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Coexpression cluster:C1456

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Full id: C1456_medial_amygdala_brain_hippocampus_occipital_putamen_parietal



Phase1 CAGE Peaks

Hg19::chr19:47113203..47113232,+p@chr19:47113203..47113232
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Hg19::chr19:47113300..47113328,+p@chr19:47113300..47113328
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Hg19::chr19:47113368..47113396,+p@chr19:47113368..47113396
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Hg19::chr19:47113445..47113466,+p@chr19:47113445..47113466
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Hg19::chr19:47113473..47113571,+p@chr19:47113473..47113571
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Hg19::chr19:47113683..47113695,+p@chr19:47113683..47113695
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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube8.91e-1857
neural rod8.91e-1857
future spinal cord8.91e-1857
neural keel8.91e-1857
cerebral hemisphere1.98e-1732
gray matter6.18e-1734
brain grey matter6.18e-1734
regional part of brain3.97e-1659
telencephalon4.47e-1634
regional part of telencephalon1.73e-1533
central nervous system2.07e-1582
regional part of cerebral cortex6.07e-1522
cerebral cortex1.92e-1425
pallium1.92e-1425
regional part of forebrain7.02e-1441
forebrain7.02e-1441
future forebrain7.02e-1441
neocortex1.01e-1320
neural plate1.20e-1386
presumptive neural plate1.20e-1386
anterior neural tube1.91e-1342
brain4.43e-1369
future brain4.43e-1369
neurectoderm2.41e-1290
cell layer6.81e-12312
epithelium1.16e-11309
adult organism1.62e-11115
regional part of nervous system2.60e-1194
nervous system2.60e-1194
pre-chordal neural plate4.26e-1161
anatomical cluster1.99e-09286
tube5.51e-09194
organism subdivision5.70e-09365
anatomical conduit1.42e-08241
head5.20e-08123
anterior region of body2.02e-07129
craniocervical region2.02e-07129


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.