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Coexpression cluster:C3619: Difference between revisions

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|tf_chipseq_enrich=TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329009747227234
|tf_chipseq_enrich=TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329009747227234
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}}
}}

Revision as of 16:14, 26 November 2012


Full id: C3619_cerebellum_occipital_caudate_putamen_Fibroblast_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr17:26698422..26698461,+p6@SARM1
Hg19::chr3:141105795..141105814,+p@chr3:141105795..141105814
+
Hg19::chr3:141105820..141105861,+p@chr3:141105820..141105861
+


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 tube1.81e-3956
neural rod1.81e-3956
future spinal cord1.81e-3956
neural keel1.81e-3956
regional part of nervous system8.08e-3753
regional part of brain8.08e-3753
nervous system6.69e-3289
regional part of forebrain8.90e-3241
forebrain8.90e-3241
anterior neural tube8.90e-3241
future forebrain8.90e-3241
central nervous system1.79e-3081
brain4.27e-2868
future brain4.27e-2868
brain grey matter7.09e-2634
gray matter7.09e-2634
telencephalon9.42e-2634
cerebral hemisphere8.04e-2532
adult organism2.03e-24114
neurectoderm2.56e-2486
regional part of telencephalon4.10e-2432
neural plate2.77e-2382
presumptive neural plate2.77e-2382
regional part of cerebral cortex1.18e-2122
structure with developmental contribution from neural crest6.83e-21132
neocortex8.90e-2020
tube2.99e-19192
pre-chordal neural plate4.84e-1861
cerebral cortex5.27e-1825
pallium5.27e-1825
ecto-epithelium4.47e-17104
ectoderm-derived structure2.60e-16171
ectoderm2.60e-16171
presumptive ectoderm2.60e-16171
organ system subdivision1.31e-15223
anatomical conduit1.31e-14240
anatomical cluster1.92e-13373
basal ganglion1.01e-099
nuclear complex of neuraxis1.01e-099
aggregate regional part of brain1.01e-099
collection of basal ganglia1.01e-099
cerebral subcortex1.01e-099
multi-tissue structure1.02e-09342
neural nucleus1.99e-099
nucleus of brain1.99e-099
epithelium3.06e-09306
posterior neural tube6.95e-0915
chordal neural plate6.95e-0915
cell layer7.19e-09309
telencephalic nucleus1.07e-077
gyrus1.40e-076
diencephalon1.94e-077
future diencephalon1.94e-077
aorta8.01e-0721
aortic system8.01e-0721
brainstem9.35e-076


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
TRIM28#10155212.39368336350830.008368344129438470.0329009747227234



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.