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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0001049!6.05e-15!57;UBERON:0005068!6.05e-15!57;UBERON:0006241!6.05e-15!57;UBERON:0007135!6.05e-15!57;UBERON:0001893!7.31e-13!34;UBERON:0002020!7.56e-13!34;UBERON:0003528!7.56e-13!34;UBERON:0002791!2.35e-12!33;UBERON:0002616!3.05e-12!59;UBERON:0000955!3.75e-12!69;UBERON:0006238!3.75e-12!69;UBERON:0001869!1.17e-11!32;UBERON:0001017!1.63e-11!82;UBERON:0003080!2.47e-11!42;UBERON:0005743!3.21e-11!86;UBERON:0002780!4.46e-11!41;UBERON:0001890!4.46e-11!41;UBERON:0006240!4.46e-11!41;UBERON:0003075!3.65e-10!86;UBERON:0007284!3.65e-10!86;UBERON:0000073!1.04e-09!94;UBERON:0001016!1.04e-09!94;UBERON:0002346!3.50e-09!90;UBERON:0002619!4.23e-09!22;UBERON:0000956!1.55e-08!25;UBERON:0000203!1.55e-08!25;UBERON:0004111!1.61e-08!241;UBERON:0001950!2.87e-08!20;UBERON:0000025!3.35e-08!194;UBERON:0000033!5.57e-08!123;UBERON:0007023!5.68e-08!115;UBERON:0000153!8.43e-08!129;UBERON:0007811!8.43e-08!129;UBERON:0000477!2.22e-07!286;UBERON:0003056!2.27e-07!61;UBERON:0000119!2.42e-07!312;UBERON:0000483!3.57e-07!309
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}}
}}

Revision as of 19:57, 8 August 2012


Full id: C4351_Reticulocytes_splenic_plasma_chronic_liver_optic_b



Phase1 CAGE Peaks

Hg19::chr3:98312434..98312474,-p1@CPOX
Hg19::chr3:98312478..98312489,-p3@CPOX
Hg19::chr3:98312500..98312515,-p2@CPOX


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube6.05e-1557
neural rod6.05e-1557
future spinal cord6.05e-1557
neural keel6.05e-1557
telencephalon7.31e-1334
gray matter7.56e-1334
brain grey matter7.56e-1334
regional part of telencephalon2.35e-1233
regional part of brain3.05e-1259
brain3.75e-1269
future brain3.75e-1269
cerebral hemisphere1.17e-1132
central nervous system1.63e-1182
anterior neural tube2.47e-1142
regional part of forebrain4.46e-1141
forebrain4.46e-1141
future forebrain4.46e-1141
neural plate3.65e-1086
presumptive neural plate3.65e-1086
regional part of nervous system1.04e-0994
nervous system1.04e-0994
neurectoderm3.50e-0990
regional part of cerebral cortex4.23e-0922
cerebral cortex1.55e-0825
pallium1.55e-0825
anatomical conduit1.61e-08241
neocortex2.87e-0820
tube3.35e-08194
head5.57e-08123
adult organism5.68e-08115
anterior region of body8.43e-08129
craniocervical region8.43e-08129
anatomical cluster2.22e-07286
pre-chordal neural plate2.27e-0761
cell layer2.42e-07312
epithelium3.57e-07309


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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