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Coexpression cluster:C1954: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00250192732867277!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287754667737621!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229881781038563!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.16749522578862e-05!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00353106148235943!ZNF143#7702;3:8.10052593133674:0.00362487051209098:0.0183366197526044
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00250192732867277!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287754667737621!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229881781038563!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.16749522578862e-05!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00353106148235943!ZNF143#7702;3:8.10052593133674:0.00362487051209098:0.0183366197526044
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}}
}}

Revision as of 15:12, 26 November 2012


Full id: C1954_occipital_parietal_temporal_duodenum_brain_Neurons_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr5:146833190..146833201,-p10@DPYSL3
Hg19::chr5:146833206..146833217,-p9@DPYSL3
Hg19::chr5:146833222..146833261,-p1@DPYSL3
Hg19::chr5:146833451..146833484,-p5@DPYSL3
Hg19::chr5:146833803..146833825,-p14@DPYSL3


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
central nervous system1.03e-2981
nervous system2.88e-2889
anatomical cluster3.65e-26373
neural plate6.10e-2382
presumptive neural plate6.10e-2382
structure with developmental contribution from neural crest3.02e-22132
brain1.84e-2168
future brain1.84e-2168
neural tube4.00e-2156
neural rod4.00e-2156
future spinal cord4.00e-2156
neural keel4.00e-2156
neurectoderm1.84e-2086
ectoderm-derived structure6.56e-20171
ectoderm6.56e-20171
presumptive ectoderm6.56e-20171
adult organism1.32e-19114
tube1.50e-19192
regional part of nervous system2.79e-1953
regional part of brain2.79e-1953
multi-cellular organism9.23e-17656
anatomical conduit2.69e-16240
embryo2.83e-15592
regional part of forebrain3.92e-1541
forebrain3.92e-1541
anterior neural tube3.92e-1541
future forebrain3.92e-1541
multi-tissue structure6.93e-15342
pre-chordal neural plate8.56e-1561
ecto-epithelium1.18e-14104
germ layer1.56e-14560
germ layer / neural crest1.56e-14560
embryonic tissue1.56e-14560
presumptive structure1.56e-14560
germ layer / neural crest derived structure1.56e-14560
epiblast (generic)1.56e-14560
embryonic structure2.19e-14564
organ system subdivision2.39e-14223
brain grey matter2.96e-1434
gray matter2.96e-1434
telencephalon5.78e-1434
regional part of telencephalon3.52e-1332
developing anatomical structure4.12e-13581
cerebral hemisphere5.05e-1332
anatomical group2.52e-12625
epithelium2.53e-12306
anatomical system4.01e-12624
cell layer5.90e-12309
splanchnic layer of lateral plate mesoderm1.42e-1083
cerebral cortex4.91e-1025
pallium4.91e-1025
artery1.38e-0942
arterial blood vessel1.38e-0942
arterial system1.38e-0942
organ part4.01e-09218
regional part of cerebral cortex1.45e-0822
organ4.89e-08503
neocortex1.46e-0720
systemic artery2.13e-0733
systemic arterial system2.13e-0733
epithelial tube open at both ends2.76e-0759
blood vessel2.76e-0759
blood vasculature2.76e-0759
vascular cord2.76e-0759
posterior neural tube2.84e-0715
chordal neural plate2.84e-0715
heart3.30e-0724
primitive heart tube3.30e-0724
primary heart field3.30e-0724
anterior lateral plate mesoderm3.30e-0724
heart tube3.30e-0724
heart primordium3.30e-0724
cardiac mesoderm3.30e-0724
cardiogenic plate3.30e-0724
heart rudiment3.30e-0724
primary circulatory organ9.47e-0727


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#1066455.360256373075030.0002259278299937090.00250192732867277
EGR1#195843.990543275848110.0067800983001440.0287754667737621
RAD21#5885510.35503389545638.39503550283973e-060.000229881781038563
SMC3#9126515.04493284493281.29633924985553e-065.16749522578862e-05
YY1#752854.911170749853860.00034993140821360.00353106148235943
ZNF143#770238.100525931336740.003624870512090980.0183366197526044



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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