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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 19:36, 8 August 2012


Full id: C3989_pineal_pituitary_optic_spinal_corpus_substantia_thalamus



Phase1 CAGE Peaks

Hg19::chr1:61542891..61542920,+p12@NFIA
Hg19::chr3:101405675..101405733,+p@chr3:101405675..101405733
+
Hg19::chr7:7606626..7606650,-p@chr7:7606626..7606650
-


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>


Uber Anatomy
Ontology termp-valuen
adult organism3.53e-43115
regional part of nervous system9.09e-2994
nervous system9.09e-2994
central nervous system2.05e-2882
neural tube6.51e-2857
neural rod6.51e-2857
future spinal cord6.51e-2857
neural keel6.51e-2857
brain7.19e-2569
future brain7.19e-2569
regional part of forebrain2.78e-2341
forebrain2.78e-2341
future forebrain2.78e-2341
anterior neural tube3.48e-2342
regional part of brain4.51e-2359
telencephalon8.22e-1934
gray matter8.63e-1934
brain grey matter8.63e-1934
regional part of telencephalon3.37e-1833
cerebral hemisphere1.81e-1732
neural plate3.07e-1786
presumptive neural plate3.07e-1786
neurectoderm3.82e-1790
regional part of cerebral cortex9.49e-1422
pre-chordal neural plate3.19e-1361
cerebral cortex3.54e-1325
pallium3.54e-1325
neocortex1.27e-1220
anterior region of body2.47e-10129
craniocervical region2.47e-10129
ectoderm7.33e-10173
presumptive ectoderm7.33e-10173
ectoderm-derived structure1.03e-09169
head6.70e-09123
nucleus of brain3.48e-079
neural nucleus3.48e-079
basal ganglion3.65e-079
nuclear complex of neuraxis3.65e-079
aggregate regional part of brain3.65e-079
collection of basal ganglia3.65e-079
cerebral subcortex3.65e-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)

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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.