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Coexpression cluster:C1996: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0042605!peptide antigen binding!0.0050777110561639!445347$GO:0042287!MHC protein binding!0.0050777110561639!445347$GO:0003823!antigen binding!0.0229600847756976!445347$GO:0042277!peptide binding!0.0229600847756976!445347
|gostat_on_coexpression_clusters=GO:0042605!peptide antigen binding!0.0050777110561639!445347$GO:0042287!MHC protein binding!0.0050777110561639!445347$GO:0003823!antigen binding!0.0229600847756976!445347$GO:0042277!peptide binding!0.0229600847756976!445347
|id=C1996
|id=C1996
|ontology_enrichment_celltype=CL:0000037!1.35e-32!172;CL:0000566!1.35e-32!172;CL:0000988!1.07e-29!182;CL:0002032!2.77e-29!165;CL:0000837!2.77e-29!165;CL:0000738!4.71e-27!140;CL:0002087!6.58e-24!119;CL:0002031!1.41e-23!124;CL:0000763!3.19e-19!112;CL:0000049!3.19e-19!112;CL:0000766!1.36e-15!76;CL:0000839!7.21e-15!70;CL:0000557!6.58e-14!71;CL:0002194!6.47e-13!63;CL:0000576!6.47e-13!63;CL:0000040!6.47e-13!63;CL:0000559!6.47e-13!63;CL:0002009!5.01e-12!65;CL:0000791!7.70e-12!18;CL:0000789!7.70e-12!18;CL:0002420!7.70e-12!18;CL:0002419!7.70e-12!18;CL:0000790!7.70e-12!18;CL:0000625!8.22e-11!11;CL:0000084!9.22e-11!25;CL:0000827!9.22e-11!25;CL:0000838!7.39e-10!52;CL:0002057!7.43e-10!42;CL:0000542!1.95e-09!53;CL:0000051!1.95e-09!53;CL:0000860!1.77e-08!45;CL:0000134!1.71e-07!358;CL:0002320!3.74e-07!365
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!8.65e-23!102;UBERON:0003061!8.65e-23!102;UBERON:0002193!3.30e-20!112;UBERON:0007023!1.67e-17!115;UBERON:0002371!5.02e-12!80;UBERON:0000178!1.40e-10!15;UBERON:0000179!1.40e-10!15;UBERON:0000463!1.40e-10!15;UBERON:0002405!3.09e-10!115;UBERON:0001474!5.59e-10!86;UBERON:0004765!1.35e-07!101;UBERON:0001434!1.35e-07!101;UBERON:0002384!1.58e-07!375
}}
}}

Revision as of 14:18, 21 May 2012


Full id: C1996_Natural_CD8_NK_CD4_Peripheral_blood_Whole



Phase1 CAGE Peaks

Hg19::chr7:38357069..38357141,-p1@TARP
Hg19::chr7:38357145..38357165,-p6@TARP
Hg19::chr7:38357177..38357188,-p8@TARP
Hg19::chr7:38357258..38357299,-p2@TARP
Hg19::chr7:38375259..38375289,-p2@uc010kxk.1


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:0042605peptide antigen binding0.0050777110561639
GO:0042287MHC protein binding0.0050777110561639
GO:0003823antigen binding0.0229600847756976
GO:0042277peptide binding0.0229600847756976



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 cell1.35e-32172
angioblastic mesenchymal cell1.35e-32172
hematopoietic cell1.07e-29182
hematopoietic oligopotent progenitor cell2.77e-29165
hematopoietic multipotent progenitor cell2.77e-29165
leukocyte4.71e-27140
nongranular leukocyte6.58e-24119
hematopoietic lineage restricted progenitor cell1.41e-23124
myeloid cell3.19e-19112
common myeloid progenitor3.19e-19112
myeloid leukocyte1.36e-1576
myeloid lineage restricted progenitor cell7.21e-1570
granulocyte monocyte progenitor cell6.58e-1471
monopoietic cell6.47e-1363
monocyte6.47e-1363
monoblast6.47e-1363
promonocyte6.47e-1363
macrophage dendritic cell progenitor5.01e-1265
mature alpha-beta T cell7.70e-1218
alpha-beta T cell7.70e-1218
immature T cell7.70e-1218
mature T cell7.70e-1218
immature alpha-beta T cell7.70e-1218
CD8-positive, alpha-beta T cell8.22e-1111
T cell9.22e-1125
pro-T cell9.22e-1125
lymphoid lineage restricted progenitor cell7.39e-1052
CD14-positive, CD16-negative classical monocyte7.43e-1042
lymphocyte1.95e-0953
common lymphoid progenitor1.95e-0953
classical monocyte1.77e-0845
mesenchymal cell1.71e-07358
connective tissue cell3.74e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.65e-23102
blood island8.65e-23102
hemolymphoid system3.30e-20112
adult organism1.67e-17115
bone marrow5.02e-1280
blood1.40e-1015
haemolymphatic fluid1.40e-1015
organism substance1.40e-1015
immune system3.09e-10115
bone element5.59e-1086
skeletal element1.35e-07101
skeletal system1.35e-07101
connective tissue1.58e-07375


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.