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Coexpression cluster:C2589

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Full id: C2589_neuroblastoma_occipital_small_medial_amygdala_frontal_parietal



Phase1 CAGE Peaks

Hg19::chr1:50575466..50575485,+p3@ELAVL4
Hg19::chr1:50575491..50575526,+p2@ELAVL4
Hg19::chr1:50575553..50575567,+p6@ELAVL4
Hg19::chr9:23826183..23826194,-p5@ELAVL2


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:0003730mRNA 3'-UTR binding1.31015399186089e-06
GO:0003729mRNA binding1.31249355256064e-05
GO:0003723RNA binding0.00743630928123174



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
neural cell6.76e-0925
neuronal stem cell4.61e-088
Uber Anatomy
Ontology termp-valuen
central nervous system1.55e-5682
regional part of nervous system1.33e-5394
nervous system1.33e-5394
neural tube4.33e-5157
neural rod4.33e-5157
future spinal cord4.33e-5157
neural keel4.33e-5157
brain8.85e-4569
future brain8.85e-4569
regional part of brain2.54e-4259
regional part of forebrain4.63e-4141
forebrain4.63e-4141
future forebrain4.63e-4141
anterior neural tube1.11e-3942
neurectoderm3.83e-3790
neural plate3.30e-3686
presumptive neural plate3.30e-3686
telencephalon4.09e-3534
gray matter4.32e-3534
brain grey matter4.32e-3534
regional part of telencephalon5.52e-3433
cerebral hemisphere1.65e-3332
adult organism1.79e-33115
ectoderm3.15e-29173
presumptive ectoderm3.15e-29173
ectoderm-derived structure3.76e-28169
cerebral cortex3.50e-2725
pallium3.50e-2725
pre-chordal neural plate5.27e-2761
regional part of cerebral cortex6.33e-2622
anterior region of body8.19e-25129
craniocervical region8.19e-25129
neocortex7.43e-2420
head1.08e-22123
posterior neural tube3.27e-1215
chordal neural plate3.27e-1215
organ part6.66e-10219
temporal lobe1.06e-097
segmental subdivision of hindbrain1.34e-0912
hindbrain1.34e-0912
presumptive hindbrain1.34e-0912
basal ganglion1.67e-099
nuclear complex of neuraxis1.67e-099
aggregate regional part of brain1.67e-099
collection of basal ganglia1.67e-099
cerebral subcortex1.67e-099
nucleus of brain2.72e-099
neural nucleus2.72e-099
embryo1.07e-08612
segmental subdivision of nervous system1.35e-0813
gyrus3.78e-086
organ5.03e-08511
tube1.64e-07194
telencephalic nucleus1.91e-077
embryonic structure1.95e-07605
developing anatomical structure1.95e-07605
diencephalon2.77e-077
future diencephalon2.77e-077
germ layer3.68e-07604
embryonic tissue3.68e-07604
presumptive structure3.68e-07604
epiblast (generic)3.68e-07604
parietal lobe4.75e-075
regional part of metencephalon5.10e-079
metencephalon5.10e-079
future metencephalon5.10e-079
occipital lobe5.46e-075


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


No analysis results for this cluster

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.