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Coexpression cluster:C2492

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Full id: C2492_medial_brain_temporal_postcentral_cerebellum_pons_eye



Phase1 CAGE Peaks

Hg19::chr19:42473625..42473655,-p@chr19:42473625..42473655
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Hg19::chr19:42479863..42479884,-p@chr19:42479863..42479884
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Hg19::chr19:42479906..42479929,-p@chr19:42479906..42479929
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Hg19::chr19:42492239..42492251,-p5@ATP1A3


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
central nervous system5.22e-6181
nervous system2.95e-6089
neural tube6.50e-6056
neural rod6.50e-6056
future spinal cord6.50e-6056
neural keel6.50e-6056
regional part of nervous system4.91e-5853
regional part of brain4.91e-5853
brain4.79e-5468
future brain4.79e-5468
regional part of forebrain1.62e-4941
forebrain1.62e-4941
anterior neural tube1.62e-4941
future forebrain1.62e-4941
neurectoderm9.14e-4886
neural plate1.09e-4682
presumptive neural plate1.09e-4682
cerebral hemisphere8.91e-4432
telencephalon1.22e-4334
brain grey matter1.30e-4334
gray matter1.30e-4334
regional part of cerebral cortex1.65e-4022
regional part of telencephalon2.82e-4032
adult organism1.22e-39114
neocortex7.83e-3720
pre-chordal neural plate3.54e-3661
ecto-epithelium3.44e-35104
cerebral cortex5.57e-3525
pallium5.57e-3525
ectoderm-derived structure1.02e-31171
ectoderm1.02e-31171
presumptive ectoderm1.02e-31171
structure with developmental contribution from neural crest2.21e-31132
organ system subdivision3.73e-21223
tube3.08e-14192
gyrus2.54e-136
brainstem6.47e-126
posterior neural tube1.22e-1115
chordal neural plate1.22e-1115
parietal lobe5.00e-115
temporal lobe7.55e-116
occipital lobe8.61e-115
limbic system2.06e-105
basal ganglion4.21e-109
nuclear complex of neuraxis4.21e-109
aggregate regional part of brain4.21e-109
collection of basal ganglia4.21e-109
cerebral subcortex4.21e-109
neural nucleus4.40e-109
nucleus of brain4.40e-109
segmental subdivision of hindbrain7.76e-1012
hindbrain7.76e-1012
presumptive hindbrain7.76e-1012
anatomical cluster1.86e-09373
segmental subdivision of nervous system5.95e-0913
corpus striatum7.68e-094
striatum7.68e-094
ventral part of telencephalon7.68e-094
future corpus striatum7.68e-094
organ part8.81e-09218
anatomical conduit1.01e-08240
regional part of diencephalon1.31e-084
frontal cortex2.12e-073
diencephalon2.51e-077
future diencephalon2.51e-077
caudate-putamen5.09e-073
dorsal striatum5.09e-073
telencephalic nucleus5.09e-077
pons5.97e-073


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.