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Coexpression cluster:C3842: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;2:41.8113335595521:0.000754340825991485:0.00593421222700547
|tf_chipseq_enrich=CTBP2#1488;2:41.8113335595521:0.000754340825991485:0.00593421222700547
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}}
}}

Revision as of 16:23, 26 November 2012


Full id: C3842_anaplastic_neuroectodermal_mesenchymal_neuroblastoma_Mesothelial_Fibroblast_gall



Phase1 CAGE Peaks

Hg19::chr1:107682694..107682765,+p1@NTNG1
Hg19::chr1:107682962..107683001,+p6@NTNG1
Hg19::chr1:107683775..107683816,+p2@NTNG1


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
skin fibroblast1.28e-1123
fibroblast1.02e-1076
kidney tubule cell3.13e-0710
nephron tubule epithelial cell3.13e-0710
Uber Anatomy
Ontology termp-valuen
neurectoderm8.19e-1486
structure with developmental contribution from neural crest8.77e-13132
neural tube1.03e-1256
neural rod1.03e-1256
future spinal cord1.03e-1256
neural keel1.03e-1256
ectoderm-derived structure5.69e-12171
ectoderm5.69e-12171
presumptive ectoderm5.69e-12171
neural plate6.20e-1282
presumptive neural plate6.20e-1282
regional part of nervous system1.07e-1153
regional part of brain1.07e-1153
nervous system1.77e-1189
ecto-epithelium1.05e-10104
multi-tissue structure1.28e-09342
central nervous system2.29e-0981
pre-chordal neural plate6.45e-0961
regional part of forebrain7.53e-0941
forebrain7.53e-0941
anterior neural tube7.53e-0941
future forebrain7.53e-0941
cerebral hemisphere2.90e-0832
cell layer4.29e-08309
epithelium4.51e-08306
telencephalon4.98e-0834
cerebral cortex6.34e-0825
pallium6.34e-0825
brain grey matter6.58e-0834
gray matter6.58e-0834
surface structure9.04e-0899
multi-cellular organism1.02e-07656
brain1.45e-0768
future brain1.45e-0768
regional part of telencephalon2.10e-0732
skin of body2.53e-0741
nephron tubule epithelium3.13e-0710
integument4.98e-0746
integumental system4.98e-0746
organ part5.91e-07218
anatomical system6.64e-07624
dermis7.73e-079
dermatome7.73e-079
future dermis7.73e-079
neocortex8.43e-0720
anatomical group8.70e-07625


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
CTBP2#1488241.81133355955210.0007543408259914850.00593421222700547



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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