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Coexpression cluster:C2932: Difference between revisions

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|tf_chipseq_enrich=TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323506920625073!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158736071079241
|tf_chipseq_enrich=TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323506920625073!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158736071079241
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}}
}}

Revision as of 15:49, 26 November 2012


Full id: C2932_occipital_astrocytoma_gall_medial_postcentral_parietal_brain



Phase1 CAGE Peaks

Hg19::chr8:94929594..94929608,+p21@PDP1
Hg19::chr8:94929969..94929980,+p8@PDP1
Hg19::chr8:94930034..94930089,+p2@PDP1
Hg19::chr8:94930100..94930120,+p5@PDP1


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>disease_data<br>

Cell Type
Ontology termp-valuen
neural cell9.64e-0925
embryonic cell1.65e-08250
Uber Anatomy
Ontology termp-valuen
central nervous system4.91e-3681
nervous system1.04e-3589
brain2.37e-3168
future brain2.37e-3168
neural tube1.74e-3056
neural rod1.74e-3056
future spinal cord1.74e-3056
neural keel1.74e-3056
regional part of nervous system1.11e-2953
regional part of brain1.11e-2953
regional part of forebrain6.34e-2641
forebrain6.34e-2641
anterior neural tube6.34e-2641
future forebrain6.34e-2641
neural plate6.68e-2582
presumptive neural plate6.68e-2582
telencephalon2.01e-2434
cerebral hemisphere3.19e-2432
brain grey matter3.74e-2434
gray matter3.74e-2434
neurectoderm1.16e-2386
regional part of telencephalon3.24e-2332
ectoderm-derived structure5.83e-23171
ectoderm5.83e-23171
presumptive ectoderm5.83e-23171
ecto-epithelium1.76e-22104
anatomical conduit3.05e-22240
anatomical cluster8.90e-22373
structure with developmental contribution from neural crest4.41e-21132
pre-chordal neural plate7.65e-2161
tube9.08e-21192
cerebral cortex1.10e-1925
pallium1.10e-1925
regional part of cerebral cortex2.38e-1722
cell layer6.28e-17309
epithelium6.85e-17306
neocortex4.75e-1620
organ system subdivision2.57e-14223
anatomical system1.20e-11624
anatomical group1.66e-11625
embryo1.67e-11592
multi-cellular organism2.56e-11656
multi-tissue structure7.62e-10342
developing anatomical structure7.92e-10581
embryonic structure1.13e-09564
germ layer1.25e-09560
germ layer / neural crest1.25e-09560
embryonic tissue1.25e-09560
presumptive structure1.25e-09560
germ layer / neural crest derived structure1.25e-09560
epiblast (generic)1.25e-09560
organ part3.60e-08218
adult organism3.53e-07114
vasculature5.82e-0778
vascular system5.82e-0778
Disease
Ontology termp-valuen
squamous cell carcinoma8.62e-0714


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#687243.343046285745290.008005664898701650.0323506920625073
TCF7L2#693438.077632422353010.002978381685834620.0158736071079241



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.

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