430$GO:0048598!embryonic morphogenesis!0.0202127547381958!253430$GO:0009792!embryonic development ending in birth or egg hatching!0.0202127547381958!253430$GO:0043009!chordate embryonic development!0.0202127547381958!253430$GO:0035295!tube development!0.0237543708322871!253430$GO:0005768!endosome!0.0374388860274241!53917$GO:0009790!embryonic development!0.0436597004450281!253430$GO:0019318!hexose metabolic process!0.046962490367732!253430$GO:0005996!monosaccharide metabolic process!0.046962490367732!253430
|id=C1588
|id=C1588
|ontology_enrichment_celltype=CL:0002057!5.76e-27!42;CL:0000766!1.28e-23!76;CL:0000860!1.62e-23!45;CL:0000738!9.54e-23!140;CL:0000557!1.32e-20!71;CL:0002009!4.80e-19!65;CL:0002087!2.91e-18!119;CL:0002031!3.51e-18!124;CL:0000037!6.52e-18!172;CL:0000566!6.52e-18!172;CL:0002194!7.17e-18!63;CL:0000576!7.17e-18!63;CL:0000040!7.17e-18!63;CL:0000559!7.17e-18!63;CL:0000839!2.20e-17!70;CL:0000988!6.65e-17!182;CL:0002032!3.74e-16!165;CL:0000837!3.74e-16!165;CL:0000763!1.08e-14!112;CL:0000049!1.08e-14!112;CL:0002320!2.61e-12!365;CL:0000134!2.65e-11!358;CL:0000219!7.89e-10!390;CL:0000048!1.22e-09!430;CL:0000723!1.45e-08!436;CL:0000034!2.87e-08!444;CL:0002393!2.01e-07!9;CL:0002397!2.01e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!4.15e-22!102;UBERON:0003061!4.15e-22!102;UBERON:0002193!8.07e-22!112;UBERON:0001474!2.59e-18!86;UBERON:0002371!6.68e-18!80;UBERON:0004765!4.47e-15!101;UBERON:0001434!4.47e-15!101;UBERON:0002405!4.89e-14!115;UBERON:0002384!1.72e-12!375;UBERON:0002204!1.75e-09!167
}}
}}

Revision as of 14:13, 21 May 2012


Full id: C1588_Eosinophils_CD14CD16_CD14_Neutrophils_Basophils_Whole_embryonic



Phase1 CAGE Peaks

Hg19::chr10:60027628..60027641,-p2@IPMK
Hg19::chr5:176730629..176730638,-p5@RAB24
Hg19::chr5:176730640..176730649,-p4@RAB24
Hg19::chr5:176730651..176730666,-p3@RAB24
Hg19::chr5:176730676..176730730,-p1@RAB24


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


GO IDGO nameFDR corrected p-value
GO:0050516inositol polyphosphate multikinase activity0.0044742070763476
GO:0046853inositol and derivative phosphorylation0.0044742070763476
GO:0046835carbohydrate phosphorylation0.00760447274511088
GO:0008440inositol trisphosphate 3-kinase activity0.00760447274511088
GO:0006020inositol metabolic process0.00760447274511088
GO:0051766inositol trisphosphate kinase activity0.00760447274511088
GO:0001839neural plate morphogenesis0.00760447274511088
GO:0001841neural tube formation0.00760447274511088
GO:0001840neural plate development0.00760447274511088
GO:0001838embryonic epithelial tube formation0.00760447274511088
GO:0021915neural tube development0.00772624213739308
GO:0016331morphogenesis of embryonic epithelium0.00820029831559406
GO:0006914autophagy0.00894525314623864
GO:0005793ER-Golgi intermediate compartment0.0137339145107121
GO:0005770late endosome0.0152013327330055
GO:0002009morphogenesis of an epithelium0.0173540881453391
GO:0004428inositol or phosphatidylinositol kinase activity0.0173540881453391
GO:0035239tube morphogenesis0.0202127547381958
GO:0048598embryonic morphogenesis0.0202127547381958
GO:0009792embryonic development ending in birth or egg hatching0.0202127547381958
GO:0043009chordate embryonic development0.0202127547381958
GO:0035295tube development0.0237543708322871
GO:0005768endosome0.0374388860274241
GO:0009790embryonic development0.0436597004450281
GO:0019318hexose metabolic process0.046962490367732
GO:0005996monosaccharide metabolic process0.046962490367732



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
CD14-positive, CD16-negative classical monocyte5.76e-2742
myeloid leukocyte1.28e-2376
classical monocyte1.62e-2345
leukocyte9.54e-23140
granulocyte monocyte progenitor cell1.32e-2071
macrophage dendritic cell progenitor4.80e-1965
nongranular leukocyte2.91e-18119
hematopoietic lineage restricted progenitor cell3.51e-18124
hematopoietic stem cell6.52e-18172
angioblastic mesenchymal cell6.52e-18172
monopoietic cell7.17e-1863
monocyte7.17e-1863
monoblast7.17e-1863
promonocyte7.17e-1863
myeloid lineage restricted progenitor cell2.20e-1770
hematopoietic cell6.65e-17182
hematopoietic oligopotent progenitor cell3.74e-16165
hematopoietic multipotent progenitor cell3.74e-16165
myeloid cell1.08e-14112
common myeloid progenitor1.08e-14112
connective tissue cell2.61e-12365
mesenchymal cell2.65e-11358
motile cell7.89e-10390
multi fate stem cell1.22e-09430
somatic stem cell1.45e-08436
stem cell2.87e-08444
intermediate monocyte2.01e-079
CD14-positive, CD16-positive monocyte2.01e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.15e-22102
blood island4.15e-22102
hemolymphoid system8.07e-22112
bone element2.59e-1886
bone marrow6.68e-1880
skeletal element4.47e-15101
skeletal system4.47e-15101
immune system4.89e-14115
connective tissue1.72e-12375
musculoskeletal system1.75e-09167


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.