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Coexpression cluster:C4318: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!8.53e-93!114;UBERON:0001049!2.64e-58!56;UBERON:0005068!2.64e-58!56;UBERON:0006241!2.64e-58!56;UBERON:0007135!2.64e-58!56;UBERON:0000073!2.24e-53!53;UBERON:0002616!2.24e-53!53;UBERON:0000955!4.83e-46!68;UBERON:0006238!4.83e-46!68;UBERON:0002346!1.62e-44!86;UBERON:0002780!2.45e-44!41;UBERON:0001890!2.45e-44!41;UBERON:0003080!2.45e-44!41;UBERON:0006240!2.45e-44!41;UBERON:0001017!2.70e-44!81;UBERON:0003075!5.13e-44!82;UBERON:0007284!5.13e-44!82;UBERON:0001016!3.53e-40!89;UBERON:0010371!1.85e-37!104;UBERON:0003528!4.20e-34!34;UBERON:0002020!4.20e-34!34;UBERON:0001893!8.21e-34!34;UBERON:0010314!2.17e-32!132;UBERON:0002791!1.88e-31!32;UBERON:0001869!6.16e-31!32;UBERON:0003056!8.07e-30!61;UBERON:0004121!6.88e-27!171;UBERON:0000924!6.88e-27!171;UBERON:0006601!6.88e-27!171;UBERON:0002619!9.61e-26!22;UBERON:0001950!8.39e-23!20;UBERON:0000956!5.29e-22!25;UBERON:0000203!5.29e-22!25;UBERON:0011216!8.10e-17!223;UBERON:0004111!6.66e-16!240;UBERON:0000025!2.33e-15!192;UBERON:0003076!1.40e-14!15;UBERON:0003057!1.40e-14!15;UBERON:0002420!2.57e-14!9;UBERON:0007245!2.57e-14!9;UBERON:0010009!2.57e-14!9;UBERON:0010011!2.57e-14!9;UBERON:0000454!2.57e-14!9;UBERON:0000125!5.35e-14!9;UBERON:0002308!5.35e-14!9;UBERON:0000477!2.48e-12!373;UBERON:0001894!3.33e-12!7;UBERON:0006222!3.33e-12!7;UBERON:0004732!1.30e-11!13;UBERON:0000064!1.87e-11!218;UBERON:0009663!2.32e-11!7;UBERON:0000483!6.95e-11!306;UBERON:0000119!1.36e-10!309;UBERON:0004733!3.86e-10!12;UBERON:0002028!3.86e-10!12;UBERON:0007277!3.86e-10!12;UBERON:0002298!7.86e-10!6;UBERON:0000481!9.69e-10!342;UBERON:0000200!2.14e-09!6;UBERON:0000062!8.42e-09!503;UBERON:0000349!1.92e-08!5;UBERON:0002021!2.76e-08!5;UBERON:0000468!3.22e-08!656;UBERON:0002784!4.46e-08!4;UBERON:0001872!1.28e-07!5;UBERON:0003296!1.37e-07!4;UBERON:0010133!1.37e-07!4;UBERON:0000923!5.42e-07!560;UBERON:0010316!5.42e-07!560;UBERON:0005291!5.42e-07!560;UBERON:0006598!5.42e-07!560;UBERON:0010317!5.42e-07!560;UBERON:0002532!5.42e-07!560;UBERON:0000467!7.85e-07!624;UBERON:0000480!8.91e-07!625;UBERON:0002050!9.14e-07!564
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}}
}}

Revision as of 16:40, 26 November 2012


Full id: C4318_spinal_medulla_thalamus_melanoma_occipital_breast_amygdala



Phase1 CAGE Peaks

Hg19::chr3:195295690..195295718,-p@chr3:195295690..195295718
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Hg19::chr3:195295735..195295762,-p@chr3:195295735..195295762
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Hg19::chr3:195295785..195295796,-p@chr3:195295785..195295796
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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 organism8.53e-93114
neural tube2.64e-5856
neural rod2.64e-5856
future spinal cord2.64e-5856
neural keel2.64e-5856
regional part of nervous system2.24e-5353
regional part of brain2.24e-5353
brain4.83e-4668
future brain4.83e-4668
neurectoderm1.62e-4486
regional part of forebrain2.45e-4441
forebrain2.45e-4441
anterior neural tube2.45e-4441
future forebrain2.45e-4441
central nervous system2.70e-4481
neural plate5.13e-4482
presumptive neural plate5.13e-4482
nervous system3.53e-4089
ecto-epithelium1.85e-37104
brain grey matter4.20e-3434
gray matter4.20e-3434
telencephalon8.21e-3434
structure with developmental contribution from neural crest2.17e-32132
regional part of telencephalon1.88e-3132
cerebral hemisphere6.16e-3132
pre-chordal neural plate8.07e-3061
ectoderm-derived structure6.88e-27171
ectoderm6.88e-27171
presumptive ectoderm6.88e-27171
regional part of cerebral cortex9.61e-2622
neocortex8.39e-2320
cerebral cortex5.29e-2225
pallium5.29e-2225
organ system subdivision8.10e-17223
anatomical conduit6.66e-16240
tube2.33e-15192
posterior neural tube1.40e-1415
chordal neural plate1.40e-1415
basal ganglion2.57e-149
nuclear complex of neuraxis2.57e-149
aggregate regional part of brain2.57e-149
collection of basal ganglia2.57e-149
cerebral subcortex2.57e-149
neural nucleus5.35e-149
nucleus of brain5.35e-149
anatomical cluster2.48e-12373
diencephalon3.33e-127
future diencephalon3.33e-127
segmental subdivision of nervous system1.30e-1113
organ part1.87e-11218
telencephalic nucleus2.32e-117
epithelium6.95e-11306
cell layer1.36e-10309
segmental subdivision of hindbrain3.86e-1012
hindbrain3.86e-1012
presumptive hindbrain3.86e-1012
brainstem7.86e-106
multi-tissue structure9.69e-10342
gyrus2.14e-096
organ8.42e-09503
limbic system1.92e-085
occipital lobe2.76e-085
multi-cellular organism3.22e-08656
regional part of diencephalon4.46e-084
parietal lobe1.28e-075
gland of diencephalon1.37e-074
neuroendocrine gland1.37e-074
germ layer5.42e-07560
germ layer / neural crest5.42e-07560
embryonic tissue5.42e-07560
presumptive structure5.42e-07560
germ layer / neural crest derived structure5.42e-07560
epiblast (generic)5.42e-07560
anatomical system7.85e-07624
anatomical group8.91e-07625
embryonic structure9.14e-07564


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.