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Coexpression cluster:C2872: Difference between revisions

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|ontology_enrichment_disease=DOID:171!3.91e-07!10
|ontology_enrichment_disease=DOID:171!3.91e-07!10
|ontology_enrichment_uberon=UBERON:0001017!1.39e-56!82;UBERON:0000073!4.70e-56!94;UBERON:0001016!4.70e-56!94;UBERON:0005743!2.40e-54!86;UBERON:0001049!1.61e-51!57;UBERON:0005068!1.61e-51!57;UBERON:0006241!1.61e-51!57;UBERON:0007135!1.61e-51!57;UBERON:0000955!4.75e-47!69;UBERON:0006238!4.75e-47!69;UBERON:0002616!1.73e-42!59;UBERON:0002780!7.65e-38!41;UBERON:0001890!7.65e-38!41;UBERON:0006240!7.65e-38!41;UBERON:0003080!1.37e-36!42;UBERON:0002346!4.42e-36!90;UBERON:0002020!9.91e-36!34;UBERON:0003528!9.91e-36!34;UBERON:0001893!1.07e-35!34;UBERON:0002791!1.18e-34!33;UBERON:0001869!2.06e-33!32;UBERON:0003075!1.89e-32!86;UBERON:0007284!1.89e-32!86;UBERON:0000924!5.62e-30!173;UBERON:0006601!5.62e-30!173;UBERON:0004121!4.64e-27!169;UBERON:0000956!2.39e-26!25;UBERON:0000203!2.39e-26!25;UBERON:0003056!2.77e-23!61;UBERON:0002619!9.84e-23!22;UBERON:0000033!3.01e-21!123;UBERON:0001950!1.39e-20!20;UBERON:0000153!5.49e-20!129;UBERON:0007811!5.49e-20!129;UBERON:0007023!4.37e-16!115;UBERON:0003076!1.28e-15!15;UBERON:0003057!1.28e-15!15;UBERON:0004732!1.17e-13!13;UBERON:0004733!1.50e-12!12;UBERON:0002028!1.50e-12!12;UBERON:0007277!1.50e-12!12;UBERON:0002308!9.83e-11!9;UBERON:0000125!9.83e-11!9;UBERON:0002420!1.77e-10!9;UBERON:0007245!1.77e-10!9;UBERON:0010009!1.77e-10!9;UBERON:0010011!1.77e-10!9;UBERON:0000454!1.77e-10!9;UBERON:0002680!1.17e-09!9;UBERON:0001895!1.17e-09!9;UBERON:0010092!1.17e-09!9;UBERON:0009663!1.37e-08!7;UBERON:0000200!1.68e-07!6;UBERON:0002298!2.17e-07!8;UBERON:0001871!2.45e-07!7;UBERON:0000064!2.69e-07!219;UBERON:0002021!5.84e-07!5;UBERON:0001872!8.77e-07!5;UBERON:0000025!8.82e-07!194
|ontology_enrichment_uberon=UBERON:0001017!1.39e-56!82;UBERON:0000073!4.70e-56!94;UBERON:0001016!4.70e-56!94;UBERON:0005743!2.40e-54!86;UBERON:0001049!1.61e-51!57;UBERON:0005068!1.61e-51!57;UBERON:0006241!1.61e-51!57;UBERON:0007135!1.61e-51!57;UBERON:0000955!4.75e-47!69;UBERON:0006238!4.75e-47!69;UBERON:0002616!1.73e-42!59;UBERON:0002780!7.65e-38!41;UBERON:0001890!7.65e-38!41;UBERON:0006240!7.65e-38!41;UBERON:0003080!1.37e-36!42;UBERON:0002346!4.42e-36!90;UBERON:0002020!9.91e-36!34;UBERON:0003528!9.91e-36!34;UBERON:0001893!1.07e-35!34;UBERON:0002791!1.18e-34!33;UBERON:0001869!2.06e-33!32;UBERON:0003075!1.89e-32!86;UBERON:0007284!1.89e-32!86;UBERON:0000924!5.62e-30!173;UBERON:0006601!5.62e-30!173;UBERON:0004121!4.64e-27!169;UBERON:0000956!2.39e-26!25;UBERON:0000203!2.39e-26!25;UBERON:0003056!2.77e-23!61;UBERON:0002619!9.84e-23!22;UBERON:0000033!3.01e-21!123;UBERON:0001950!1.39e-20!20;UBERON:0000153!5.49e-20!129;UBERON:0007811!5.49e-20!129;UBERON:0007023!4.37e-16!115;UBERON:0003076!1.28e-15!15;UBERON:0003057!1.28e-15!15;UBERON:0004732!1.17e-13!13;UBERON:0004733!1.50e-12!12;UBERON:0002028!1.50e-12!12;UBERON:0007277!1.50e-12!12;UBERON:0002308!9.83e-11!9;UBERON:0000125!9.83e-11!9;UBERON:0002420!1.77e-10!9;UBERON:0007245!1.77e-10!9;UBERON:0010009!1.77e-10!9;UBERON:0010011!1.77e-10!9;UBERON:0000454!1.77e-10!9;UBERON:0002680!1.17e-09!9;UBERON:0001895!1.17e-09!9;UBERON:0010092!1.17e-09!9;UBERON:0009663!1.37e-08!7;UBERON:0000200!1.68e-07!6;UBERON:0002298!2.17e-07!8;UBERON:0001871!2.45e-07!7;UBERON:0000064!2.69e-07!219;UBERON:0002021!5.84e-07!5;UBERON:0001872!8.77e-07!5;UBERON:0000025!8.82e-07!194
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}}
}}

Revision as of 18:40, 8 August 2012


Full id: C2872_neuroepithelioma_neuroblastoma_Astrocyte_Neurons_carcinoid_astrocytoma_Neural



Phase1 CAGE Peaks

Hg19::chr6:99282438..99282457,+p2@POU3F2
Hg19::chr6:99282461..99282472,+p7@POU3F2
Hg19::chr6:99282475..99282501,+p1@POU3F2
Hg19::chr6:99282722..99282737,+p6@POU3F2


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>


Uber Anatomy
Ontology termp-valuen
central nervous system1.39e-5682
regional part of nervous system4.70e-5694
nervous system4.70e-5694
neural tube1.61e-5157
neural rod1.61e-5157
future spinal cord1.61e-5157
neural keel1.61e-5157
brain4.75e-4769
future brain4.75e-4769
regional part of brain1.73e-4259
regional part of forebrain7.65e-3841
forebrain7.65e-3841
future forebrain7.65e-3841
anterior neural tube1.37e-3642
neurectoderm4.42e-3690
gray matter9.91e-3634
brain grey matter9.91e-3634
telencephalon1.07e-3534
regional part of telencephalon1.18e-3433
cerebral hemisphere2.06e-3332
neural plate1.89e-3286
presumptive neural plate1.89e-3286
ectoderm5.62e-30173
presumptive ectoderm5.62e-30173
ectoderm-derived structure4.64e-27169
cerebral cortex2.39e-2625
pallium2.39e-2625
pre-chordal neural plate2.77e-2361
regional part of cerebral cortex9.84e-2322
head3.01e-21123
neocortex1.39e-2020
anterior region of body5.49e-20129
craniocervical region5.49e-20129
adult organism4.37e-16115
posterior neural tube1.28e-1515
chordal neural plate1.28e-1515
segmental subdivision of nervous system1.17e-1313
segmental subdivision of hindbrain1.50e-1212
hindbrain1.50e-1212
presumptive hindbrain1.50e-1212
nucleus of brain9.83e-119
neural nucleus9.83e-119
basal ganglion1.77e-109
nuclear complex of neuraxis1.77e-109
aggregate regional part of brain1.77e-109
collection of basal ganglia1.77e-109
cerebral subcortex1.77e-109
regional part of metencephalon1.17e-099
metencephalon1.17e-099
future metencephalon1.17e-099
telencephalic nucleus1.37e-087
gyrus1.68e-076
brainstem2.17e-078
temporal lobe2.45e-077
organ part2.69e-07219
occipital lobe5.84e-075
parietal lobe8.77e-075
tube8.82e-07194
Disease
Ontology termp-valuen
neuroectodermal tumor3.91e-0710


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


No analysis results for this cluster

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.