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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!4.46e-39!115;UBERON:0001049!1.97e-26!57;UBERON:0005068!1.97e-26!57;UBERON:0006241!1.97e-26!57;UBERON:0007135!1.97e-26!57;UBERON:0002616!1.41e-23!59;UBERON:0003080!7.21e-22!42;UBERON:0002780!9.81e-22!41;UBERON:0001890!9.81e-22!41;UBERON:0006240!9.81e-22!41;UBERON:0001017!4.95e-20!82;UBERON:0000955!1.31e-19!69;UBERON:0006238!1.31e-19!69;UBERON:0005743!5.07e-19!86;UBERON:0001893!2.88e-18!34;UBERON:0002020!3.31e-18!34;UBERON:0003528!3.31e-18!34;UBERON:0002791!1.18e-17!33;UBERON:0003075!3.24e-17!86;UBERON:0007284!3.24e-17!86;UBERON:0001869!5.25e-17!32;UBERON:0000073!1.87e-16!94;UBERON:0001016!1.87e-16!94;UBERON:0002346!5.23e-15!90;UBERON:0002619!4.99e-14!22;UBERON:0000153!9.63e-14!129;UBERON:0007811!9.63e-14!129;UBERON:0000956!3.03e-13!25;UBERON:0000203!3.03e-13!25;UBERON:0001950!5.98e-13!20;UBERON:0000033!1.22e-12!123;UBERON:0003056!1.37e-11!61;UBERON:0004121!1.66e-11!169;UBERON:0000924!2.39e-10!173;UBERON:0006601!2.39e-10!173
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}}
}}

Revision as of 20:01, 8 August 2012


Full id: C4440_left_heart_medial_middle_parietal_hippocampus_occipital



Phase1 CAGE Peaks

Hg19::chr4:89205685..89205696,-p5@PPM1K
Hg19::chr4:89205705..89205720,-p1@PPM1K
Hg19::chr8:22861538..22861557,+p14@RHOBTB2


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 lineage1.53e-1024
pro-B cell1.53e-1024
lymphocyte4.53e-0853
common lymphoid progenitor4.53e-0853
lymphoid lineage restricted progenitor cell9.67e-0852
Uber Anatomy
Ontology termp-valuen
adult organism4.46e-39115
neural tube1.97e-2657
neural rod1.97e-2657
future spinal cord1.97e-2657
neural keel1.97e-2657
regional part of brain1.41e-2359
anterior neural tube7.21e-2242
regional part of forebrain9.81e-2241
forebrain9.81e-2241
future forebrain9.81e-2241
central nervous system4.95e-2082
brain1.31e-1969
future brain1.31e-1969
telencephalon2.88e-1834
gray matter3.31e-1834
brain grey matter3.31e-1834
regional part of telencephalon1.18e-1733
neural plate3.24e-1786
presumptive neural plate3.24e-1786
cerebral hemisphere5.25e-1732
regional part of nervous system1.87e-1694
nervous system1.87e-1694
neurectoderm5.23e-1590
regional part of cerebral cortex4.99e-1422
anterior region of body9.63e-14129
craniocervical region9.63e-14129
cerebral cortex3.03e-1325
pallium3.03e-1325
neocortex5.98e-1320
head1.22e-12123
pre-chordal neural plate1.37e-1161
ectoderm-derived structure1.66e-11169
ectoderm2.39e-10173
presumptive ectoderm2.39e-10173


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.