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Coexpression cluster:C3929

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Full id: C3929_clear_Renal_acute_CD133_placenta_CD34_diaphragm



Phase1 CAGE Peaks

Hg19::chr1:208084668..208084701,-p2@CD34
Hg19::chr1:208084709..208084727,-p6@CD34
Hg19::chr1:208084729..208084734,-p9@CD34


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
endothelial cell2.52e-1236
endothelial cell of vascular tree5.96e-1024
meso-epithelial cell2.11e-0945
Uber Anatomy
Ontology termp-valuen
adult organism4.77e-46114
neural tube2.69e-2456
neural rod2.69e-2456
future spinal cord2.69e-2456
neural keel2.69e-2456
regional part of nervous system2.59e-2253
regional part of brain2.59e-2253
regional part of forebrain1.56e-2041
forebrain1.56e-2041
anterior neural tube1.56e-2041
future forebrain1.56e-2041
telencephalon2.03e-1834
brain grey matter2.81e-1834
gray matter2.81e-1834
regional part of telencephalon6.18e-1732
cerebral hemisphere6.50e-1732
neural plate1.16e-1682
presumptive neural plate1.16e-1682
central nervous system1.76e-1581
brain2.40e-1568
future brain2.40e-1568
neurectoderm2.81e-1586
anatomical conduit5.07e-14240
tube5.09e-14192
structure with developmental contribution from neural crest2.47e-13132
cerebral cortex4.21e-1325
pallium4.21e-1325
nervous system1.02e-1289
pre-chordal neural plate1.36e-1261
ecto-epithelium2.74e-11104
anatomical cluster2.95e-11373
regional part of cerebral cortex3.06e-1122
neocortex3.19e-1120
organ part4.47e-08218
organ system subdivision1.78e-07223
epithelium7.38e-07306


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.