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Coexpression cluster:C2657

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Full id: C2657_retinoblastoma_nonsmall_acute_myelodysplastic_large_hepatoblastoma_brain



Phase1 CAGE Peaks

Hg19::chr2:115897297..115897302,-p@chr2:115897297..115897302
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Hg19::chr2:115918904..115918922,-p1@LOC389023
Hg19::chr2:115918927..115918946,-p2@LOC389023
Hg19::chr2:115919049..115919088,+p2@DPP10


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


GO IDGO nameFDR corrected p-value
GO:0004274dipeptidyl-peptidase IV activity0.0041014168530947
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.0041014168530947
GO:0008239dipeptidyl-peptidase activity0.0041014168530947
GO:0008238exopeptidase activity0.0302749322971859
GO:0008236serine-type peptidase activity0.0406903724635975
GO:0017171serine hydrolase activity0.0406903724635975



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
neuronal stem cell1.13e-088
embryonic stem cell4.14e-085
Uber Anatomy
Ontology termp-valuen
central nervous system1.43e-4781
nervous system8.27e-4389
neural tube4.43e-4156
neural rod4.43e-4156
future spinal cord4.43e-4156
neural keel4.43e-4156
regional part of nervous system1.01e-3953
regional part of brain1.01e-3953
brain7.85e-3768
future brain7.85e-3768
brain grey matter1.04e-3534
gray matter1.04e-3534
telencephalon1.64e-3534
regional part of forebrain1.51e-3441
forebrain1.51e-3441
anterior neural tube1.51e-3441
future forebrain1.51e-3441
cerebral hemisphere1.55e-3332
regional part of telencephalon3.93e-3332
neocortex2.88e-2920
regional part of cerebral cortex4.90e-2922
neural plate2.65e-2882
presumptive neural plate2.65e-2882
neurectoderm2.41e-2686
cerebral cortex7.13e-2525
pallium7.13e-2525
pre-chordal neural plate1.47e-2461
ecto-epithelium7.12e-22104
adult organism1.01e-21114
organ system subdivision2.38e-19223
ectoderm-derived structure7.04e-18171
ectoderm7.04e-18171
presumptive ectoderm7.04e-18171
structure with developmental contribution from neural crest4.30e-15132
basal ganglion6.68e-139
nuclear complex of neuraxis6.68e-139
aggregate regional part of brain6.68e-139
collection of basal ganglia6.68e-139
cerebral subcortex6.68e-139
neural nucleus2.56e-129
nucleus of brain2.56e-129
gyrus1.80e-106
tube4.24e-10192
telencephalic nucleus8.73e-107
parietal lobe6.58e-095
temporal lobe7.83e-096
occipital lobe8.02e-095
posterior neural tube4.88e-0815
chordal neural plate4.88e-0815
testis6.00e-078
segmental subdivision of hindbrain9.79e-0712
hindbrain9.79e-0712
presumptive hindbrain9.79e-0712


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
JUND#372735.245997956403270.01043432751748420.0387040322346403



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.