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|full_id=C4831_smooth_aorta_optic_granulosa_colon_globus_substantia
|full_id=C4831_smooth_aorta_optic_granulosa_colon_globus_substantia
|id=C4831
|id=C4831
|ontology_enrichment_celltype=CL:0000055!7.67e-13!180
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.31e-35!115;UBERON:0001049!5.17e-25!57;UBERON:0005068!5.17e-25!57;UBERON:0006241!5.17e-25!57;UBERON:0007135!5.17e-25!57;UBERON:0002616!2.10e-22!59;UBERON:0001017!2.95e-22!82;UBERON:0005743!3.45e-21!86;UBERON:0003075!9.60e-21!86;UBERON:0007284!9.60e-21!86;UBERON:0000955!3.27e-20!69;UBERON:0006238!3.27e-20!69;UBERON:0000073!6.05e-20!94;UBERON:0001016!6.05e-20!94;UBERON:0003080!3.33e-19!42;UBERON:0002780!7.32e-19!41;UBERON:0001890!7.32e-19!41;UBERON:0006240!7.32e-19!41;UBERON:0002346!1.47e-18!90;UBERON:0004121!3.16e-18!169;UBERON:0000475!5.98e-17!365;UBERON:0000924!6.65e-17!173;UBERON:0006601!6.65e-17!173;UBERON:0000033!2.37e-15!123;UBERON:0002020!3.24e-15!34;UBERON:0003528!3.24e-15!34;UBERON:0001893!4.76e-15!34;UBERON:0000153!7.80e-15!129;UBERON:0007811!7.80e-15!129;UBERON:0002791!1.48e-14!33;UBERON:0003056!2.96e-14!61;UBERON:0001869!9.08e-14!32;UBERON:0000481!8.89e-11!347;UBERON:0000468!1.45e-10!659;UBERON:0000956!2.83e-10!25;UBERON:0000203!2.83e-10!25;UBERON:0002619!3.84e-10!22;UBERON:0000062!1.47e-09!511;UBERON:0001950!3.70e-09!20;UBERON:0000064!4.82e-09!219;UBERON:0000483!1.17e-08!309;UBERON:0000119!3.07e-08!312;UBERON:0000467!6.21e-08!625;UBERON:0000480!9.16e-08!626;UBERON:0000477!3.63e-07!286;UBERON:0003076!5.17e-07!15;UBERON:0003057!5.17e-07!15;UBERON:0000922!7.07e-07!612
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Revision as of 14:53, 21 May 2012


Full id: C4831_smooth_aorta_optic_granulosa_colon_globus_substantia



Phase1 CAGE Peaks

Hg19::chr9:79520989..79521001,-p3@PRUNE2
Hg19::chr9:79521006..79521040,-p1@PRUNE2
Hg19::chr9:79521045..79521056,-p4@PRUNE2


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
non-terminally differentiated cell7.67e-13180
Uber Anatomy
Ontology termp-valuen
adult organism8.31e-35115
neural tube5.17e-2557
neural rod5.17e-2557
future spinal cord5.17e-2557
neural keel5.17e-2557
regional part of brain2.10e-2259
central nervous system2.95e-2282
neural plate9.60e-2186
presumptive neural plate9.60e-2186
brain3.27e-2069
future brain3.27e-2069
regional part of nervous system6.05e-2094
nervous system6.05e-2094
anterior neural tube3.33e-1942
regional part of forebrain7.32e-1941
forebrain7.32e-1941
future forebrain7.32e-1941
neurectoderm1.47e-1890
ectoderm-derived structure3.16e-18169
organism subdivision5.98e-17365
ectoderm6.65e-17173
presumptive ectoderm6.65e-17173
head2.37e-15123
gray matter3.24e-1534
brain grey matter3.24e-1534
telencephalon4.76e-1534
anterior region of body7.80e-15129
craniocervical region7.80e-15129
regional part of telencephalon1.48e-1433
pre-chordal neural plate2.96e-1461
cerebral hemisphere9.08e-1432
multi-tissue structure8.89e-11347
multi-cellular organism1.45e-10659
cerebral cortex2.83e-1025
pallium2.83e-1025
regional part of cerebral cortex3.84e-1022
organ1.47e-09511
neocortex3.70e-0920
organ part4.82e-09219
epithelium1.17e-08309
cell layer3.07e-08312
anatomical system6.21e-08625
anatomical group9.16e-08626
anatomical cluster3.63e-07286
posterior neural tube5.17e-0715
chordal neural plate5.17e-0715
embryo7.07e-07612


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.