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Coexpression cluster:C1876: Difference between revisions

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|tf_chipseq_enrich=SETDB1#9869;4:32.2560209424084:1.85197955342303e-06:6.8636938459882e-05!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135469172249826!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00919564642822748!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00352799366178397
|tf_chipseq_enrich=SETDB1#9869;4:32.2560209424084:1.85197955342303e-06:6.8636938459882e-05!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135469172249826!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00919564642822748!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00352799366178397
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}}
}}

Revision as of 15:09, 26 November 2012


Full id: C1876_neuroectodermal_breast_Hepatic_acute_left_Endothelial_spleen



Phase1 CAGE Peaks

Hg19::chr21:27945275..27945302,-p5@CYYR1
Hg19::chr21:27945464..27945495,-p4@CYYR1
Hg19::chr21:27945502..27945527,-p3@CYYR1
Hg19::chr21:27945531..27945559,-p2@CYYR1
Hg19::chr21:27945562..27945618,-p1@CYYR1


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
adult organism6.03e-39114
ectoderm-derived structure4.36e-23171
ectoderm4.36e-23171
presumptive ectoderm4.36e-23171
neurectoderm2.31e-2286
ecto-epithelium2.54e-21104
neural plate3.80e-2082
presumptive neural plate3.80e-2082
anatomical cluster3.58e-19373
neural tube9.08e-1956
neural rod9.08e-1956
future spinal cord9.08e-1956
neural keel9.08e-1956
central nervous system2.12e-1781
nervous system3.55e-1789
regional part of nervous system3.72e-1753
regional part of brain3.72e-1753
structure with developmental contribution from neural crest4.50e-17132
pre-chordal neural plate5.54e-1561
multi-cellular organism5.64e-15656
cell layer7.14e-14309
regional part of forebrain7.20e-1441
forebrain7.20e-1441
anterior neural tube7.20e-1441
future forebrain7.20e-1441
anatomical conduit9.53e-14240
embryo1.21e-13592
epithelium2.38e-13306
brain4.76e-1368
future brain4.76e-1368
developing anatomical structure1.17e-11581
brain grey matter1.19e-1134
gray matter1.19e-1134
telencephalon1.50e-1134
embryonic structure3.90e-11564
anatomical system4.23e-11624
anatomical group5.69e-11625
regional part of telencephalon8.47e-1132
cerebral hemisphere9.98e-1132
tube1.05e-10192
organ part1.25e-10218
germ layer1.56e-10560
germ layer / neural crest1.56e-10560
embryonic tissue1.56e-10560
presumptive structure1.56e-10560
germ layer / neural crest derived structure1.56e-10560
epiblast (generic)1.56e-10560
organ system subdivision1.65e-10223
multi-tissue structure2.86e-10342
cerebral cortex2.68e-0925
pallium2.68e-0925
blood vessel endothelium1.36e-0818
endothelium1.36e-0818
cardiovascular system endothelium1.36e-0818
regional part of cerebral cortex5.12e-0822
neocortex2.17e-0720
simple squamous epithelium7.56e-0722


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
SETDB1#9869432.25602094240841.85197955342303e-066.8636938459882e-05
TAF1#687253.343046285745290.002394600090870310.0135469172249826
TBP#690853.706770687096390.001428755106721120.00919564642822748
YY1#752854.911170749853860.00034993140821360.00352799366178397



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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