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Coexpression cluster:C1955

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Full id: C1955_Fibroblast_osteoclastoma_Mallassezderived_mesothelioma_pagetoid_mesenchymal_Mesothelial



Phase1 CAGE Peaks

Hg19::chr5:167181769..167181798,+p17@ODZ2
Hg19::chr5:167181849..167181893,+p3@ODZ2
Hg19::chr5:167181899..167181909,+p14@ODZ2
Hg19::chr5:167181917..167181979,+p1@ODZ2
Hg19::chr5:167181984..167182000,+p9@ODZ2


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
non-terminally differentiated cell1.68e-14180
fibroblast1.04e-1375
skin fibroblast2.59e-1123
embryonic cell1.86e-07248
ectodermal cell3.62e-0771
mesothelial cell4.85e-0719
endo-epithelial cell9.45e-0743
Uber Anatomy
Ontology termp-valuen
head2.88e-18123
organism subdivision7.61e-17365
anterior region of body3.69e-16129
craniocervical region3.69e-16129
ectoderm2.70e-15173
presumptive ectoderm2.70e-15173
ectoderm-derived structure5.16e-14169
skin of body2.58e-1340
surface structure2.17e-1195
neurectoderm2.68e-1190
brain1.34e-1069
future brain1.34e-1069
integument1.69e-1045
integumental system1.69e-1045
neural plate5.44e-1086
presumptive neural plate5.44e-1086
regional part of brain2.26e-0959
central nervous system5.39e-0982
cerebral hemisphere1.51e-0832
pre-chordal neural plate1.51e-0861
gray matter3.96e-0834
brain grey matter3.96e-0834
regional part of nervous system6.72e-0894
nervous system6.72e-0894
neural tube6.74e-0857
neural rod6.74e-0857
future spinal cord6.74e-0857
neural keel6.74e-0857
telencephalon1.38e-0734
cerebral cortex1.86e-0725
pallium1.86e-0725
subdivision of head2.66e-0748
organ part2.97e-07219
regional part of telencephalon3.12e-0733


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
ZNF263#1012758.221841637010682.6606316672286e-050.00057258131195897



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.