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Coexpression cluster:C4069

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Full id: C4069_medulloblastoma_uterus_cervix_ovary_trachea_heart_throat



Phase1 CAGE Peaks

Hg19::chr21:17791855..17791869,+p14@LINC00478
Hg19::chr21:17791874..17791892,+p6@LINC00478
Hg19::chr21:17791908..17791940,+p3@LINC00478


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism4.43e-21114
anatomical cluster1.98e-17373
organ system subdivision5.51e-16223
central nervous system2.06e-1581
nervous system6.96e-1489
neural tube1.03e-1256
neural rod1.03e-1256
future spinal cord1.03e-1256
neural keel1.03e-1256
brain3.61e-1268
future brain3.61e-1268
regional part of nervous system1.77e-1153
regional part of brain1.77e-1153
neurectoderm4.85e-1186
multi-cellular organism6.83e-11656
neural plate1.51e-1082
presumptive neural plate1.51e-1082
structure with developmental contribution from neural crest3.25e-10132
ectoderm-derived structure1.57e-09171
ectoderm1.57e-09171
presumptive ectoderm1.57e-09171
regional part of forebrain1.63e-0941
forebrain1.63e-0941
anterior neural tube1.63e-0941
future forebrain1.63e-0941
germ layer3.41e-09560
germ layer / neural crest3.41e-09560
embryonic tissue3.41e-09560
presumptive structure3.41e-09560
germ layer / neural crest derived structure3.41e-09560
epiblast (generic)3.41e-09560
embryonic structure3.68e-09564
developing anatomical structure6.34e-09581
anatomical conduit1.33e-08240
multi-tissue structure1.33e-08342
embryo1.93e-08592
anatomical system6.39e-08624
anatomical group8.46e-08625
tissue1.10e-07773
brain grey matter3.21e-0734
gray matter3.21e-0734
telencephalon5.04e-0734
cerebral hemisphere9.27e-0732
regional part of telencephalon9.79e-0732


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
EP300#203336.77394172622320.003216880500103790.0167707174437348
ESR1#2099330.76860329615453.43136389821584e-050.000677572724836007
GATA2#2624312.7449317335540.0004829527704283790.00437345915119826
RAD21#5885310.35503389545630.0009004912073565420.00665203007533667
TRIM28#10155318.59052504526250.0001555969297255280.00197333184500357



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.