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Coexpression cluster:C4345: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.72e-38!57;UBERON:0005068!1.72e-38!57;UBERON:0006241!1.72e-38!57;UBERON:0007135!1.72e-38!57;UBERON:0007023!1.40e-36!115;UBERON:0002616!2.15e-34!59;UBERON:0002780!6.16e-34!41;UBERON:0001890!6.16e-34!41;UBERON:0006240!6.16e-34!41;UBERON:0003080!9.20e-33!42;UBERON:0001017!3.76e-32!82;UBERON:0000955!5.11e-32!69;UBERON:0006238!5.11e-32!69;UBERON:0005743!4.44e-31!86;UBERON:0002346!6.94e-31!90;UBERON:0003075!6.15e-30!86;UBERON:0007284!6.15e-30!86;UBERON:0002020!1.78e-29!34;UBERON:0003528!1.78e-29!34;UBERON:0001893!2.15e-29!34;UBERON:0002791!2.36e-28!33;UBERON:0001869!5.86e-28!32;UBERON:0000073!3.13e-27!94;UBERON:0001016!3.13e-27!94;UBERON:0003056!4.10e-25!61;UBERON:0002619!8.20e-23!22;UBERON:0000033!1.38e-21!123;UBERON:0000153!4.17e-21!129;UBERON:0007811!4.17e-21!129;UBERON:0001950!6.02e-21!20;UBERON:0000924!7.69e-21!173;UBERON:0006601!7.69e-21!173;UBERON:0000956!1.27e-20!25;UBERON:0000203!1.27e-20!25;UBERON:0004121!6.88e-20!169;UBERON:0000475!7.00e-14!365;UBERON:0002420!1.02e-10!9;UBERON:0007245!1.02e-10!9;UBERON:0010009!1.02e-10!9;UBERON:0010011!1.02e-10!9;UBERON:0000454!1.02e-10!9;UBERON:0002308!2.29e-10!9;UBERON:0000125!2.29e-10!9;UBERON:0009663!1.60e-08!7;UBERON:0000200!6.34e-08!6;UBERON:0000483!9.56e-08!309;UBERON:0000064!9.59e-08!219;UBERON:0000119!1.03e-07!312;UBERON:0001871!1.93e-07!7;UBERON:0000025!2.40e-07!194;UBERON:0003076!2.70e-07!15;UBERON:0003057!2.70e-07!15;UBERON:0001872!6.91e-07!5;UBERON:0000477!8.29e-07!286;UBERON:0002298!8.86e-07!8
|ontology_enrichment_uberon=UBERON:0001049!4.93e-54!56;UBERON:0005068!4.93e-54!56;UBERON:0006241!4.93e-54!56;UBERON:0007135!4.93e-54!56;UBERON:0000073!1.13e-49!53;UBERON:0002616!1.13e-49!53;UBERON:0001017!3.61e-48!81;UBERON:0000955!1.06e-46!68;UBERON:0006238!1.06e-46!68;UBERON:0002780!1.33e-46!41;UBERON:0001890!1.33e-46!41;UBERON:0003080!1.33e-46!41;UBERON:0006240!1.33e-46!41;UBERON:0001016!1.45e-41!89;UBERON:0001869!3.46e-40!32;UBERON:0003528!6.54e-40!34;UBERON:0002020!6.54e-40!34;UBERON:0001893!1.02e-39!34;UBERON:0003075!2.01e-38!82;UBERON:0007284!2.01e-38!82;UBERON:0007023!1.20e-37!114;UBERON:0002791!3.12e-37!32;UBERON:0002346!7.54e-36!86;UBERON:0010371!2.86e-34!104;UBERON:0003056!3.04e-34!61;UBERON:0002619!4.13e-32!22;UBERON:0000956!9.03e-30!25;UBERON:0000203!9.03e-30!25;UBERON:0001950!2.12e-29!20;UBERON:0004121!4.55e-26!171;UBERON:0000924!4.55e-26!171;UBERON:0006601!4.55e-26!171;UBERON:0010314!1.14e-23!132;UBERON:0011216!6.55e-23!223;UBERON:0002420!5.63e-12!9;UBERON:0007245!5.63e-12!9;UBERON:0010009!5.63e-12!9;UBERON:0010011!5.63e-12!9;UBERON:0000454!5.63e-12!9;UBERON:0000125!1.90e-11!9;UBERON:0002308!1.90e-11!9;UBERON:0000200!1.64e-10!6;UBERON:0002298!5.57e-10!6;UBERON:0000025!2.53e-09!192;UBERON:0003076!2.98e-09!15;UBERON:0003057!2.98e-09!15;UBERON:0000477!3.96e-09!373;UBERON:0001872!4.54e-09!5;UBERON:0000349!5.42e-09!5;UBERON:0002021!5.97e-09!5;UBERON:0001871!7.28e-09!6;UBERON:0009663!7.28e-09!7;UBERON:0000064!2.31e-08!218;UBERON:0001894!3.55e-08!7;UBERON:0006222!3.55e-08!7;UBERON:0000369!5.55e-08!4;UBERON:0002435!5.55e-08!4;UBERON:0000204!5.55e-08!4;UBERON:0010082!5.55e-08!4;UBERON:0004111!1.17e-07!240;UBERON:0000481!4.89e-07!342;UBERON:0000483!9.22e-07!306
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}}
}}

Revision as of 15:52, 19 October 2012


Full id: C4345_caudate_melanoma_merkel_smallcell_occipital_pons_amygdala



Phase1 CAGE Peaks

Hg19::chr3:76359866..76359898,+p5@ROBO2
Hg19::chr3:76360015..76360051,+p3@ROBO2
Hg19::chr3:76360054..76360097,+p4@ROBO2


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
neural tube4.93e-5456
neural rod4.93e-5456
future spinal cord4.93e-5456
neural keel4.93e-5456
regional part of nervous system1.13e-4953
regional part of brain1.13e-4953
central nervous system3.61e-4881
brain1.06e-4668
future brain1.06e-4668
regional part of forebrain1.33e-4641
forebrain1.33e-4641
anterior neural tube1.33e-4641
future forebrain1.33e-4641
nervous system1.45e-4189
cerebral hemisphere3.46e-4032
brain grey matter6.54e-4034
gray matter6.54e-4034
telencephalon1.02e-3934
neural plate2.01e-3882
presumptive neural plate2.01e-3882
adult organism1.20e-37114
regional part of telencephalon3.12e-3732
neurectoderm7.54e-3686
ecto-epithelium2.86e-34104
pre-chordal neural plate3.04e-3461
regional part of cerebral cortex4.13e-3222
cerebral cortex9.03e-3025
pallium9.03e-3025
neocortex2.12e-2920
ectoderm-derived structure4.55e-26171
ectoderm4.55e-26171
presumptive ectoderm4.55e-26171
structure with developmental contribution from neural crest1.14e-23132
organ system subdivision6.55e-23223
basal ganglion5.63e-129
nuclear complex of neuraxis5.63e-129
aggregate regional part of brain5.63e-129
collection of basal ganglia5.63e-129
cerebral subcortex5.63e-129
neural nucleus1.90e-119
nucleus of brain1.90e-119
gyrus1.64e-106
brainstem5.57e-106
tube2.53e-09192
posterior neural tube2.98e-0915
chordal neural plate2.98e-0915
anatomical cluster3.96e-09373
parietal lobe4.54e-095
limbic system5.42e-095
occipital lobe5.97e-095
temporal lobe7.28e-096
telencephalic nucleus7.28e-097
organ part2.31e-08218
diencephalon3.55e-087
future diencephalon3.55e-087
corpus striatum5.55e-084
striatum5.55e-084
ventral part of telencephalon5.55e-084
future corpus striatum5.55e-084
anatomical conduit1.17e-07240
multi-tissue structure4.89e-07342
epithelium9.22e-07306


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.

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