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Coexpression cluster:C4078: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115398288390486!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279974884945594!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172016584914066!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325964384034946!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000852469350668577!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140479631042936!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109601789968019
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115398288390486!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279974884945594!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172016584914066!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325964384034946!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000852469350668577!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140479631042936!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109601789968019
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}}
}}

Revision as of 16:32, 26 November 2012


Full id: C4078_Mast_Endothelial_Lymphatic_Melanocyte_melanoma_Hep2_Hepatic



Phase1 CAGE Peaks

Hg19::chr21:42540033..42540062,+p2@BACE2
Hg19::chr21:42540070..42540107,+p1@BACE2
Hg19::chr21:42540108..42540124,+p3@BACE2


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
vasculature2.45e-1878
vascular system2.45e-1878
vessel4.72e-1868
splanchnic layer of lateral plate mesoderm6.43e-1683
epithelial tube open at both ends1.14e-1559
blood vessel1.14e-1559
blood vasculature1.14e-1559
vascular cord1.14e-1559
epithelial tube1.53e-15117
anatomical cluster8.01e-15373
cardiovascular system6.16e-13109
circulatory system1.40e-12112
organism subdivision6.65e-12264
epithelium8.82e-12306
cell layer1.02e-11309
blood vessel endothelium9.97e-1118
endothelium9.97e-1118
cardiovascular system endothelium9.97e-1118
multi-tissue structure1.62e-10342
primordium4.38e-10160
anatomical conduit4.52e-10240
artery4.65e-1042
arterial blood vessel4.65e-1042
arterial system4.65e-1042
systemic artery2.89e-0933
systemic arterial system2.89e-0933
multi-cellular organism7.80e-09656
simple squamous epithelium9.80e-0922
compound organ1.41e-0868
squamous epithelium2.83e-0825
trunk7.78e-08199
unilaminar epithelium8.33e-08148
organ segment2.30e-0798
organ part3.21e-07218
larynx3.38e-079
anatomical system4.79e-07624
tube7.50e-07192
anatomical group7.94e-07625


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
CEBPB#105137.971147625824820.001974187055288560.0115398288390486
CTCF#1066435.360256373075030.0064925092527670.0279974884945594
CTCFL#140690319.74647435897440.0001298372005551160.00172016584914066
E2F1#186934.907389214879320.008460985347239390.0325964384034946
GATA3#2625327.2365163572064.94721007899563e-050.000852469350668577
ZBTB7A#5134137.35190930787590.002516255860282270.0140479631042936
ZNF263#1012738.221841637010680.001799043925565870.0109601789968019



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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