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Coexpression cluster:C3984: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!2.28e-64!89;UBERON:0001017!4.29e-63!81;UBERON:0000073!4.47e-63!53;UBERON:0002616!4.47e-63!53;UBERON:0001049!1.50e-62!56;UBERON:0005068!1.50e-62!56;UBERON:0006241!1.50e-62!56;UBERON:0007135!1.50e-62!56;UBERON:0003528!2.67e-59!34;UBERON:0002020!2.67e-59!34;UBERON:0001893!3.19e-59!34;UBERON:0002780!1.28e-58!41;UBERON:0001890!1.28e-58!41;UBERON:0003080!1.28e-58!41;UBERON:0006240!1.28e-58!41;UBERON:0001869!4.41e-55!32;UBERON:0002619!7.33e-55!22;UBERON:0000955!8.46e-55!68;UBERON:0006238!8.46e-55!68;UBERON:0002791!1.38e-54!32;UBERON:0001950!6.23e-50!20;UBERON:0000956!9.25e-48!25;UBERON:0000203!9.25e-48!25;UBERON:0002346!5.68e-46!86;UBERON:0003075!5.20e-44!82;UBERON:0007284!5.20e-44!82;UBERON:0003056!1.05e-41!61;UBERON:0004121!1.23e-36!171;UBERON:0000924!1.23e-36!171;UBERON:0006601!1.23e-36!171;UBERON:0010371!1.28e-36!104;UBERON:0007023!4.61e-36!114;UBERON:0011216!6.78e-26!223;UBERON:0010314!9.10e-25!132;UBERON:0000200!1.62e-17!6;UBERON:0002298!2.50e-15!6;UBERON:0001872!2.62e-14!5;UBERON:0001871!2.71e-14!6;UBERON:0002021!2.92e-14!5;UBERON:0000349!5.15e-14!5;UBERON:0000025!1.21e-13!192;UBERON:0002420!3.28e-13!9;UBERON:0007245!3.28e-13!9;UBERON:0010009!3.28e-13!9;UBERON:0010011!3.28e-13!9;UBERON:0000454!3.28e-13!9;UBERON:0000125!5.97e-13!9;UBERON:0002308!5.97e-13!9;UBERON:0000477!3.48e-11!373;UBERON:0000064!5.64e-10!218;UBERON:0001870!1.19e-09!3;UBERON:0004111!7.11e-09!240;UBERON:0000988!8.81e-09!3;UBERON:0009663!1.09e-08!7;UBERON:0000922!2.75e-08!592;UBERON:0001896!3.09e-08!3;UBERON:0005290!3.09e-08!3;UBERON:0010096!3.09e-08!3;UBERON:0003076!1.32e-07!15;UBERON:0003057!1.32e-07!15;UBERON:0004733!2.67e-07!12;UBERON:0002028!2.67e-07!12;UBERON:0007277!2.67e-07!12;UBERON:0002771!4.89e-07!2;UBERON:0002702!5.17e-07!2;UBERON:0000483!5.50e-07!306;UBERON:0000923!6.73e-07!560;UBERON:0010316!6.73e-07!560;UBERON:0005291!6.73e-07!560;UBERON:0006598!6.73e-07!560;UBERON:0010317!6.73e-07!560;UBERON:0002532!6.73e-07!560;UBERON:0000119!8.08e-07!309;UBERON:0002050!9.71e-07!564
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}}
}}

Revision as of 16:28, 26 November 2012


Full id: C3984_carcinoid_merkel_neuroblastoma_parietal_medial_occipital_middle



Phase1 CAGE Peaks

Hg19::chr1:50513716..50513743,+p5@ELAVL4
Hg19::chr1:50513788..50513817,+p7@ELAVL4
Hg19::chr9:23821301..23821313,-p6@ELAVL2


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


GO IDGO nameFDR corrected p-value
GO:0003730mRNA 3'-UTR binding1.31015399186089e-06
GO:0003729mRNA binding1.31249355256064e-05
GO:0003723RNA binding0.00743630928123174



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>


Cell Type
Ontology termp-valuen
neuronal stem cell7.98e-088
Merkel cell3.36e-072
neuron6.74e-076
neuroblast6.74e-076
electrically signaling cell6.74e-076
Uber Anatomy
Ontology termp-valuen
nervous system2.28e-6489
central nervous system4.29e-6381
regional part of nervous system4.47e-6353
regional part of brain4.47e-6353
neural tube1.50e-6256
neural rod1.50e-6256
future spinal cord1.50e-6256
neural keel1.50e-6256
brain grey matter2.67e-5934
gray matter2.67e-5934
telencephalon3.19e-5934
regional part of forebrain1.28e-5841
forebrain1.28e-5841
anterior neural tube1.28e-5841
future forebrain1.28e-5841
cerebral hemisphere4.41e-5532
regional part of cerebral cortex7.33e-5522
brain8.46e-5568
future brain8.46e-5568
regional part of telencephalon1.38e-5432
neocortex6.23e-5020
cerebral cortex9.25e-4825
pallium9.25e-4825
neurectoderm5.68e-4686
neural plate5.20e-4482
presumptive neural plate5.20e-4482
pre-chordal neural plate1.05e-4161
ectoderm-derived structure1.23e-36171
ectoderm1.23e-36171
presumptive ectoderm1.23e-36171
ecto-epithelium1.28e-36104
adult organism4.61e-36114
organ system subdivision6.78e-26223
structure with developmental contribution from neural crest9.10e-25132
gyrus1.62e-176
brainstem2.50e-156
parietal lobe2.62e-145
temporal lobe2.71e-146
occipital lobe2.92e-145
limbic system5.15e-145
tube1.21e-13192
basal ganglion3.28e-139
nuclear complex of neuraxis3.28e-139
aggregate regional part of brain3.28e-139
collection of basal ganglia3.28e-139
cerebral subcortex3.28e-139
neural nucleus5.97e-139
nucleus of brain5.97e-139
anatomical cluster3.48e-11373
organ part5.64e-10218
frontal cortex1.19e-093
anatomical conduit7.11e-09240
pons8.81e-093
telencephalic nucleus1.09e-087
embryo2.75e-08592
medulla oblongata3.09e-083
myelencephalon3.09e-083
future myelencephalon3.09e-083
posterior neural tube1.32e-0715
chordal neural plate1.32e-0715
segmental subdivision of hindbrain2.67e-0712
hindbrain2.67e-0712
presumptive hindbrain2.67e-0712
middle temporal gyrus4.89e-072
middle frontal gyrus5.17e-072
epithelium5.50e-07306
germ layer6.73e-07560
germ layer / neural crest6.73e-07560
embryonic tissue6.73e-07560
presumptive structure6.73e-07560
germ layer / neural crest derived structure6.73e-07560
epiblast (generic)6.73e-07560
cell layer8.08e-07309
embryonic structure9.71e-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.