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Coexpression cluster:C4447

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Full id: C4447_mesothelioma_Wilms_leiomyoblastoma_large_endometrial_serous_merkel



Phase1 CAGE Peaks

Hg19::chr5:107007726..107007737,-p@chr5:107007726..107007737
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Hg19::chr5:107007827..107007856,-p@chr5:107007827..107007856
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Hg19::chr5:107007859..107007895,-p@chr5:107007859..107007895
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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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell1.81e-13253
Uber Anatomy
Ontology termp-valuen
anatomical cluster6.33e-30373
multi-tissue structure6.93e-22342
ectoderm-derived structure4.20e-20171
ectoderm4.20e-20171
presumptive ectoderm4.20e-20171
organ system subdivision3.95e-17223
organ part6.62e-17218
neurectoderm3.44e-1486
pre-chordal neural plate1.29e-1361
multi-cellular organism2.12e-13656
neural plate3.91e-1382
presumptive neural plate3.91e-1382
embryo4.69e-13592
central nervous system1.29e-1281
nervous system2.79e-1289
cell layer3.02e-12309
epithelium4.16e-12306
brain7.89e-1268
future brain7.89e-1268
neocortex8.76e-1220
developing anatomical structure8.94e-12581
ecto-epithelium1.07e-11104
adult organism1.16e-11114
structure with developmental contribution from neural crest1.21e-11132
anatomical system3.02e-11624
anatomical group3.33e-11625
regional part of cerebral cortex9.96e-1122
cerebral hemisphere1.09e-1032
regional part of forebrain1.29e-1041
forebrain1.29e-1041
anterior neural tube1.29e-1041
future forebrain1.29e-1041
telencephalon2.81e-1034
anatomical conduit5.19e-10240
regional part of telencephalon7.43e-1032
organ8.79e-10503
brain grey matter1.67e-0934
gray matter1.67e-0934
regional part of nervous system1.75e-0953
regional part of brain1.75e-0953
neural tube2.48e-0956
neural rod2.48e-0956
future spinal cord2.48e-0956
neural keel2.48e-0956
cerebral cortex5.53e-0925
pallium5.53e-0925
cavitated compound organ1.90e-0831
kidney2.04e-0826
kidney mesenchyme2.04e-0826
upper urinary tract2.04e-0826
kidney rudiment2.04e-0826
kidney field2.04e-0826
germ layer7.73e-08560
germ layer / neural crest7.73e-08560
embryonic tissue7.73e-08560
presumptive structure7.73e-08560
germ layer / neural crest derived structure7.73e-08560
epiblast (generic)7.73e-08560
embryonic structure1.28e-07564
compound organ1.35e-0768
trunk region element5.91e-07101
urinary system structure6.10e-0747
tube6.40e-07192
renal system8.30e-0748
endoderm-derived structure9.23e-07160
endoderm9.23e-07160
presumptive endoderm9.23e-07160
Disease
Ontology termp-valuen
cell type cancer3.35e-10143
carcinoma1.74e-09106


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
E2F1#186934.907389214879320.008460985347239390.0326989656853291
EGR1#195834.988179094810140.008056488137383440.0321972817732441
HDAC2#3066313.41562023662630.0004140761399857210.00392892686326598
MAX#414936.452555509007120.003721913834265510.0187205239326168
MYC#460935.22228187160940.007020843755740150.0295605684743296
ZNF263#1012738.221841637010680.001799043925565870.0109864547153651



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.