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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3842_anaplastic_neuroectodermal_mesenchymal_neuroblastoma_Mesothelial_Fibroblast_gall
|full_id=C3842_anaplastic_neuroectodermal_mesenchymal_neuroblastoma_Mesothelial_Fibroblast_gall
|id=C3842
|id=C3842

Revision as of 16:49, 12 September 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>


Uber Anatomy
Ontology termp-valuen
organism subdivision3.09e-25365
neurectoderm2.33e-1990
neural plate2.29e-1786
presumptive neural plate2.29e-1786
ectoderm3.48e-17173
presumptive ectoderm3.48e-17173
neural tube5.50e-1757
neural rod5.50e-1757
future spinal cord5.50e-1757
neural keel5.50e-1757
regional part of nervous system1.00e-1694
nervous system1.00e-1694
epithelium1.10e-15309
ectoderm-derived structure1.49e-15169
cell layer1.56e-15312
regional part of brain7.40e-1459
head1.03e-13123
central nervous system1.62e-1382
pre-chordal neural plate1.71e-1361
anterior region of body4.37e-13129
craniocervical region4.37e-13129
regional part of forebrain6.06e-1341
forebrain6.06e-1341
future forebrain6.06e-1341
multi-tissue structure1.72e-12347
anterior neural tube3.40e-1242
somite1.25e-1183
paraxial mesoderm1.25e-1183
presomitic mesoderm1.25e-1183
presumptive segmental plate1.25e-1183
trunk paraxial mesoderm1.25e-1183
presumptive paraxial mesoderm1.25e-1183
gray matter4.37e-1134
brain grey matter4.37e-1134
brain5.57e-1169
future brain5.57e-1169
telencephalon5.98e-1134
multi-cellular organism7.58e-11659
regional part of telencephalon1.07e-1033
trunk mesenchyme1.51e-10143
cerebral hemisphere2.16e-1032
anatomical group2.59e-10626
anatomical system2.70e-10625
dermomyotome4.60e-1070
surface structure3.42e-0995
cerebral cortex3.74e-0925
pallium3.74e-0925
anatomical cluster4.20e-09286
anatomical conduit4.47e-09241
multilaminar epithelium4.48e-0982
integument7.96e-0945
integumental system7.96e-0945
tube9.99e-09194
organ part1.52e-08219
embryo4.22e-08612
adult organism6.30e-08115
regional part of cerebral cortex8.24e-0822
skin of body9.84e-0840
muscle tissue2.84e-0763
musculature2.84e-0763
musculature of body2.84e-0763
neocortex3.70e-0720
embryonic structure3.92e-07605
developing anatomical structure3.92e-07605
germ layer4.29e-07604
embryonic tissue4.29e-07604
presumptive structure4.29e-07604
epiblast (generic)4.29e-07604
skeletal muscle tissue5.64e-0761
striated muscle tissue5.64e-0761
myotome5.64e-0761


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.