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Coexpression cluster:C3818: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.07e-41!115;UBERON:0001049!1.03e-32!57;UBERON:0005068!1.03e-32!57;UBERON:0006241!1.03e-32!57;UBERON:0007135!1.03e-32!57;UBERON:0002616!9.39e-28!59;UBERON:0000955!3.14e-27!69;UBERON:0006238!3.14e-27!69;UBERON:0001017!3.27e-27!82;UBERON:0005743!1.75e-26!86;UBERON:0000073!1.30e-25!94;UBERON:0001016!1.30e-25!94;UBERON:0003080!9.09e-25!42;UBERON:0002780!3.23e-24!41;UBERON:0001890!3.23e-24!41;UBERON:0006240!3.23e-24!41;UBERON:0003075!3.62e-24!86;UBERON:0007284!3.62e-24!86;UBERON:0002346!3.27e-23!90;UBERON:0000153!6.55e-20!129;UBERON:0007811!6.55e-20!129;UBERON:0002020!1.12e-19!34;UBERON:0003528!1.12e-19!34;UBERON:0001893!1.21e-19!34;UBERON:0000033!2.33e-19!123;UBERON:0003056!3.54e-19!61;UBERON:0002791!4.91e-19!33;UBERON:0001869!2.65e-18!32;UBERON:0004121!1.39e-17!169;UBERON:0000924!2.94e-17!173;UBERON:0006601!2.94e-17!173;UBERON:0002619!1.01e-14!22;UBERON:0000956!2.71e-14!25;UBERON:0000203!2.71e-14!25;UBERON:0001950!1.17e-13!20;UBERON:0003076!5.23e-09!15;UBERON:0003057!5.23e-09!15;UBERON:0000064!1.84e-08!219;UBERON:0004732!6.45e-08!13;UBERON:0004733!3.04e-07!12;UBERON:0002028!3.04e-07!12;UBERON:0007277!3.04e-07!12;UBERON:0002308!6.97e-07!9;UBERON:0000125!6.97e-07!9;UBERON:0002420!8.49e-07!9;UBERON:0007245!8.49e-07!9;UBERON:0010009!8.49e-07!9;UBERON:0010011!8.49e-07!9;UBERON:0000454!8.49e-07!9
|ontology_enrichment_uberon=UBERON:0007023!8.12e-40!114;UBERON:0001049!7.69e-32!56;UBERON:0005068!7.69e-32!56;UBERON:0006241!7.69e-32!56;UBERON:0007135!7.69e-32!56;UBERON:0000073!6.36e-30!53;UBERON:0002616!6.36e-30!53;UBERON:0000955!1.11e-26!68;UBERON:0006238!1.11e-26!68;UBERON:0001017!6.79e-26!81;UBERON:0003075!2.43e-24!82;UBERON:0007284!2.43e-24!82;UBERON:0001016!2.65e-24!89;UBERON:0002346!7.27e-24!86;UBERON:0002780!1.17e-23!41;UBERON:0001890!1.17e-23!41;UBERON:0003080!1.17e-23!41;UBERON:0006240!1.17e-23!41;UBERON:0001893!3.85e-19!34;UBERON:0003528!4.22e-19!34;UBERON:0002020!4.22e-19!34;UBERON:0003056!1.78e-18!61;UBERON:0002791!7.44e-18!32;UBERON:0011216!8.71e-18!223;UBERON:0001869!9.16e-18!32;UBERON:0010371!3.03e-17!104;UBERON:0002619!5.92e-15!22;UBERON:0004121!9.24e-15!171;UBERON:0000924!9.24e-15!171;UBERON:0006601!9.24e-15!171;UBERON:0000956!2.03e-14!25;UBERON:0000203!2.03e-14!25;UBERON:0001950!6.61e-14!20;UBERON:0010314!8.13e-14!132;UBERON:0003076!2.95e-09!15;UBERON:0003057!2.95e-09!15;UBERON:0004732!3.71e-08!13;UBERON:0000064!4.02e-08!218;UBERON:0000477!5.68e-08!373;UBERON:0000481!6.65e-08!342;UBERON:0004733!1.81e-07!12;UBERON:0002028!1.81e-07!12;UBERON:0007277!1.81e-07!12
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259569526281172!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273855823510931!ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163090131269644!SETDB1#9869;2:26.880017452007:0.00181446890796441:0.0108933845871979!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370739491455821!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156378009311489!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00389030244366426
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}}
}}

Revision as of 15:26, 19 October 2012


Full id: C3818_pineal_cerebellum_thalamus_optic_occipital_globus_pituitary



Phase1 CAGE Peaks

Hg19::chr19:52097613..52097642,-p1@FLJ30403
Hg19::chr19:52097643..52097664,-p2@FLJ30403
Hg19::chr19:57183322..57183358,+p1@FJ997633


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
adult organism8.12e-40114
neural tube7.69e-3256
neural rod7.69e-3256
future spinal cord7.69e-3256
neural keel7.69e-3256
regional part of nervous system6.36e-3053
regional part of brain6.36e-3053
brain1.11e-2668
future brain1.11e-2668
central nervous system6.79e-2681
neural plate2.43e-2482
presumptive neural plate2.43e-2482
nervous system2.65e-2489
neurectoderm7.27e-2486
regional part of forebrain1.17e-2341
forebrain1.17e-2341
anterior neural tube1.17e-2341
future forebrain1.17e-2341
telencephalon3.85e-1934
brain grey matter4.22e-1934
gray matter4.22e-1934
pre-chordal neural plate1.78e-1861
regional part of telencephalon7.44e-1832
organ system subdivision8.71e-18223
cerebral hemisphere9.16e-1832
ecto-epithelium3.03e-17104
regional part of cerebral cortex5.92e-1522
ectoderm-derived structure9.24e-15171
ectoderm9.24e-15171
presumptive ectoderm9.24e-15171
cerebral cortex2.03e-1425
pallium2.03e-1425
neocortex6.61e-1420
structure with developmental contribution from neural crest8.13e-14132
posterior neural tube2.95e-0915
chordal neural plate2.95e-0915
segmental subdivision of nervous system3.71e-0813
organ part4.02e-08218
anatomical cluster5.68e-08373
multi-tissue structure6.65e-08342
segmental subdivision of hindbrain1.81e-0712
hindbrain1.81e-0712
presumptive hindbrain1.81e-0712


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
ATF3#467214.97544968400580.005768294540793880.0259569526281172
BCLAF1#9774214.43509840674790.006201147435546130.0273855823510931
ESR1#2099220.51240219743630.003099741577095180.0163090131269644
SETDB1#9869226.8800174520070.001814468907964410.0108933845871979
SIX5#147912211.3911435703060.009873820081429030.0370739491455821
ZBTB33#10009221.10981668665410.002928597060603240.0156378009311489
ZNF143#7702313.50087655222790.0004062804962997170.00389030244366426



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.