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Coexpression cluster:C1041: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003104!1.24e-12!160;UBERON:0009142!1.24e-12!160;UBERON:0000468!1.86e-12!656;UBERON:0000481!2.59e-12!342;UBERON:0000475!3.51e-12!264;UBERON:0004872!6.73e-12!83;UBERON:0002385!7.36e-12!64;UBERON:0001015!7.36e-12!64;UBERON:0000383!7.36e-12!64;UBERON:0001134!2.74e-11!62;UBERON:0002036!2.74e-11!62;UBERON:0003082!2.74e-11!62;UBERON:0005256!3.58e-11!122;UBERON:0003914!3.81e-11!117;UBERON:0002100!5.98e-11!199;UBERON:0007503!6.31e-11!78;UBERON:0000477!7.71e-11!373;UBERON:0007524!8.01e-11!73;UBERON:0000486!1.10e-10!83;UBERON:0002329!1.58e-10!71;UBERON:0003059!1.58e-10!71;UBERON:0007282!1.58e-10!71;UBERON:0004290!1.58e-10!71;UBERON:0009618!1.58e-10!71;UBERON:0003077!1.86e-10!72;UBERON:0007285!1.86e-10!72;UBERON:0001637!2.42e-10!42;UBERON:0003509!2.42e-10!42;UBERON:0004572!2.42e-10!42;UBERON:0002049!4.44e-10!78;UBERON:0007798!4.44e-10!78;UBERON:0003103!3.14e-09!68;UBERON:0004573!6.62e-09!33;UBERON:0004571!6.62e-09!33;UBERON:0007500!7.80e-09!59;UBERON:0001981!7.80e-09!59;UBERON:0004537!7.80e-09!59;UBERON:0006965!7.80e-09!59;UBERON:0000467!1.02e-08!624;UBERON:0000119!1.03e-08!309;UBERON:0000483!1.14e-08!306;UBERON:0007100!1.19e-08!27;UBERON:0000480!1.74e-08!625;UBERON:0001009!1.83e-08!112;UBERON:0000055!2.94e-08!68;UBERON:0004535!2.24e-07!109;UBERON:0000490!2.50e-07!148;UBERON:0004111!3.36e-07!240;UBERON:0000948!6.17e-07!24;UBERON:0005498!6.17e-07!24;UBERON:0004140!6.17e-07!24;UBERON:0009881!6.17e-07!24;UBERON:0004141!6.17e-07!24;UBERON:0003084!6.17e-07!24;UBERON:0007005!6.17e-07!24;UBERON:0004139!6.17e-07!24;UBERON:0004291!6.17e-07!24
|ontology_enrichment_uberon=UBERON:0003104!1.24e-12!160;UBERON:0009142!1.24e-12!160;UBERON:0000468!1.86e-12!656;UBERON:0000481!2.59e-12!342;UBERON:0000475!3.51e-12!264;UBERON:0004872!6.73e-12!83;UBERON:0002385!7.36e-12!64;UBERON:0001015!7.36e-12!64;UBERON:0000383!7.36e-12!64;UBERON:0001134!2.74e-11!62;UBERON:0002036!2.74e-11!62;UBERON:0003082!2.74e-11!62;UBERON:0005256!3.58e-11!122;UBERON:0003914!3.81e-11!117;UBERON:0002100!5.98e-11!199;UBERON:0007503!6.31e-11!78;UBERON:0000477!7.71e-11!373;UBERON:0007524!8.01e-11!73;UBERON:0000486!1.10e-10!83;UBERON:0002329!1.58e-10!71;UBERON:0003059!1.58e-10!71;UBERON:0007282!1.58e-10!71;UBERON:0004290!1.58e-10!71;UBERON:0009618!1.58e-10!71;UBERON:0003077!1.86e-10!72;UBERON:0007285!1.86e-10!72;UBERON:0001637!2.42e-10!42;UBERON:0003509!2.42e-10!42;UBERON:0004572!2.42e-10!42;UBERON:0002049!4.44e-10!78;UBERON:0007798!4.44e-10!78;UBERON:0003103!3.14e-09!68;UBERON:0004573!6.62e-09!33;UBERON:0004571!6.62e-09!33;UBERON:0007500!7.80e-09!59;UBERON:0001981!7.80e-09!59;UBERON:0004537!7.80e-09!59;UBERON:0006965!7.80e-09!59;UBERON:0000467!1.02e-08!624;UBERON:0000119!1.03e-08!309;UBERON:0000483!1.14e-08!306;UBERON:0007100!1.19e-08!27;UBERON:0000480!1.74e-08!625;UBERON:0001009!1.83e-08!112;UBERON:0000055!2.94e-08!68;UBERON:0004535!2.24e-07!109;UBERON:0000490!2.50e-07!148;UBERON:0004111!3.36e-07!240;UBERON:0000948!6.17e-07!24;UBERON:0005498!6.17e-07!24;UBERON:0004140!6.17e-07!24;UBERON:0009881!6.17e-07!24;UBERON:0004141!6.17e-07!24;UBERON:0003084!6.17e-07!24;UBERON:0007005!6.17e-07!24;UBERON:0004139!6.17e-07!24;UBERON:0004291!6.17e-07!24
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}}
}}

Revision as of 14:38, 26 November 2012


Full id: C1041_heart_hepatic_left_mesodermal_smooth_spindle_skeletal



Phase1 CAGE Peaks

Hg19::chr15:63334938..63334957,+p1@TPM1
Hg19::chr15:63336209..63336321,+p6@TPM1
Hg19::chr15:63336244..63336312,-p@chr15:63336244..63336312
-
Hg19::chr15:63349171..63349210,+p9@TPM1
Hg19::chr15:63349224..63349289,+p5@TPM1
Hg19::chr15:63351752..63351785,+p@chr15:63351752..63351785
+
Hg19::chr15:63353058..63353095,+p10@TPM1
Hg19::chr15:63354403..63354419,+p14@TPM1


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
mesenchyme1.24e-12160
entire embryonic mesenchyme1.24e-12160
multi-cellular organism1.86e-12656
multi-tissue structure2.59e-12342
organism subdivision3.51e-12264
splanchnic layer of lateral plate mesoderm6.73e-1283
muscle tissue7.36e-1264
musculature7.36e-1264
musculature of body7.36e-1264
skeletal muscle tissue2.74e-1162
striated muscle tissue2.74e-1162
myotome2.74e-1162
trunk mesenchyme3.58e-11122
epithelial tube3.81e-11117
trunk5.98e-11199
epithelial vesicle6.31e-1178
anatomical cluster7.71e-11373
dense mesenchyme tissue8.01e-1173
multilaminar epithelium1.10e-1083
somite1.58e-1071
presomitic mesoderm1.58e-1071
presumptive segmental plate1.58e-1071
dermomyotome1.58e-1071
trunk paraxial mesoderm1.58e-1071
paraxial mesoderm1.86e-1072
presumptive paraxial mesoderm1.86e-1072
artery2.42e-1042
arterial blood vessel2.42e-1042
arterial system2.42e-1042
vasculature4.44e-1078
vascular system4.44e-1078
compound organ3.14e-0968
systemic artery6.62e-0933
systemic arterial system6.62e-0933
epithelial tube open at both ends7.80e-0959
blood vessel7.80e-0959
blood vasculature7.80e-0959
vascular cord7.80e-0959
anatomical system1.02e-08624
cell layer1.03e-08309
epithelium1.14e-08306
primary circulatory organ1.19e-0827
anatomical group1.74e-08625
circulatory system1.83e-08112
vessel2.94e-0868
cardiovascular system2.24e-07109
unilaminar epithelium2.50e-07148
anatomical conduit3.36e-07240
heart6.17e-0724
primitive heart tube6.17e-0724
primary heart field6.17e-0724
anterior lateral plate mesoderm6.17e-0724
heart tube6.17e-0724
heart primordium6.17e-0724
cardiac mesoderm6.17e-0724
cardiogenic plate6.17e-0724
heart rudiment6.17e-0724


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.

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