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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4843_Small_amniotic_uterus_Amniotic_smooth_Mesenchymal_salivary
|full_id=C4843_Small_amniotic_uterus_Amniotic_smooth_Mesenchymal_salivary
|id=C4843
|id=C4843

Revision as of 17:59, 12 September 2012


Full id: C4843_Small_amniotic_uterus_Amniotic_smooth_Mesenchymal_salivary



Phase1 CAGE Peaks

Hg19::chrX:107683009..107683088,+p1@COL4A5
Hg19::chrX:107683096..107683121,+p3@COL4A5
Hg19::chrX:107683216..107683245,+p6@COL4A5


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
epithelial cell2.47e-17254
embryonic cell7.69e-16248
mesodermal cell3.36e-09119
contractile cell1.17e-0859
smooth muscle cell1.59e-0842
smooth muscle myoblast1.59e-0842
muscle cell9.35e-0854
muscle precursor cell1.26e-0757
myoblast1.26e-0757
multi-potent skeletal muscle stem cell1.26e-0757
electrically responsive cell1.57e-0760
electrically active cell1.57e-0760
Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.14e-27347
cell layer6.27e-24312
epithelium7.93e-24309
anatomical cluster1.03e-22286
multi-cellular organism4.03e-20659
embryo6.30e-19612
anatomical conduit1.47e-18241
anatomical system1.67e-16625
embryonic structure1.72e-16605
developing anatomical structure1.72e-16605
anatomical group1.82e-16626
mesenchyme2.17e-16238
entire embryonic mesenchyme2.17e-16238
organism subdivision3.93e-16365
germ layer5.10e-16604
embryonic tissue5.10e-16604
presumptive structure5.10e-16604
epiblast (generic)5.10e-16604
endoderm-derived structure6.54e-15169
endoderm6.54e-15169
presumptive endoderm6.54e-15169
trunk mesenchyme3.71e-14143
organ part5.52e-13219
unilaminar epithelium4.27e-12138
tube4.90e-12194
primordium3.42e-11168
trunk5.00e-11216
digestive system9.73e-11155
digestive tract9.73e-11155
primitive gut9.73e-11155
epithelial tube2.33e-10118
vasculature4.44e-1079
vascular system4.44e-1079
organ6.78e-10511
multilaminar epithelium1.19e-0982
splanchnic layer of lateral plate mesoderm5.41e-0984
reproductive structure6.73e-0959
reproductive system6.73e-0959
subdivision of digestive tract7.25e-09129
endodermal part of digestive tract7.25e-09129
muscle tissue1.41e-0863
musculature1.41e-0863
musculature of body1.41e-0863
skeletal muscle tissue4.25e-0861
striated muscle tissue4.25e-0861
myotome4.25e-0861
gland1.35e-0759
reproductive organ1.97e-0748
respiratory system2.04e-0772
ectoderm-derived structure3.02e-07169
endo-epithelium3.03e-0782
somite3.30e-0783
paraxial mesoderm3.30e-0783
presomitic mesoderm3.30e-0783
presumptive segmental plate3.30e-0783
trunk paraxial mesoderm3.30e-0783
presumptive paraxial mesoderm3.30e-0783
blood vessel3.72e-0760
epithelial tube open at both ends3.72e-0760
blood vasculature3.72e-0760
vascular cord3.72e-0760
dermomyotome3.84e-0770
mixed endoderm/mesoderm-derived structure3.90e-07130
vessel4.10e-0769
immaterial anatomical entity5.44e-07126
extraembryonic structure5.60e-0724
female organism6.77e-0741


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
CHD2#1106310.34402283411690.0009033701102746880.00663341566104044
SETDB1#9869340.32002617801051.52461559299059e-050.000360328870595936
TRIM28#10155318.59052504526250.0001555969297255280.00198247990040312
ZNF263#1012738.221841637010680.001799043925565870.0110303128180213



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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