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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:38, 8 August 2012


Full id: C2829_pineal_cerebellum_occipital_thalamus_medial_globus_parietal



Phase1 CAGE Peaks

Hg19::chr5:77656342..77656362,+p2@SCAMP1
Hg19::chr5:77656368..77656380,+p5@SCAMP1
Hg19::chr5:77656382..77656393,+p6@SCAMP1
Hg19::chr5:77656394..77656413,+p3@SCAMP1


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
adult organism1.27e-28115
regional part of nervous system5.30e-2894
nervous system5.30e-2894
central nervous system1.87e-2782
neural tube2.96e-2657
neural rod2.96e-2657
future spinal cord2.96e-2657
neural keel2.96e-2657
brain3.63e-2469
future brain3.63e-2469
anterior neural tube5.35e-2342
regional part of forebrain2.19e-2241
forebrain2.19e-2241
future forebrain2.19e-2241
regional part of brain3.84e-2159
head1.49e-18123
gray matter3.05e-1834
brain grey matter3.05e-1834
telencephalon5.43e-1834
anterior region of body5.91e-18129
craniocervical region5.91e-18129
neural plate2.07e-1786
presumptive neural plate2.07e-1786
regional part of telencephalon2.15e-1733
cerebral hemisphere3.27e-1732
neurectoderm2.13e-1690
ectoderm-derived structure5.88e-16169
pre-chordal neural plate1.79e-1561
ectoderm2.04e-15173
presumptive ectoderm2.04e-15173
regional part of cerebral cortex1.43e-1422
cerebral cortex1.39e-1325
pallium1.39e-1325
neocortex1.75e-1320
organ1.14e-11511
embryo4.41e-09612
multi-cellular organism3.30e-08659
embryonic structure9.32e-08605
developing anatomical structure9.32e-08605
germ layer1.72e-07604
embryonic tissue1.72e-07604
presumptive structure1.72e-07604
epiblast (generic)1.72e-07604
anatomical group3.02e-07626
anatomical system3.38e-07625


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.