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Coexpression cluster:C4243: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0230003518477883!BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183932228006061!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329282455178368
|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0230003518477883!BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183932228006061!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329282455178368
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}}
}}

Revision as of 16:38, 26 November 2012


Full id: C4243_CD4_cerebellum_CD8_medial_Peripheral_occipital_parietal



Phase1 CAGE Peaks

Hg19::chr2:69871079..69871100,-p6@AAK1
Hg19::chr6:154568673..154568692,-p3@IPCEF1
Hg19::chr6:154568722..154568735,-p4@IPCEF1


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
adult organism7.79e-56114
neural tube3.47e-3456
neural rod3.47e-3456
future spinal cord3.47e-3456
neural keel3.47e-3456
regional part of nervous system2.47e-3253
regional part of brain2.47e-3253
regional part of forebrain1.01e-2741
forebrain1.01e-2741
anterior neural tube1.01e-2741
future forebrain1.01e-2741
central nervous system1.07e-2481
brain1.16e-2368
future brain1.16e-2368
telencephalon3.95e-2334
brain grey matter1.13e-2234
gray matter1.13e-2234
neural plate2.82e-2282
presumptive neural plate2.82e-2282
cerebral hemisphere8.21e-2232
regional part of telencephalon1.99e-2132
neurectoderm2.13e-2086
nervous system2.19e-2089
neocortex1.45e-1820
regional part of cerebral cortex4.96e-1822
pre-chordal neural plate5.65e-1861
cerebral cortex2.54e-1625
pallium2.54e-1625
ecto-epithelium1.58e-14104
organ system subdivision2.91e-11223
structure with developmental contribution from neural crest7.12e-11132
blood3.81e-0915
haemolymphatic fluid3.81e-0915
organism substance3.81e-0915
basal ganglion3.21e-089
nuclear complex of neuraxis3.21e-089
aggregate regional part of brain3.21e-089
collection of basal ganglia3.21e-089
cerebral subcortex3.21e-089
neural nucleus7.63e-089
nucleus of brain7.63e-089
posterior neural tube9.59e-0815
chordal neural plate9.59e-0815
gyrus9.90e-086
hemopoietic organ1.92e-077
immune organ1.92e-077
ectoderm-derived structure2.49e-07171
ectoderm2.49e-07171
presumptive ectoderm2.49e-07171


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
BATF#10538216.23853452820240.004917462407809970.0230003518477883
BCL11A#53335218.91297006907140.003639406248379680.0183932228006061
TRIM28#10155212.39368336350830.008368344129438470.0329282455178368



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.