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Coexpression cluster:C2493: Difference between revisions

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|full_id=C2493_neuroblastoma_acute_teratocarcinoma_small_merkel_rhabdomyosarcoma_occipital
|full_id=C2493_neuroblastoma_acute_teratocarcinoma_small_merkel_rhabdomyosarcoma_occipital
|id=C2493
|id=C2493
|ontology_enrichment_celltype=CL:0002319!1.24e-08!25;CL:0000540!2.89e-08!6;CL:0000031!2.89e-08!6;CL:0000404!2.89e-08!6;CL:0000047!8.30e-08!8;CL:0002322!1.73e-07!5
|ontology_enrichment_celltype=CL:0002322!4.87e-11!5;CL:0000188!5.85e-08!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:169!4.66e-07!6
|ontology_enrichment_uberon=UBERON:0000073!3.51e-51!94;UBERON:0001016!3.51e-51!94;UBERON:0001017!1.68e-49!82;UBERON:0005743!6.97e-48!86;UBERON:0001049!2.59e-41!57;UBERON:0005068!2.59e-41!57;UBERON:0006241!2.59e-41!57;UBERON:0007135!2.59e-41!57;UBERON:0000955!3.34e-39!69;UBERON:0006238!3.34e-39!69;UBERON:0002616!3.00e-35!59;UBERON:0002780!2.01e-33!41;UBERON:0001890!2.01e-33!41;UBERON:0006240!2.01e-33!41;UBERON:0003080!2.33e-32!42;UBERON:0003075!1.52e-31!86;UBERON:0007284!1.52e-31!86;UBERON:0002346!1.29e-30!90;UBERON:0001869!1.41e-30!32;UBERON:0002020!1.47e-30!34;UBERON:0003528!1.47e-30!34;UBERON:0001893!1.67e-30!34;UBERON:0002791!3.49e-29!33;UBERON:0000956!2.76e-25!25;UBERON:0000203!2.76e-25!25;UBERON:0004121!4.65e-25!169;UBERON:0002619!5.35e-25!22;UBERON:0000924!8.16e-25!173;UBERON:0006601!8.16e-25!173;UBERON:0001950!6.10e-23!20;UBERON:0003056!8.80e-23!61;UBERON:0007023!1.25e-19!115;UBERON:0000153!1.02e-18!129;UBERON:0007811!1.02e-18!129;UBERON:0000033!8.18e-18!123;UBERON:0003076!5.89e-10!15;UBERON:0003057!5.89e-10!15;UBERON:0004732!1.14e-09!13;UBERON:0000200!1.36e-09!6;UBERON:0004733!1.30e-08!12;UBERON:0002028!1.30e-08!12;UBERON:0007277!1.30e-08!12;UBERON:0001872!1.64e-08!5;UBERON:0002021!5.32e-08!5;UBERON:0002308!6.86e-07!9;UBERON:0000125!6.86e-07!9
|ontology_enrichment_uberon=UBERON:0001016!3.97e-45!89;UBERON:0001049!9.56e-43!56;UBERON:0005068!9.56e-43!56;UBERON:0006241!9.56e-43!56;UBERON:0007135!9.56e-43!56;UBERON:0001017!1.68e-41!81;UBERON:0000073!4.38e-40!53;UBERON:0002616!4.38e-40!53;UBERON:0000955!4.15e-37!68;UBERON:0006238!4.15e-37!68;UBERON:0002780!1.33e-32!41;UBERON:0001890!1.33e-32!41;UBERON:0003080!1.33e-32!41;UBERON:0006240!1.33e-32!41;UBERON:0003528!4.81e-32!34;UBERON:0002020!4.81e-32!34;UBERON:0001893!6.02e-32!34;UBERON:0001869!2.13e-31!32;UBERON:0003075!4.47e-31!82;UBERON:0007284!4.47e-31!82;UBERON:0002346!3.99e-29!86;UBERON:0002619!5.67e-29!22;UBERON:0001950!7.66e-29!20;UBERON:0002791!1.94e-28!32;UBERON:0010371!2.98e-25!104;UBERON:0000956!5.11e-25!25;UBERON:0000203!5.11e-25!25;UBERON:0003056!8.41e-23!61;UBERON:0004121!8.67e-22!171;UBERON:0000924!8.67e-22!171;UBERON:0006601!8.67e-22!171;UBERON:0010314!1.63e-17!132;UBERON:0007023!2.35e-17!114;UBERON:0011216!3.05e-14!223;UBERON:0000200!3.32e-14!6;UBERON:0001872!3.59e-12!5;UBERON:0003076!4.66e-11!15;UBERON:0003057!4.66e-11!15;UBERON:0002298!1.16e-09!6;UBERON:0004733!1.29e-08!12;UBERON:0002028!1.29e-08!12;UBERON:0007277!1.29e-08!12;UBERON:0000013!1.67e-08!5;UBERON:0002410!1.67e-08!5;UBERON:0000125!1.92e-08!9;UBERON:0002308!1.92e-08!9;UBERON:0001871!3.78e-08!6;UBERON:0000025!3.84e-08!192;UBERON:0004732!7.28e-08!13;UBERON:0000988!7.91e-08!3;UBERON:0001870!8.48e-08!3;UBERON:0000483!6.12e-07!306;UBERON:0000119!9.25e-07!309
|tf_chipseq_enrich=GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0108992042744595
|tf_chipseq_enrich=GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0108992042744595
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}}
}}

Revision as of 14:05, 19 October 2012


Full id: C2493_neuroblastoma_acute_teratocarcinoma_small_merkel_rhabdomyosarcoma_occipital



Phase1 CAGE Peaks

Hg19::chr19:4279009..4279053,+p2@SHD
Hg19::chr19:4279059..4279071,+p4@SHD
Hg19::chr19:4279079..4279090,+p12@SHD
Hg19::chr19:4279507..4279523,+p6@SHD


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>disease_data<br>

Cell Type
Ontology termp-valuen
embryonic stem cell4.87e-115
cell of skeletal muscle5.85e-089
Uber Anatomy
Ontology termp-valuen
nervous system3.97e-4589
neural tube9.56e-4356
neural rod9.56e-4356
future spinal cord9.56e-4356
neural keel9.56e-4356
central nervous system1.68e-4181
regional part of nervous system4.38e-4053
regional part of brain4.38e-4053
brain4.15e-3768
future brain4.15e-3768
regional part of forebrain1.33e-3241
forebrain1.33e-3241
anterior neural tube1.33e-3241
future forebrain1.33e-3241
brain grey matter4.81e-3234
gray matter4.81e-3234
telencephalon6.02e-3234
cerebral hemisphere2.13e-3132
neural plate4.47e-3182
presumptive neural plate4.47e-3182
neurectoderm3.99e-2986
regional part of cerebral cortex5.67e-2922
neocortex7.66e-2920
regional part of telencephalon1.94e-2832
ecto-epithelium2.98e-25104
cerebral cortex5.11e-2525
pallium5.11e-2525
pre-chordal neural plate8.41e-2361
ectoderm-derived structure8.67e-22171
ectoderm8.67e-22171
presumptive ectoderm8.67e-22171
structure with developmental contribution from neural crest1.63e-17132
adult organism2.35e-17114
organ system subdivision3.05e-14223
gyrus3.32e-146
parietal lobe3.59e-125
posterior neural tube4.66e-1115
chordal neural plate4.66e-1115
brainstem1.16e-096
segmental subdivision of hindbrain1.29e-0812
hindbrain1.29e-0812
presumptive hindbrain1.29e-0812
sympathetic nervous system1.67e-085
autonomic nervous system1.67e-085
neural nucleus1.92e-089
nucleus of brain1.92e-089
temporal lobe3.78e-086
tube3.84e-08192
segmental subdivision of nervous system7.28e-0813
pons7.91e-083
frontal cortex8.48e-083
epithelium6.12e-07306
cell layer9.25e-07309
Disease
Ontology termp-valuen
neuroendocrine tumor4.66e-076


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
GATA2#262439.55869880016550.001818151618357440.0108992042744595



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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