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Coexpression cluster:C3511: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324611288178802!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319891861985397!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153874772550471
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324611288178802!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319891861985397!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153874772550471
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}}
}}

Revision as of 16:10, 26 November 2012


Full id: C3511_Mesenchymal_Dendritic_Macrophage_Hepatic_Renal_Osteoblast_Melanocyte



Phase1 CAGE Peaks

Hg19::chr15:73976545..73976624,+p2@CD276
Hg19::chr15:73976691..73976704,+p3@CD276
Hg19::chr15:73976715..73976760,+p1@CD276


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
epithelial tube6.56e-15117
multi-cellular organism1.57e-14656
organism subdivision1.62e-14264
mesenchyme2.43e-14160
entire embryonic mesenchyme2.43e-14160
epithelial vesicle2.76e-1378
vasculature2.86e-1378
vascular system2.86e-1378
trunk9.10e-13199
splanchnic layer of lateral plate mesoderm2.09e-1283
multilaminar epithelium4.12e-1283
artery2.96e-1142
arterial blood vessel2.96e-1142
arterial system2.96e-1142
unilaminar epithelium3.70e-11148
epithelial tube open at both ends5.03e-1159
blood vessel5.03e-1159
blood vasculature5.03e-1159
vascular cord5.03e-1159
somite6.37e-1171
presomitic mesoderm6.37e-1171
presumptive segmental plate6.37e-1171
dermomyotome6.37e-1171
trunk paraxial mesoderm6.37e-1171
trunk mesenchyme9.98e-11122
dense mesenchyme tissue1.06e-1073
anatomical system1.12e-10624
skeletal muscle tissue1.56e-1062
striated muscle tissue1.56e-1062
myotome1.56e-1062
paraxial mesoderm1.70e-1072
presumptive paraxial mesoderm1.70e-1072
anatomical group1.89e-10625
vessel2.71e-1068
muscle tissue6.11e-1064
musculature6.11e-1064
musculature of body6.11e-1064
cell layer8.28e-10309
epithelium1.78e-09306
embryo3.28e-08592
systemic artery3.77e-0833
systemic arterial system3.77e-0833
urinary system structure4.42e-0847
renal system6.64e-0848
developing anatomical structure1.27e-07581
nephron epithelium1.30e-0715
renal tubule1.30e-0715
nephron tubule1.30e-0715
nephron1.30e-0715
uriniferous tubule1.30e-0715
nephrogenic mesenchyme1.30e-0715
cardiovascular system1.69e-07109
circulatory system2.93e-07112
excretory tube4.11e-0716
kidney epithelium4.11e-0716
mesoderm4.86e-07315
mesoderm-derived structure4.86e-07315
presumptive mesoderm4.86e-07315


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
E2F1#186934.907389214879320.008460985347239390.0324611288178802
EGR1#195834.988179094810140.008056488137383440.0319891861985397
GABPB1#255337.067683836182170.002832212825417420.0153874772550471



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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