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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3929_clear_Renal_acute_CD133_placenta_CD34_diaphragm
|full_id=C3929_clear_Renal_acute_CD133_placenta_CD34_diaphragm
|id=C3929
|id=C3929

Revision as of 16:56, 12 September 2012


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>

Uber Anatomy
Ontology termp-valuen
adult organism1.89e-59115
neural tube7.81e-2957
neural rod7.81e-2957
future spinal cord7.81e-2957
neural keel7.81e-2957
anterior neural tube1.59e-2342
regional part of brain2.76e-2359
regional part of forebrain8.24e-2341
forebrain8.24e-2341
future forebrain8.24e-2341
neural plate1.12e-2286
presumptive neural plate1.12e-2286
anatomical conduit1.64e-21241
tube7.84e-21194
neurectoderm9.16e-2190
brain5.02e-2069
future brain5.02e-2069
central nervous system7.98e-2082
gray matter2.29e-1934
brain grey matter2.29e-1934
telencephalon3.22e-1934
regional part of telencephalon1.12e-1833
anatomical cluster2.31e-18286
cerebral hemisphere4.85e-1832
regional part of nervous system2.17e-1694
nervous system2.17e-1694
cerebral cortex2.76e-1425
pallium2.76e-1425
pre-chordal neural plate6.13e-1461
regional part of cerebral cortex9.33e-1322
neocortex8.09e-1220
anterior region of body2.06e-11129
craniocervical region2.06e-11129
epithelium1.32e-10309
organ part1.73e-10219
cell layer3.24e-10312
head3.24e-10123
compound organ8.48e-0869
ectoderm-derived structure1.15e-07169
anatomical system4.13e-07625
ectoderm4.21e-07173
presumptive ectoderm4.21e-07173
anatomical group5.04e-07626
multi-cellular organism7.03e-07659
endothelium9.80e-0718
blood vessel endothelium9.80e-0718
cardiovascular system endothelium9.80e-0718


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.

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