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Coexpression cluster:C3947: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.33e-38!56;UBERON:0005068!3.33e-38!56;UBERON:0006241!3.33e-38!56;UBERON:0007135!3.33e-38!56;UBERON:0000073!7.70e-38!53;UBERON:0002616!7.70e-38!53;UBERON:0000955!1.01e-30!68;UBERON:0006238!1.01e-30!68;UBERON:0002780!4.08e-30!41;UBERON:0001890!4.08e-30!41;UBERON:0003080!4.08e-30!41;UBERON:0006240!4.08e-30!41;UBERON:0002346!4.21e-30!86;UBERON:0001017!4.43e-30!81;UBERON:0003075!5.42e-30!82;UBERON:0007284!5.42e-30!82;UBERON:0001016!1.74e-29!89;UBERON:0003528!1.48e-28!34;UBERON:0002020!1.48e-28!34;UBERON:0001893!1.67e-28!34;UBERON:0001869!1.32e-27!32;UBERON:0002791!6.44e-27!32;UBERON:0003056!7.45e-26!61;UBERON:0007023!3.82e-25!114;UBERON:0010371!5.39e-23!104;UBERON:0000956!1.85e-20!25;UBERON:0000203!1.85e-20!25;UBERON:0004121!3.13e-20!171;UBERON:0000924!3.13e-20!171;UBERON:0006601!3.13e-20!171;UBERON:0010314!8.32e-19!132;UBERON:0002619!2.00e-18!22;UBERON:0001950!2.46e-16!20;UBERON:0011216!9.02e-16!223;UBERON:0000064!5.44e-15!218;UBERON:0002420!4.79e-10!9;UBERON:0007245!4.79e-10!9;UBERON:0010009!4.79e-10!9;UBERON:0010011!4.79e-10!9;UBERON:0000454!4.79e-10!9;UBERON:0000125!1.48e-09!9;UBERON:0002308!1.48e-09!9;UBERON:0000477!1.59e-09!373;UBERON:0000025!2.83e-09!192;UBERON:0003076!3.44e-09!15;UBERON:0003057!3.44e-09!15;UBERON:0004733!7.93e-09!12;UBERON:0002028!7.93e-09!12;UBERON:0007277!7.93e-09!12;UBERON:0004111!1.07e-08!240;UBERON:0000200!4.23e-08!6;UBERON:0000481!4.88e-08!342;UBERON:0009663!5.56e-08!7;UBERON:0004732!6.69e-08!13;UBERON:0000483!3.69e-07!306;UBERON:0000119!3.93e-07!309;UBERON:0000349!6.76e-07!5
|ontology_enrichment_uberon=UBERON:0001049!3.33e-38!56;UBERON:0005068!3.33e-38!56;UBERON:0006241!3.33e-38!56;UBERON:0007135!3.33e-38!56;UBERON:0000073!7.70e-38!53;UBERON:0002616!7.70e-38!53;UBERON:0000955!1.01e-30!68;UBERON:0006238!1.01e-30!68;UBERON:0002780!4.08e-30!41;UBERON:0001890!4.08e-30!41;UBERON:0003080!4.08e-30!41;UBERON:0006240!4.08e-30!41;UBERON:0002346!4.21e-30!86;UBERON:0001017!4.43e-30!81;UBERON:0003075!5.42e-30!82;UBERON:0007284!5.42e-30!82;UBERON:0001016!1.74e-29!89;UBERON:0003528!1.48e-28!34;UBERON:0002020!1.48e-28!34;UBERON:0001893!1.67e-28!34;UBERON:0001869!1.32e-27!32;UBERON:0002791!6.44e-27!32;UBERON:0003056!7.45e-26!61;UBERON:0007023!3.82e-25!114;UBERON:0010371!5.39e-23!104;UBERON:0000956!1.85e-20!25;UBERON:0000203!1.85e-20!25;UBERON:0004121!3.13e-20!171;UBERON:0000924!3.13e-20!171;UBERON:0006601!3.13e-20!171;UBERON:0010314!8.32e-19!132;UBERON:0002619!2.00e-18!22;UBERON:0001950!2.46e-16!20;UBERON:0011216!9.02e-16!223;UBERON:0000064!5.44e-15!218;UBERON:0002420!4.79e-10!9;UBERON:0007245!4.79e-10!9;UBERON:0010009!4.79e-10!9;UBERON:0010011!4.79e-10!9;UBERON:0000454!4.79e-10!9;UBERON:0000125!1.48e-09!9;UBERON:0002308!1.48e-09!9;UBERON:0000477!1.59e-09!373;UBERON:0000025!2.83e-09!192;UBERON:0003076!3.44e-09!15;UBERON:0003057!3.44e-09!15;UBERON:0004733!7.93e-09!12;UBERON:0002028!7.93e-09!12;UBERON:0007277!7.93e-09!12;UBERON:0004111!1.07e-08!240;UBERON:0000200!4.23e-08!6;UBERON:0000481!4.88e-08!342;UBERON:0009663!5.56e-08!7;UBERON:0004732!6.69e-08!13;UBERON:0000483!3.69e-07!306;UBERON:0000119!3.93e-07!309;UBERON:0000349!6.76e-07!5
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}}
}}

Revision as of 16:27, 26 November 2012


Full id: C3947_cerebellum_amygdala_parietal_middle_caudate_occipital_olfactory



Phase1 CAGE Peaks

Hg19::chr1:228604454..228604504,-p3@TRIM17
Hg19::chr1:228604544..228604568,-p1@TRIM17
Hg19::chr1:228604572..228604589,-p4@TRIM17


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 tube3.33e-3856
neural rod3.33e-3856
future spinal cord3.33e-3856
neural keel3.33e-3856
regional part of nervous system7.70e-3853
regional part of brain7.70e-3853
brain1.01e-3068
future brain1.01e-3068
regional part of forebrain4.08e-3041
forebrain4.08e-3041
anterior neural tube4.08e-3041
future forebrain4.08e-3041
neurectoderm4.21e-3086
central nervous system4.43e-3081
neural plate5.42e-3082
presumptive neural plate5.42e-3082
nervous system1.74e-2989
brain grey matter1.48e-2834
gray matter1.48e-2834
telencephalon1.67e-2834
cerebral hemisphere1.32e-2732
regional part of telencephalon6.44e-2732
pre-chordal neural plate7.45e-2661
adult organism3.82e-25114
ecto-epithelium5.39e-23104
cerebral cortex1.85e-2025
pallium1.85e-2025
ectoderm-derived structure3.13e-20171
ectoderm3.13e-20171
presumptive ectoderm3.13e-20171
structure with developmental contribution from neural crest8.32e-19132
regional part of cerebral cortex2.00e-1822
neocortex2.46e-1620
organ system subdivision9.02e-16223
organ part5.44e-15218
basal ganglion4.79e-109
nuclear complex of neuraxis4.79e-109
aggregate regional part of brain4.79e-109
collection of basal ganglia4.79e-109
cerebral subcortex4.79e-109
neural nucleus1.48e-099
nucleus of brain1.48e-099
anatomical cluster1.59e-09373
tube2.83e-09192
posterior neural tube3.44e-0915
chordal neural plate3.44e-0915
segmental subdivision of hindbrain7.93e-0912
hindbrain7.93e-0912
presumptive hindbrain7.93e-0912
anatomical conduit1.07e-08240
gyrus4.23e-086
multi-tissue structure4.88e-08342
telencephalic nucleus5.56e-087
segmental subdivision of nervous system6.69e-0813
epithelium3.69e-07306
cell layer3.93e-07309
limbic system6.76e-075


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)

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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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