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Difference between revisions of "Coexpression cluster:C4114"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0007023!2.13e-24!115;UBERON:0000025!6.85e-21!194;UBERON:0004111!1.21e-20!241;UBERON:0000477!1.57e-17!286;UBERON:0000119!2.93e-13!312;UBERON:0001049!3.27e-13!57;UBERON:0005068!3.27e-13!57;UBERON:0006241!3.27e-13!57;UBERON:0007135!3.27e-13!57;UBERON:0000483!3.29e-13!309;UBERON:0002616!1.10e-12!59;UBERON:0001986!9.51e-12!18;UBERON:0004638!9.51e-12!18;UBERON:0004852!9.51e-12!18;UBERON:0003080!1.98e-10!42;UBERON:0000487!1.98e-10!22;UBERON:0002780!6.50e-10!41;UBERON:0001890!6.50e-10!41;UBERON:0006240!6.50e-10!41;UBERON:0000955!7.67e-10!69;UBERON:0006238!7.67e-10!69;UBERON:0003075!3.37e-09!86;UBERON:0007284!3.37e-09!86;UBERON:0000468!9.39e-09!659;UBERON:0002346!1.44e-08!90;UBERON:0005743!1.53e-08!86;UBERON:0003915!1.82e-08!9;UBERON:0004700!1.82e-08!9;UBERON:0001917!1.82e-08!9;UBERON:0002020!2.12e-08!34;UBERON:0003528!2.12e-08!34;UBERON:0001017!2.87e-08!82;UBERON:0003914!3.50e-08!118;UBERON:0006914!3.76e-08!25;UBERON:0001893!6.70e-08!34;UBERON:0000467!7.11e-08!625;UBERON:0004872!8.09e-08!84;UBERON:0000480!9.56e-08!626;UBERON:0002791!1.23e-07!33;UBERON:0001869!2.88e-07!32;UBERON:0001009!6.11e-07!113;UBERON:0000055!8.23e-07!69;UBERON:0000073!9.09e-07!94;UBERON:0001016!9.09e-07!94
 
|ontology_enrichment_uberon=UBERON:0007023!2.13e-24!115;UBERON:0000025!6.85e-21!194;UBERON:0004111!1.21e-20!241;UBERON:0000477!1.57e-17!286;UBERON:0000119!2.93e-13!312;UBERON:0001049!3.27e-13!57;UBERON:0005068!3.27e-13!57;UBERON:0006241!3.27e-13!57;UBERON:0007135!3.27e-13!57;UBERON:0000483!3.29e-13!309;UBERON:0002616!1.10e-12!59;UBERON:0001986!9.51e-12!18;UBERON:0004638!9.51e-12!18;UBERON:0004852!9.51e-12!18;UBERON:0003080!1.98e-10!42;UBERON:0000487!1.98e-10!22;UBERON:0002780!6.50e-10!41;UBERON:0001890!6.50e-10!41;UBERON:0006240!6.50e-10!41;UBERON:0000955!7.67e-10!69;UBERON:0006238!7.67e-10!69;UBERON:0003075!3.37e-09!86;UBERON:0007284!3.37e-09!86;UBERON:0000468!9.39e-09!659;UBERON:0002346!1.44e-08!90;UBERON:0005743!1.53e-08!86;UBERON:0003915!1.82e-08!9;UBERON:0004700!1.82e-08!9;UBERON:0001917!1.82e-08!9;UBERON:0002020!2.12e-08!34;UBERON:0003528!2.12e-08!34;UBERON:0001017!2.87e-08!82;UBERON:0003914!3.50e-08!118;UBERON:0006914!3.76e-08!25;UBERON:0001893!6.70e-08!34;UBERON:0000467!7.11e-08!625;UBERON:0004872!8.09e-08!84;UBERON:0000480!9.56e-08!626;UBERON:0002791!1.23e-07!33;UBERON:0001869!2.88e-07!32;UBERON:0001009!6.11e-07!113;UBERON:0000055!8.23e-07!69;UBERON:0000073!9.09e-07!94;UBERON:0001016!9.09e-07!94
 +
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899036951279306!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444858534418109!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00643504909018683
 
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}}
 
}}

Revision as of 03:56, 5 September 2012


Full id: C4114_lung_heart_Endothelial_kidney_Mesenchymal_placenta_squamous



Phase1 CAGE Peaks

  Short description
Hg19::chr2:102953710..102953727,+ p1@IL1RL1
Hg19::chr2:102953739..102953750,+ p5@IL1RL1
Hg19::chr2:102953753..102953765,+ p4@IL1RL1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism2.13e-24115
tube6.85e-21194
anatomical conduit1.21e-20241
anatomical cluster1.57e-17286
cell layer2.93e-13312
neural tube3.27e-1357
neural rod3.27e-1357
future spinal cord3.27e-1357
neural keel3.27e-1357
epithelium3.29e-13309
regional part of brain1.10e-1259
endothelium9.51e-1218
blood vessel endothelium9.51e-1218
cardiovascular system endothelium9.51e-1218
anterior neural tube1.98e-1042
simple squamous epithelium1.98e-1022
regional part of forebrain6.50e-1041
forebrain6.50e-1041
future forebrain6.50e-1041
brain7.67e-1069
future brain7.67e-1069
neural plate3.37e-0986
presumptive neural plate3.37e-0986
multi-cellular organism9.39e-09659
neurectoderm1.44e-0890
endothelial tube1.82e-089
arterial system endothelium1.82e-089
endothelium of artery1.82e-089
gray matter2.12e-0834
brain grey matter2.12e-0834
central nervous system2.87e-0882
epithelial tube3.50e-08118
squamous epithelium3.76e-0825
telencephalon6.70e-0834
anatomical system7.11e-08625
splanchnic layer of lateral plate mesoderm8.09e-0884
anatomical group9.56e-08626
regional part of telencephalon1.23e-0733
cerebral hemisphere2.88e-0732
circulatory system6.11e-07113
vessel8.23e-0769
regional part of nervous system9.09e-0794
nervous system9.09e-0794


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235338.99795530889440.001372499272417130.00899036951279306
JUN#3725312.51282919233630.0005103313992726250.00444858534418109
STAT3#6774310.51946499715420.0008589184530415310.00643504909018683



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.