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Coexpression cluster:C4475: Difference between revisions

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|full_id=C4475_duodenum_parietal_H9_frontal_insula_immature_pons
|full_id=C4475_duodenum_parietal_H9_frontal_insula_immature_pons
|id=C4475
|id=C4475
|ontology_enrichment_celltype=CL:0000791!5.02e-08!18;CL:0000789!5.02e-08!18;CL:0002420!5.02e-08!18;CL:0002419!5.02e-08!18;CL:0000790!5.02e-08!18
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.30e-40!86;UBERON:0001017!1.90e-38!82;UBERON:0000073!5.99e-37!94;UBERON:0001016!5.99e-37!94;UBERON:0007023!1.79e-32!115;UBERON:0001049!4.88e-32!57;UBERON:0005068!4.88e-32!57;UBERON:0006241!4.88e-32!57;UBERON:0007135!4.88e-32!57;UBERON:0000955!6.23e-31!69;UBERON:0006238!6.23e-31!69;UBERON:0003075!1.02e-30!86;UBERON:0007284!1.02e-30!86;UBERON:0002346!3.88e-29!90;UBERON:0002616!4.60e-27!59;UBERON:0003056!1.73e-26!61;UBERON:0002780!2.61e-26!41;UBERON:0001890!2.61e-26!41;UBERON:0006240!2.61e-26!41;UBERON:0003080!4.74e-26!42;UBERON:0001893!3.73e-22!34;UBERON:0002020!4.33e-22!34;UBERON:0003528!4.33e-22!34;UBERON:0001869!1.27e-21!32;UBERON:0002791!2.07e-21!33;UBERON:0000153!1.01e-19!129;UBERON:0007811!1.01e-19!129;UBERON:0004121!2.69e-19!169;UBERON:0000924!1.01e-18!173;UBERON:0006601!1.01e-18!173;UBERON:0000033!1.28e-18!123;UBERON:0000956!3.78e-17!25;UBERON:0000203!3.78e-17!25;UBERON:0002619!2.30e-16!22;UBERON:0001950!2.26e-15!20;UBERON:0000064!2.97e-10!219;UBERON:0003076!2.86e-07!15;UBERON:0003057!2.86e-07!15
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Revision as of 14:49, 21 May 2012


Full id: C4475_duodenum_parietal_H9_frontal_insula_immature_pons



Phase1 CAGE Peaks

Hg19::chr5:146258140..146258149,-p16@PPP2R2B
Hg19::chr5:146258158..146258169,-p11@PPP2R2B
Hg19::chr5:146258291..146258364,-p1@PPP2R2B


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
mature alpha-beta T cell5.02e-0818
alpha-beta T cell5.02e-0818
immature T cell5.02e-0818
mature T cell5.02e-0818
immature alpha-beta T cell5.02e-0818
Uber Anatomy
Ontology termp-valuen
central nervous system1.90e-3882
regional part of nervous system5.99e-3794
nervous system5.99e-3794
adult organism1.79e-32115
neural tube4.88e-3257
neural rod4.88e-3257
future spinal cord4.88e-3257
neural keel4.88e-3257
brain6.23e-3169
future brain6.23e-3169
neural plate1.02e-3086
presumptive neural plate1.02e-3086
neurectoderm3.88e-2990
regional part of brain4.60e-2759
pre-chordal neural plate1.73e-2661
regional part of forebrain2.61e-2641
forebrain2.61e-2641
future forebrain2.61e-2641
anterior neural tube4.74e-2642
telencephalon3.73e-2234
gray matter4.33e-2234
brain grey matter4.33e-2234
cerebral hemisphere1.27e-2132
regional part of telencephalon2.07e-2133
anterior region of body1.01e-19129
craniocervical region1.01e-19129
ectoderm-derived structure2.69e-19169
ectoderm1.01e-18173
presumptive ectoderm1.01e-18173
head1.28e-18123
cerebral cortex3.78e-1725
pallium3.78e-1725
regional part of cerebral cortex2.30e-1622
neocortex2.26e-1520
organ part2.97e-10219
posterior neural tube2.86e-0715
chordal neural plate2.86e-0715


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.