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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!1.27e-45!115;UBERON:0001049!1.70e-26!57;UBERON:0005068!1.70e-26!57;UBERON:0006241!1.70e-26!57;UBERON:0007135!1.70e-26!57;UBERON:0002616!4.75e-23!59;UBERON:0003080!2.26e-21!42;UBERON:0002780!6.57e-21!41;UBERON:0001890!6.57e-21!41;UBERON:0006240!6.57e-21!41;UBERON:0001017!2.86e-20!82;UBERON:0000955!3.57e-19!69;UBERON:0006238!3.57e-19!69;UBERON:0005743!4.87e-19!86;UBERON:0002020!9.41e-18!34;UBERON:0003528!9.41e-18!34;UBERON:0001893!1.31e-17!34;UBERON:0002791!4.54e-17!33;UBERON:0000073!7.07e-17!94;UBERON:0001016!7.07e-17!94;UBERON:0001869!2.25e-16!32;UBERON:0003075!1.63e-15!86;UBERON:0007284!1.63e-15!86;UBERON:0002619!5.48e-14!22;UBERON:0002346!1.46e-13!90;UBERON:0001950!5.57e-13!20;UBERON:0000956!1.41e-12!25;UBERON:0000203!1.41e-12!25;UBERON:0003056!8.81e-11!61;UBERON:0000025!1.50e-08!194;UBERON:0000153!5.10e-08!129;UBERON:0007811!5.10e-08!129;UBERON:0000033!5.60e-07!123;UBERON:0002308!9.97e-07!9;UBERON:0000125!9.97e-07!9
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Revision as of 19:47, 8 August 2012


Full id: C4168_optic_substantia_spinal_left_pineal_globus_thalamus



Phase1 CAGE Peaks

Hg19::chr2:198669308..198669328,+p1@PLCL1
Hg19::chr2:198669338..198669358,+p2@PLCL1
Hg19::chr2:198669365..198669376,+p3@PLCL1


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
leukocyte6.77e-08140
Uber Anatomy
Ontology termp-valuen
adult organism1.27e-45115
neural tube1.70e-2657
neural rod1.70e-2657
future spinal cord1.70e-2657
neural keel1.70e-2657
regional part of brain4.75e-2359
anterior neural tube2.26e-2142
regional part of forebrain6.57e-2141
forebrain6.57e-2141
future forebrain6.57e-2141
central nervous system2.86e-2082
brain3.57e-1969
future brain3.57e-1969
gray matter9.41e-1834
brain grey matter9.41e-1834
telencephalon1.31e-1734
regional part of telencephalon4.54e-1733
regional part of nervous system7.07e-1794
nervous system7.07e-1794
cerebral hemisphere2.25e-1632
neural plate1.63e-1586
presumptive neural plate1.63e-1586
regional part of cerebral cortex5.48e-1422
neurectoderm1.46e-1390
neocortex5.57e-1320
cerebral cortex1.41e-1225
pallium1.41e-1225
pre-chordal neural plate8.81e-1161
tube1.50e-08194
anterior region of body5.10e-08129
craniocervical region5.10e-08129
head5.60e-07123
nucleus of brain9.97e-079
neural nucleus9.97e-079


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.