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Coexpression cluster:C1645: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249478501128282!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352290387428697!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276251388417541!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229220683106164!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714051080610836
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249478501128282!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352290387428697!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276251388417541!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229220683106164!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714051080610836
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}}
}}

Revision as of 15:01, 26 November 2012


Full id: C1645_temporal_non_occipital_parietal_duodenum_neuroblastoma_brain



Phase1 CAGE Peaks

Hg19::chr11:79151822..79151890,-p1@ODZ4
Hg19::chr11:79151896..79151911,-p8@ODZ4
Hg19::chr11:79151994..79152022,-p2@ODZ4
Hg19::chr11:79152025..79152047,-p5@ODZ4
Hg19::chr11:79152060..79152082,-p4@ODZ4


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
nervous system1.42e-3289
neural tube5.44e-3256
neural rod5.44e-3256
future spinal cord5.44e-3256
neural keel5.44e-3256
neural plate6.93e-3182
presumptive neural plate6.93e-3182
central nervous system7.31e-3181
regional part of nervous system1.20e-2953
regional part of brain1.20e-2953
ecto-epithelium3.09e-29104
neurectoderm7.72e-2886
ectoderm-derived structure2.42e-26171
ectoderm2.42e-26171
presumptive ectoderm2.42e-26171
pre-chordal neural plate9.49e-2661
brain5.98e-2568
future brain5.98e-2568
structure with developmental contribution from neural crest7.07e-25132
regional part of forebrain1.31e-2441
forebrain1.31e-2441
anterior neural tube1.31e-2441
future forebrain1.31e-2441
brain grey matter1.91e-2334
gray matter1.91e-2334
telencephalon6.64e-2334
cerebral hemisphere3.12e-2232
regional part of telencephalon4.19e-2232
cerebral cortex1.35e-1825
pallium1.35e-1825
regional part of cerebral cortex1.54e-1622
neocortex2.82e-1520
cell layer4.69e-14309
multi-tissue structure1.07e-13342
epithelium2.25e-13306
anatomical cluster1.47e-11373
adult organism3.73e-11114
multi-cellular organism6.36e-11656
organ part1.00e-10218
organ system subdivision2.68e-10223
anatomical system2.87e-10624
anatomical group4.08e-10625
embryo9.71e-10592
developing anatomical structure2.95e-09581
posterior neural tube1.70e-0815
chordal neural plate1.70e-0815
tube8.35e-08192
embryonic structure3.73e-07564
germ layer7.62e-07560
germ layer / neural crest7.62e-07560
embryonic tissue7.62e-07560
presumptive structure7.62e-07560
germ layer / neural crest derived structure7.62e-07560
epiblast (generic)7.62e-07560


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
CTCF#1066455.360256373075030.0002259278299937090.00249478501128282
E2F1#186954.907389214879320.0003512818099256460.00352290387428697
MYC#460955.22228187160940.0002573944848850610.00276251388417541
RAD21#5885510.35503389545638.39503550283973e-060.000229220683106164
SPI1#668846.563458806818180.0009957429636454020.00714051080610836



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.