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Coexpression cluster:C1821

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Full id: C1821_cerebellum_spinal_thalamus_pineal_occipital_middle_parietal



Phase1 CAGE Peaks

Hg19::chr19:4035616..4035635,+p@chr19:4035616..4035635
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Hg19::chr19:4035684..4035711,+p@chr19:4035684..4035711
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Hg19::chr19:4035761..4035793,+p@chr19:4035761..4035793
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Hg19::chr19:4035797..4035831,+p@chr19:4035797..4035831
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Hg19::chr19:4035896..4035915,+p@chr19:4035896..4035915
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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>


Uber Anatomy
Ontology termp-valuen
neural tube1.32e-2456
neural rod1.32e-2456
future spinal cord1.32e-2456
neural keel1.32e-2456
regional part of nervous system4.66e-2353
regional part of brain4.66e-2353
regional part of forebrain1.17e-2041
forebrain1.17e-2041
anterior neural tube1.17e-2041
future forebrain1.17e-2041
nervous system1.64e-1989
central nervous system1.67e-1981
brain2.95e-1968
future brain2.95e-1968
adult organism3.97e-18114
brain grey matter8.12e-1734
gray matter8.12e-1734
telencephalon1.69e-1634
regional part of telencephalon1.51e-1532
neurectoderm2.06e-1586
cerebral hemisphere3.15e-1532
neural plate2.48e-1482
presumptive neural plate2.48e-1482
regional part of cerebral cortex2.50e-1222
cerebral cortex1.28e-1125
pallium1.28e-1125
neocortex3.70e-1120
pre-chordal neural plate5.27e-1161
ecto-epithelium1.19e-08104
organ system subdivision7.96e-08223
ectoderm-derived structure6.24e-07171
ectoderm6.24e-07171
presumptive ectoderm6.24e-07171
neural nucleus8.18e-079
nucleus of brain8.18e-079
basal ganglion9.26e-079
nuclear complex of neuraxis9.26e-079
aggregate regional part of brain9.26e-079
collection of basal ganglia9.26e-079
cerebral subcortex9.26e-079
Disease
Ontology termp-valuen
cancer1.74e-07235
disease of cellular proliferation7.00e-07239


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#23512440.09262472885037.78750287036555e-073.41300466755395e-05



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.