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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1012_heart_left_bile_Mast_epitheloid_aorta_umbilical
|full_id=C1012_heart_left_bile_Mast_epitheloid_aorta_umbilical
|id=C1012
|id=C1012

Revision as of 13:25, 12 September 2012


Full id: C1012_heart_left_bile_Mast_epitheloid_aorta_umbilical



Phase1 CAGE Peaks

Hg19::chr12:20521429..20521511,+p@chr12:20521429..20521511
+
Hg19::chr12:20522622..20522638,+p1@PDE3A
Hg19::chr12:20522763..20522783,+p5@PDE3A
Hg19::chr12:20522789..20522814,+p2@PDE3A
Hg19::chr12:20522816..20522841,+p4@PDE3A
Hg19::chr12:20522842..20522861,+p6@PDE3A
Hg19::chr12:20522891..20522907,+p8@PDE3A
Hg19::chr12:20523085..20523111,+p7@PDE3A


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
contractile cell6.65e-0759
electrically responsive cell7.06e-0760
electrically active cell7.06e-0760
Uber Anatomy
Ontology termp-valuen
adult organism3.80e-31115
anatomical cluster7.52e-22286
tube5.17e-20194
multi-cellular organism4.10e-19659
circulatory system3.39e-16113
splanchnic layer of lateral plate mesoderm9.86e-1684
anatomical conduit1.56e-15241
embryo6.63e-15612
cardiovascular system1.17e-14110
multi-tissue structure1.46e-14347
anatomical system2.68e-13625
embryonic structure2.96e-13605
developing anatomical structure2.96e-13605
anatomical group4.74e-13626
germ layer7.08e-13604
embryonic tissue7.08e-13604
presumptive structure7.08e-13604
epiblast (generic)7.08e-13604
cell layer7.94e-13312
epithelium3.22e-12309
neural tube5.95e-1257
neural rod5.95e-1257
future spinal cord5.95e-1257
neural keel5.95e-1257
regional part of brain6.23e-1259
vasculature1.83e-1179
vascular system1.83e-1179
central nervous system3.31e-1182
epithelial tube7.67e-11118
blood vessel1.22e-1060
epithelial tube open at both ends1.22e-1060
blood vasculature1.22e-1060
vascular cord1.22e-1060
regional part of nervous system8.58e-1094
nervous system8.58e-1094
vessel9.89e-1069
primary circulatory organ1.77e-0927
neural plate2.06e-0986
presumptive neural plate2.06e-0986
neurectoderm2.91e-0990
brain8.62e-0969
future brain8.62e-0969
muscle tissue3.43e-0863
musculature3.43e-0863
musculature of body3.43e-0863
artery6.88e-0842
arterial blood vessel6.88e-0842
arterial system6.88e-0842
anterior neural tube8.36e-0842
heart1.23e-0724
primitive heart tube1.23e-0724
primary heart field1.23e-0724
anterior lateral plate mesoderm1.23e-0724
heart tube1.23e-0724
heart primordium1.23e-0724
cardiac mesoderm1.23e-0724
cardiogenic plate1.23e-0724
heart rudiment1.23e-0724
regional part of forebrain1.37e-0741
forebrain1.37e-0741
future forebrain1.37e-0741
skeletal muscle tissue1.76e-0761
striated muscle tissue1.76e-0761
myotome1.76e-0761
organ part2.57e-07219
larynx2.58e-079
compound organ3.93e-0769
tissue4.25e-07787
gray matter8.40e-0734
brain grey matter8.40e-0734


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
CTCF#1066474.690224326440655.26249365325459e-050.000893528815887265
E2F1#186974.293965563019419.58670853279727e-050.00137004139635579
NANOG#79923725.58918117088614.22843204062973e-104.1388304957013e-08
POLR2A#543082.147453176558070.002210725788971910.0127146864185493
TAF1#687262.507284714308970.01111734475613860.040881812928642
TBP#690873.243424351209340.0006354223620492050.00521188063064925
ZNF263#1012777.194111432384342.81251959700937e-069.7167295465452e-05



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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