Personal tools

Coexpression cluster:C4367

From FANTOM5_SSTAR

Revision as of 17:26, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4367_rectum_neuroectodermal_skeletal_neuroepithelioma_diaphragm_skin_throat



Phase1 CAGE Peaks

Hg19::chr4:126236103..126236150,+p@chr4:126236103..126236150
+
Hg19::chr4:126236297..126236308,+p@chr4:126236297..126236308
+
Hg19::chr4:126236326..126236346,+p@chr4:126236326..126236346
+


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
fibroblast2.21e-1175
non-terminally differentiated cell7.92e-10180
endothelial cell of vascular tree3.32e-0924
endothelial cell6.81e-0835
meso-epithelial cell2.56e-0744
mesodermal cell4.03e-07119
Uber Anatomy
Ontology termp-valuen
anatomical cluster9.27e-21286
multi-cellular organism1.34e-19659
organism subdivision1.24e-18365
multi-tissue structure5.58e-16347
anatomical conduit3.62e-15241
cell layer1.36e-14312
epithelium4.76e-14309
anatomical system1.21e-12625
anatomical group2.29e-12626
ectoderm1.59e-11173
presumptive ectoderm1.59e-11173
tube2.46e-11194
adult organism1.20e-10115
ectoderm-derived structure2.33e-10169
vasculature9.42e-1079
vascular system9.42e-1079
embryo9.60e-10612
head3.76e-09123
neurectoderm4.81e-0990
embryonic structure6.02e-09605
developing anatomical structure6.02e-09605
anterior region of body7.12e-09129
craniocervical region7.12e-09129
germ layer1.25e-08604
embryonic tissue1.25e-08604
presumptive structure1.25e-08604
epiblast (generic)1.25e-08604
organ part2.11e-08219
circulatory system7.51e-08113
neural plate8.30e-0886
presumptive neural plate8.30e-0886
central nervous system8.80e-0882
trunk1.19e-07216
regional part of nervous system1.58e-0794
nervous system1.58e-0794
regional part of brain1.97e-0759
cardiovascular system2.71e-07110
brain5.46e-0769
future brain5.46e-0769
vessel9.87e-0769


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066435.360256373075030.0064925092527670.0280646982264697
EP300#203336.77394172622320.003216880500103790.0168025897749607
FOXA1#3169311.08141974938550.000734755275698670.00583064404214675
FOXA2#3170324.63046375266526.68983856509345e-050.00107538871771555
HNF4A#3172323.13229036295378.07584663437677e-050.00123236900445306
MYC#460935.22228187160940.007020843755740150.0295534198946333
NFYB#4801316.75979325353650.0002123649923296180.00246435415932367
RFX5#5993312.04791082719510.0005717246050312580.00485884498534133
SP1#666735.69838137814090.005403962701712170.0247439370688815
ZNF263#1012738.221841637010680.001799043925565870.0109774683653993



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.