Personal tools

Coexpression cluster:C2106

From FANTOM5_SSTAR

Revision as of 18:00, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2106_pineal_locus_hippocampus_occipital_colon_middle_parietal



Phase1 CAGE Peaks

Hg19::chr11:121501269..121501285,+p16@SORL1
Hg19::chr11:121501288..121501326,+p11@SORL1
Hg19::chr11:121502000..121502045,+p14@SORL1
Hg19::chr1:26093561..26093572,+p@chr1:26093561..26093572
+


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 organism2.92e-42115
neural tube1.09e-2857
neural rod1.09e-2857
future spinal cord1.09e-2857
neural keel1.09e-2857
regional part of forebrain3.70e-2441
forebrain3.70e-2441
future forebrain3.70e-2441
regional part of brain2.28e-2359
anterior neural tube4.19e-2342
central nervous system2.30e-2282
brain4.20e-2169
future brain4.20e-2169
gray matter8.99e-2034
brain grey matter8.99e-2034
telencephalon3.45e-1934
regional part of telencephalon9.59e-1933
cerebral hemisphere5.32e-1832
regional part of nervous system9.67e-1894
nervous system9.67e-1894
neural plate8.63e-1786
presumptive neural plate8.63e-1786
regional part of cerebral cortex3.13e-1622
neurectoderm5.76e-1690
neocortex1.18e-1420
cerebral cortex9.35e-1425
pallium9.35e-1425
pre-chordal neural plate6.33e-1261
anterior region of body2.14e-11129
craniocervical region2.14e-11129
head9.97e-11123
ectoderm-derived structure1.11e-07169
nucleus of brain1.32e-079
neural nucleus1.32e-079
basal ganglion1.64e-079
nuclear complex of neuraxis1.64e-079
aggregate regional part of brain1.64e-079
collection of basal ganglia1.64e-079
cerebral subcortex1.64e-079
ectoderm1.84e-07173
presumptive ectoderm1.84e-07173
posterior neural tube7.43e-0715
chordal neural plate7.43e-0715


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.