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Coexpression cluster:C3710: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167389657989308!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391116016857816!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663747626544639
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167389657989308!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391116016857816!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663747626544639
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}}
}}

Revision as of 16:18, 26 November 2012


Full id: C3710_Smooth_Fibroblast_heart_Neural_Preadipocyte_cholangiocellular_Lens



Phase1 CAGE Peaks

Hg19::chr18:25756974..25757018,-p2@CDH2
Hg19::chr18:25757019..25757024,-p6@CDH2
Hg19::chr18:25757066..25757103,-p1@CDH2


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>

Uber Anatomy
Ontology termp-valuen
tube1.24e-23192
epithelial tube5.75e-22117
anatomical cluster1.61e-21373
cell layer5.50e-19309
epithelium6.73e-19306
splanchnic layer of lateral plate mesoderm1.55e-1783
anatomical conduit2.55e-17240
circulatory system4.06e-17112
multi-tissue structure1.64e-16342
cardiovascular system4.72e-16109
artery5.67e-1642
arterial blood vessel5.67e-1642
arterial system5.67e-1642
multi-cellular organism7.50e-15656
vasculature4.25e-1478
vascular system4.25e-1478
mesenchyme6.00e-14160
entire embryonic mesenchyme6.00e-14160
epithelial tube open at both ends1.69e-1359
blood vessel1.69e-1359
blood vasculature1.69e-1359
vascular cord1.69e-1359
structure with developmental contribution from neural crest2.74e-13132
anatomical system2.92e-13624
systemic artery3.81e-1333
systemic arterial system3.81e-1333
anatomical group5.46e-13625
skeletal muscle tissue1.14e-1262
striated muscle tissue1.14e-1262
myotome1.14e-1262
vessel3.66e-1268
trunk mesenchyme6.50e-12122
muscle tissue6.51e-1264
musculature6.51e-1264
musculature of body6.51e-1264
primary circulatory organ1.44e-1127
epithelial vesicle1.78e-1178
dense mesenchyme tissue2.52e-1173
paraxial mesoderm4.08e-1172
presumptive paraxial mesoderm4.08e-1172
somite5.62e-1171
presomitic mesoderm5.62e-1171
presumptive segmental plate5.62e-1171
dermomyotome5.62e-1171
trunk paraxial mesoderm5.62e-1171
heart2.07e-1024
primitive heart tube2.07e-1024
primary heart field2.07e-1024
anterior lateral plate mesoderm2.07e-1024
heart tube2.07e-1024
heart primordium2.07e-1024
cardiac mesoderm2.07e-1024
cardiogenic plate2.07e-1024
heart rudiment2.07e-1024
embryo5.87e-10592
unilaminar epithelium9.54e-10148
developing anatomical structure2.99e-09581
trunk3.11e-09199
multilaminar epithelium3.65e-0983
nervous system3.66e-0989
central nervous system8.26e-0981
neural plate2.72e-0882
presumptive neural plate2.72e-0882
organism subdivision5.49e-08264
embryonic structure6.79e-08564
compound organ1.47e-0768
germ layer1.60e-07560
germ layer / neural crest1.60e-07560
embryonic tissue1.60e-07560
presumptive structure1.60e-07560
germ layer / neural crest derived structure1.60e-07560
epiblast (generic)1.60e-07560
aorta1.86e-0721
aortic system1.86e-0721
brain3.02e-0768
future brain3.02e-0768
neurectoderm7.56e-0786


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

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

TF#promotersEnrichmentp-valueq-value
EP300#203336.77394172622320.003216880500103790.0167389657989308
HDAC2#3066313.41562023662630.0004140761399857210.00391116016857816
RAD21#5885310.35503389545630.0009004912073565420.00663747626544639



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.

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