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Coexpression cluster:C2195: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106302497922132!ESR1#2099;3:23.0764524721159:0.000133910524496857:0.00175719076114176!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321405257305874
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106302497922132!ESR1#2099;3:23.0764524721159:0.000133910524496857:0.00175719076114176!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321405257305874
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}}
}}

Revision as of 15:21, 26 November 2012


Full id: C2195_liposarcoma_Smooth_Fibroblast_CD14_giant_Hepatic_mesothelioma



Phase1 CAGE Peaks

Hg19::chr12:124873357..124873401,-p1@NCOR2
Hg19::chr12:124873824..124873833,-p19@NCOR2
Hg19::chr12:124873852..124873881,-p3@NCOR2
Hg19::chr12:124873905..124873916,-p@chr12:124873905..124873916
-


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
multi-cellular organism2.44e-17656
anatomical system7.90e-17624
anatomical group1.75e-16625
epithelial tube2.05e-14117
lateral plate mesoderm2.62e-14203
tube4.62e-14192
mesoderm5.84e-14315
mesoderm-derived structure5.84e-14315
presumptive mesoderm5.84e-14315
organ2.65e-13503
artery1.04e-1242
arterial blood vessel1.04e-1242
arterial system1.04e-1242
embryo1.51e-12592
developing anatomical structure2.80e-12581
cell layer9.20e-12309
germ layer1.89e-11560
germ layer / neural crest1.89e-11560
embryonic tissue1.89e-11560
presumptive structure1.89e-11560
germ layer / neural crest derived structure1.89e-11560
epiblast (generic)1.89e-11560
epithelium4.51e-11306
embryonic structure5.30e-11564
trunk7.58e-11199
musculoskeletal system2.12e-10167
systemic artery2.75e-1033
systemic arterial system2.75e-1033
anatomical conduit3.12e-10240
epithelial tube open at both ends3.54e-1059
blood vessel3.54e-1059
blood vasculature3.54e-1059
vascular cord3.54e-1059
vasculature1.10e-0978
vascular system1.10e-0978
splanchnic layer of lateral plate mesoderm2.26e-0983
organism subdivision2.98e-09264
epithelial vesicle8.11e-0978
trunk mesenchyme1.38e-08122
mesenchyme3.12e-08160
entire embryonic mesenchyme3.12e-08160
multi-tissue structure6.52e-08342
vessel7.50e-0868
tissue3.19e-07773
unilaminar epithelium4.37e-07148
somite4.75e-0771
presomitic mesoderm4.75e-0771
presumptive segmental plate4.75e-0771
dermomyotome4.75e-0771
trunk paraxial mesoderm4.75e-0771
paraxial mesoderm6.70e-0772
presumptive paraxial mesoderm6.70e-0772
dense mesenchyme tissue9.32e-0773


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#186944.907389214879320.001724022357361790.0106302497922132
ESR1#2099323.07645247211590.0001339105244968570.00175719076114176
TAF1#687243.343046285745290.008005664898701650.0321405257305874



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.