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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><br>


Uber Anatomy
Ontology termp-valuen
neural tube2.36e-2457
neural rod2.36e-2457
future spinal cord2.36e-2457
neural keel2.36e-2457
adult organism8.98e-22115
regional part of forebrain6.49e-2141
forebrain6.49e-2141
future forebrain6.49e-2141
anterior neural tube1.65e-2042
regional part of brain2.28e-1859
brain2.33e-1869
future brain2.33e-1869
central nervous system2.79e-1882
gray matter4.49e-1734
brain grey matter4.49e-1734
regional part of nervous system7.46e-1794
nervous system7.46e-1794
telencephalon8.00e-1734
regional part of telencephalon1.97e-1633
cerebral hemisphere1.50e-1532
neurectoderm1.40e-1490
neural plate1.59e-1386
presumptive neural plate1.59e-1386
regional part of cerebral cortex1.37e-1222
cerebral cortex7.32e-1225
pallium7.32e-1225
neocortex2.15e-1120
pre-chordal neural plate7.70e-1161
anterior region of body7.50e-07129
craniocervical region7.50e-07129
nucleus of brain8.18e-079
neural nucleus8.18e-079
ectoderm8.57e-07173
presumptive ectoderm8.57e-07173
basal ganglion9.69e-079
nuclear complex of neuraxis9.69e-079
aggregate regional part of brain9.69e-079
collection of basal ganglia9.69e-079
cerebral subcortex9.69e-079


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.