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Coexpression cluster:C1263: Difference between revisions

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|tf_chipseq_enrich=TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246766805873
|tf_chipseq_enrich=TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246766805873
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}}
}}

Revision as of 14:47, 26 November 2012


Full id: C1263_neuroectodermal_glioblastoma_pons_pineal_parietal_rhabdomyosarcoma_occipital



Phase1 CAGE Peaks

Hg19::chr2:139537884..139537895,-p3@NXPH2
Hg19::chr2:139537925..139537946,-p2@NXPH2
Hg19::chr2:139537950..139537983,-p1@NXPH2
Hg19::chr2:139538247..139538266,-p5@NXPH2
Hg19::chr2:139538362..139538376,-p4@NXPH2
Hg19::chr2:139538440..139538457,-p@chr2:139538440..139538457
-
Hg19::chr2:139538474..139538479,-p@chr2:139538474..139538479
-


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>


Cell Type
Ontology termp-valuen
neuronal stem cell1.10e-128
neuron7.79e-126
neuroblast7.79e-126
electrically signaling cell7.79e-126
neural cell3.34e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system1.46e-5781
nervous system9.08e-5189
neural tube6.28e-4456
neural rod6.28e-4456
future spinal cord6.28e-4456
neural keel6.28e-4456
regional part of nervous system7.64e-4153
regional part of brain7.64e-4153
brain7.73e-4068
future brain7.73e-4068
regional part of cerebral cortex3.47e-3722
regional part of forebrain4.33e-3741
forebrain4.33e-3741
anterior neural tube4.33e-3741
future forebrain4.33e-3741
neocortex6.58e-3720
cerebral cortex6.42e-3625
pallium6.42e-3625
brain grey matter1.40e-3434
gray matter1.40e-3434
cerebral hemisphere7.85e-3432
telencephalon1.47e-3134
regional part of telencephalon2.20e-3032
neurectoderm1.27e-2986
neural plate3.13e-2982
presumptive neural plate3.13e-2982
ectoderm-derived structure2.48e-25171
ectoderm2.48e-25171
presumptive ectoderm2.48e-25171
pre-chordal neural plate8.37e-2561
adult organism1.23e-21114
structure with developmental contribution from neural crest3.15e-21132
ecto-epithelium3.16e-21104
organ system subdivision1.56e-17223
gyrus1.86e-176
brainstem5.76e-126
temporal lobe2.47e-106
occipital lobe7.46e-105
parietal lobe7.99e-105
frontal cortex1.04e-093
pons1.97e-093
anatomical cluster2.34e-09373
tube1.75e-08192
posterior neural tube2.23e-0815
chordal neural plate2.23e-0815
regional part of diencephalon3.37e-074
middle frontal gyrus6.14e-072
diencephalon7.02e-077
future diencephalon7.02e-077


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
TAF1#687273.343046285745290.0002142336319622450.00246766805873



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.