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Coexpression cluster:C3352: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!3.54e-49!81;UBERON:0007023!5.96e-49!114;UBERON:0001016!4.49e-48!89;UBERON:0001049!1.84e-43!56;UBERON:0005068!1.84e-43!56;UBERON:0006241!1.84e-43!56;UBERON:0007135!1.84e-43!56;UBERON:0000073!4.92e-41!53;UBERON:0002616!4.92e-41!53;UBERON:0000955!1.47e-38!68;UBERON:0006238!1.47e-38!68;UBERON:0003075!1.39e-37!82;UBERON:0007284!1.39e-37!82;UBERON:0002780!4.01e-35!41;UBERON:0001890!4.01e-35!41;UBERON:0003080!4.01e-35!41;UBERON:0006240!4.01e-35!41;UBERON:0002346!1.16e-34!86;UBERON:0001869!4.62e-30!32;UBERON:0003528!2.13e-29!34;UBERON:0002020!2.13e-29!34;UBERON:0003056!3.00e-29!61;UBERON:0001893!3.26e-29!34;UBERON:0010371!2.12e-28!104;UBERON:0004121!2.31e-28!171;UBERON:0000924!2.31e-28!171;UBERON:0006601!2.31e-28!171;UBERON:0002791!8.92e-28!32;UBERON:0010314!3.53e-25!132;UBERON:0011216!5.18e-25!223;UBERON:0002619!6.39e-24!22;UBERON:0000956!3.14e-23!25;UBERON:0000203!3.14e-23!25;UBERON:0001950!4.80e-22!20;UBERON:0000477!2.56e-14!373;UBERON:0000481!6.21e-12!342;UBERON:0003076!1.63e-09!15;UBERON:0003057!1.63e-09!15;UBERON:0000025!1.69e-09!192;UBERON:0004111!5.33e-09!240;UBERON:0000468!1.02e-08!656;UBERON:0000064!1.46e-08!218;UBERON:0001871!2.24e-08!6;UBERON:0004732!3.33e-08!13;UBERON:0002420!4.61e-08!9;UBERON:0007245!4.61e-08!9;UBERON:0010009!4.61e-08!9;UBERON:0010011!4.61e-08!9;UBERON:0000454!4.61e-08!9;UBERON:0000119!4.87e-08!309;UBERON:0000483!5.10e-08!306;UBERON:0000125!1.26e-07!9;UBERON:0002308!1.26e-07!9;UBERON:0004733!2.47e-07!12;UBERON:0002028!2.47e-07!12;UBERON:0007277!2.47e-07!12;UBERON:0001894!2.93e-07!7;UBERON:0006222!2.93e-07!7;UBERON:0000062!3.21e-07!503;UBERON:0000200!6.00e-07!6;UBERON:0000922!9.02e-07!592;UBERON:0002021!9.96e-07!5
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}}
}}

Revision as of 16:05, 26 November 2012


Full id: C3352_merkel_parietal_occipital_temporal_duodenum_mature_cerebellum



Phase1 CAGE Peaks

Hg19::chr13:111767485..111767533,+p8@ARHGEF7
Hg19::chr13:111767582..111767618,+p10@ARHGEF7
Hg19::chr13:111767650..111767695,+p5@ARHGEF7


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><br>

Cell Type
Ontology termp-valuen
neuronal stem cell1.72e-078
Uber Anatomy
Ontology termp-valuen
central nervous system3.54e-4981
adult organism5.96e-49114
nervous system4.49e-4889
neural tube1.84e-4356
neural rod1.84e-4356
future spinal cord1.84e-4356
neural keel1.84e-4356
regional part of nervous system4.92e-4153
regional part of brain4.92e-4153
brain1.47e-3868
future brain1.47e-3868
neural plate1.39e-3782
presumptive neural plate1.39e-3782
regional part of forebrain4.01e-3541
forebrain4.01e-3541
anterior neural tube4.01e-3541
future forebrain4.01e-3541
neurectoderm1.16e-3486
cerebral hemisphere4.62e-3032
brain grey matter2.13e-2934
gray matter2.13e-2934
pre-chordal neural plate3.00e-2961
telencephalon3.26e-2934
ecto-epithelium2.12e-28104
ectoderm-derived structure2.31e-28171
ectoderm2.31e-28171
presumptive ectoderm2.31e-28171
regional part of telencephalon8.92e-2832
structure with developmental contribution from neural crest3.53e-25132
organ system subdivision5.18e-25223
regional part of cerebral cortex6.39e-2422
cerebral cortex3.14e-2325
pallium3.14e-2325
neocortex4.80e-2220
anatomical cluster2.56e-14373
multi-tissue structure6.21e-12342
posterior neural tube1.63e-0915
chordal neural plate1.63e-0915
tube1.69e-09192
anatomical conduit5.33e-09240
multi-cellular organism1.02e-08656
organ part1.46e-08218
temporal lobe2.24e-086
segmental subdivision of nervous system3.33e-0813
basal ganglion4.61e-089
nuclear complex of neuraxis4.61e-089
aggregate regional part of brain4.61e-089
collection of basal ganglia4.61e-089
cerebral subcortex4.61e-089
cell layer4.87e-08309
epithelium5.10e-08306
neural nucleus1.26e-079
nucleus of brain1.26e-079
segmental subdivision of hindbrain2.47e-0712
hindbrain2.47e-0712
presumptive hindbrain2.47e-0712
diencephalon2.93e-077
future diencephalon2.93e-077
organ3.21e-07503
gyrus6.00e-076
embryo9.02e-07592
occipital lobe9.96e-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)

{{{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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