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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 20:22, 8 August 2012


Full id: C4850_H9_HES3GFP_teratocarcinoma_testicular_Preadipocyte_anaplastic_iPS



Phase1 CAGE Peaks

Hg19::chrX:132549456..132549473,-p2@GPC4
Hg19::chrX:132549482..132549493,-p4@GPC4
Hg19::chrX:132549506..132549526,-p1@GPC4


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 organism2.96e-18115
multi-cellular organism4.70e-18659
organ1.38e-14511
central nervous system1.58e-1482
ectoderm-derived structure1.08e-13169
head1.58e-13123
anterior region of body1.77e-13129
craniocervical region1.77e-13129
organism subdivision4.90e-13365
ectoderm7.55e-13173
presumptive ectoderm7.55e-13173
anatomical system1.24e-12625
neural tube2.01e-1257
neural rod2.01e-1257
future spinal cord2.01e-1257
neural keel2.01e-1257
anatomical group2.37e-12626
embryo2.48e-12612
regional part of nervous system6.02e-1294
nervous system6.02e-1294
neural plate6.67e-1286
presumptive neural plate6.67e-1286
regional part of brain3.74e-1159
neurectoderm9.63e-1190
brain9.99e-1169
future brain9.99e-1169
embryonic structure7.36e-10605
developing anatomical structure7.36e-10605
germ layer9.40e-10604
embryonic tissue9.40e-10604
presumptive structure9.40e-10604
epiblast (generic)9.40e-10604
organ part1.86e-09219
anterior neural tube1.24e-0842
pre-chordal neural plate1.50e-0861
regional part of forebrain1.91e-0841
forebrain1.91e-0841
future forebrain1.91e-0841
gray matter2.49e-0734
brain grey matter2.49e-0734
anatomical cavity3.93e-0770
telencephalon4.81e-0734
regional part of telencephalon5.08e-0733
multi-tissue structure6.27e-07347


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.