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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:15, 8 August 2012


Full id: C2384_mesothelioma_Monocytederived_Renal_Neutrophils_CD14_Mesenchymal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr16:67576106..67576125,+p@chr16:67576106..67576125
+
Hg19::chr16:67576295..67576332,+p@chr16:67576295..67576332
+
Hg19::chr16:67576333..67576396,+p@chr16:67576333..67576396
+
Hg19::chr16:67576398..67576436,+p@chr16:67576398..67576436
+


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
lining cell2.49e-0857
barrier cell2.49e-0857
Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.69e-13659
anatomical system1.27e-11625
anatomical group2.53e-11626
neural tube1.58e-1057
neural rod1.58e-1057
future spinal cord1.58e-1057
neural keel1.58e-1057
regional part of forebrain1.42e-0941
forebrain1.42e-0941
future forebrain1.42e-0941
gray matter1.86e-0934
brain grey matter1.86e-0934
regional part of cerebral cortex2.67e-0922
cerebral hemisphere3.11e-0932
anterior neural tube3.48e-0942
telencephalon8.80e-0934
organ9.59e-09511
regional part of telencephalon1.39e-0833
neocortex2.61e-0820
neural plate2.68e-0886
presumptive neural plate2.68e-0886
regional part of brain5.08e-0859
embryo6.52e-08612
embryonic structure7.62e-08605
developing anatomical structure7.62e-08605
germ layer8.13e-08604
embryonic tissue8.13e-08604
presumptive structure8.13e-08604
epiblast (generic)8.13e-08604
neurectoderm8.79e-0890
tube1.08e-07194
cerebral cortex1.31e-0725
pallium1.31e-0725
brain1.64e-0769
future brain1.64e-0769
central nervous system2.18e-0782
anatomical cluster3.68e-07286
anatomical conduit6.01e-07241
pre-chordal neural plate7.48e-0761
cell layer9.55e-07312


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.

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