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Coexpression cluster:C4833: Difference between revisions

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|tf_chipseq_enrich=ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110296653091972
|tf_chipseq_enrich=ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110296653091972
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}}
}}

Revision as of 16:59, 26 November 2012


Full id: C4833_lung_corpus_thalamus_optic_substantia_globus_diencephalon



Phase1 CAGE Peaks

Hg19::chr9:8857841..8857878,-p1@PTPRD
Hg19::chr9:8857883..8857892,-p14@PTPRD
Hg19::chr9:8857895..8857904,-p13@PTPRD


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 tube5.31e-3656
neural rod5.31e-3656
future spinal cord5.31e-3656
neural keel5.31e-3656
neural plate8.15e-3582
presumptive neural plate8.15e-3582
adult organism8.46e-34114
regional part of nervous system2.44e-3353
regional part of brain2.44e-3353
central nervous system1.23e-3281
neurectoderm4.74e-3286
regional part of forebrain5.49e-2841
forebrain5.49e-2841
anterior neural tube5.49e-2841
future forebrain5.49e-2841
telencephalon6.46e-2834
brain grey matter1.24e-2734
gray matter1.24e-2734
nervous system4.52e-2789
brain8.81e-2768
future brain8.81e-2768
regional part of telencephalon8.18e-2632
cerebral hemisphere9.31e-2632
ecto-epithelium9.57e-25104
structure with developmental contribution from neural crest4.90e-23132
pre-chordal neural plate7.52e-2361
cerebral cortex3.48e-1925
pallium3.48e-1925
ectoderm-derived structure2.16e-18171
ectoderm2.16e-18171
presumptive ectoderm2.16e-18171
regional part of cerebral cortex7.98e-1822
anatomical cluster3.32e-16373
neocortex6.32e-1620
organ part8.16e-14218
tube2.26e-13192
multi-tissue structure2.39e-13342
organ system subdivision7.52e-13223
embryo1.12e-12592
multi-cellular organism4.26e-12656
epithelium5.14e-12306
cell layer1.37e-11309
developing anatomical structure2.87e-11581
anatomical conduit4.17e-11240
anatomical system9.81e-11624
anatomical group1.25e-10625
neural nucleus5.34e-109
nucleus of brain5.34e-109
embryonic structure1.30e-09564
germ layer1.45e-09560
germ layer / neural crest1.45e-09560
embryonic tissue1.45e-09560
presumptive structure1.45e-09560
germ layer / neural crest derived structure1.45e-09560
epiblast (generic)1.45e-09560
posterior neural tube4.27e-0915
chordal neural plate4.27e-0915
organ2.61e-08503
telencephalic nucleus3.17e-087
basal ganglion7.13e-089
nuclear complex of neuraxis7.13e-089
aggregate regional part of brain7.13e-089
collection of basal ganglia7.13e-089
cerebral subcortex7.13e-089
brainstem6.38e-076
gyrus7.28e-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
ZNF263#1012738.221841637010680.001799043925565870.0110296653091972



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.