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Coexpression cluster:C1079

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Full id: C1079_synovial_cerebellum_small_Smooth_medulla_spinal_dura



Phase1 CAGE Peaks

Hg19::chr3:146870027..146870031,-p@chr3:146870027..146870031
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Hg19::chr3:146874115..146874120,-p@chr3:146874115..146874120
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Hg19::chr3:147072976..147072980,-p@chr3:147072976..147072980
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Hg19::chr3:147088169..147088187,-p@chr3:147088169..147088187
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Hg19::chr3:147088197..147088208,-p@chr3:147088197..147088208
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Hg19::chr3:147088209..147088251,-p@chr3:147088209..147088251
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Hg19::chr3:147088265..147088276,-p@chr3:147088265..147088276
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Hg19::chr3:147112252..147112256,-p@chr3:147112252..147112256
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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><br>


Cell Type
Ontology termp-valuen
glial cell (sensu Vertebrata)7.78e-0715
glial cell7.78e-0715
glioblast7.78e-0715
glioblast (sensu Vertebrata)7.78e-0715
Uber Anatomy
Ontology termp-valuen
central nervous system1.58e-5282
regional part of nervous system1.66e-5194
nervous system1.66e-5194
brain9.40e-5169
future brain9.40e-5169
regional part of brain8.96e-5059
neural tube8.83e-4857
neural rod8.83e-4857
future spinal cord8.83e-4857
neural keel8.83e-4857
neural plate4.47e-4586
presumptive neural plate4.47e-4586
neurectoderm1.85e-4390
regional part of forebrain4.90e-3141
forebrain4.90e-3141
future forebrain4.90e-3141
anterior neural tube5.58e-3042
ectoderm-derived structure9.01e-30169
ectoderm2.47e-29173
presumptive ectoderm2.47e-29173
head1.11e-28123
anterior region of body3.77e-27129
craniocervical region3.77e-27129
pre-chordal neural plate2.58e-2661
gray matter5.99e-2634
brain grey matter5.99e-2634
telencephalon6.87e-2634
regional part of telencephalon7.07e-2533
cerebral hemisphere9.79e-2432
posterior neural tube2.67e-1915
chordal neural plate2.67e-1915
cerebral cortex5.49e-1925
pallium5.49e-1925
adult organism1.24e-18115
segmental subdivision of nervous system6.94e-1713
regional part of cerebral cortex8.08e-1722
segmental subdivision of hindbrain8.90e-1612
hindbrain8.90e-1612
presumptive hindbrain8.90e-1612
neocortex4.40e-1520
regional part of metencephalon3.33e-129
metencephalon3.33e-129
future metencephalon3.33e-129
cerebellum6.69e-096
rhombic lip6.69e-096
cell layer1.21e-08312
nucleus of brain2.08e-089
neural nucleus2.08e-089
tube2.40e-08194
brainstem3.97e-088
vasculature of head1.07e-0711
vasculature of organ1.07e-0711
organism subdivision1.52e-07365
epithelium1.63e-07309
gyrus2.89e-076
brain vasculature5.71e-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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
SUZ12#23512212.52894522776570.01028879170298380.0382225702225989



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.