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Coexpression cluster:C3196: Difference between revisions

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|full_id=C3196_small_corpus_diencephalon_brain_chronic_CD133_CD34
|full_id=C3196_small_corpus_diencephalon_brain_chronic_CD133_CD34
|id=C3196
|id=C3196
|ontology_enrichment_celltype=CL:0000945!1.82e-07!24;CL:0000826!1.82e-07!24
|ontology_enrichment_celltype=CL:0000945!5.35e-08!24;CL:0000826!5.35e-08!24;CL:0000784!8.15e-08!3;CL:0000817!8.26e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!7.70e-48!57;UBERON:0005068!7.70e-48!57;UBERON:0006241!7.70e-48!57;UBERON:0007135!7.70e-48!57;UBERON:0007023!1.35e-42!115;UBERON:0002616!7.02e-39!59;UBERON:0002780!7.37e-37!41;UBERON:0001890!7.37e-37!41;UBERON:0006240!7.37e-37!41;UBERON:0001017!2.52e-36!82;UBERON:0000955!2.65e-36!69;UBERON:0006238!2.65e-36!69;UBERON:0003080!1.02e-35!42;UBERON:0001893!1.52e-35!34;UBERON:0005743!2.59e-35!86;UBERON:0002020!4.53e-35!34;UBERON:0003528!4.53e-35!34;UBERON:0002791!4.73e-34!33;UBERON:0001869!1.31e-32!32;UBERON:0003075!1.11e-30!86;UBERON:0007284!1.11e-30!86;UBERON:0000073!2.01e-30!94;UBERON:0001016!2.01e-30!94;UBERON:0002346!1.29e-28!90;UBERON:0002619!8.88e-28!22;UBERON:0001950!4.79e-25!20;UBERON:0000956!1.00e-23!25;UBERON:0000203!1.00e-23!25;UBERON:0003056!1.74e-22!61;UBERON:0000153!5.92e-20!129;UBERON:0007811!5.92e-20!129;UBERON:0000033!1.08e-18!123;UBERON:0002308!5.88e-13!9;UBERON:0000125!5.88e-13!9;UBERON:0003076!7.15e-13!15;UBERON:0003057!7.15e-13!15;UBERON:0002420!8.62e-13!9;UBERON:0007245!8.62e-13!9;UBERON:0010009!8.62e-13!9;UBERON:0010011!8.62e-13!9;UBERON:0000454!8.62e-13!9;UBERON:0004121!3.03e-12!169;UBERON:0000924!1.26e-11!173;UBERON:0006601!1.26e-11!173;UBERON:0001871!2.36e-11!7;UBERON:0009663!2.16e-10!7;UBERON:0002298!2.34e-09!8;UBERON:0004733!3.74e-09!12;UBERON:0002028!3.74e-09!12;UBERON:0007277!3.74e-09!12;UBERON:0004732!2.75e-08!13;UBERON:0000349!2.78e-08!5;UBERON:0001872!5.66e-08!5;UBERON:0000025!1.00e-07!194;UBERON:0002021!1.80e-07!5
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}}
}}

Revision as of 14:53, 19 October 2012


Full id: C3196_small_corpus_diencephalon_brain_chronic_CD133_CD34



Phase1 CAGE Peaks

Hg19::chr11:67415020..67415032,-p2@ACY3
Hg19::chr11:67415048..67415063,-p3@ACY3
Hg19::chr11:67415073..67415078,-p6@ACY3


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
lymphocyte of B lineage5.35e-0824
pro-B cell5.35e-0824
plasmacytoid dendritic cell8.15e-083
precursor B cell8.26e-073
Uber Anatomy
Ontology termp-valuen
neural tube1.20e-4056
neural rod1.20e-4056
future spinal cord1.20e-4056
neural keel1.20e-4056
regional part of nervous system5.87e-3653
regional part of brain5.87e-3653
telencephalon1.28e-3234
brain grey matter3.38e-3234
gray matter3.38e-3234
central nervous system8.29e-3281
brain1.88e-3168
future brain1.88e-3168
regional part of forebrain3.63e-3141
forebrain3.63e-3141
anterior neural tube3.63e-3141
future forebrain3.63e-3141
adult organism1.52e-29114
cerebral hemisphere5.67e-2932
regional part of telencephalon8.58e-2932
nervous system1.57e-2789
neural plate5.41e-2682
presumptive neural plate5.41e-2682
neurectoderm2.68e-2486
regional part of cerebral cortex1.55e-2322
cerebral cortex2.94e-2025
pallium2.94e-2025
neocortex5.30e-2020
pre-chordal neural plate5.51e-2061
ecto-epithelium2.61e-18104
neural nucleus5.14e-149
nucleus of brain5.14e-149
structure with developmental contribution from neural crest2.46e-13132
organ system subdivision8.22e-13223
ectoderm-derived structure8.66e-11171
ectoderm8.66e-11171
presumptive ectoderm8.66e-11171
basal ganglion8.84e-119
nuclear complex of neuraxis8.84e-119
aggregate regional part of brain8.84e-119
collection of basal ganglia8.84e-119
cerebral subcortex8.84e-119
temporal lobe1.21e-106
posterior neural tube1.91e-1015
chordal neural plate1.91e-1015
telencephalic nucleus2.12e-107
brainstem1.46e-096
gyrus7.73e-096
corpus striatum8.43e-094
striatum8.43e-094
ventral part of telencephalon8.43e-094
future corpus striatum8.43e-094
limbic system1.17e-075
pons1.63e-073
small intestine2.03e-074
spinal cord6.85e-073
dorsal region element6.85e-073
dorsum6.85e-073


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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