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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2452_Mesenchymal_small_neuroepithelioma_colon_Adipocyte_neuroectodermal_mature
|full_id=C2452_Mesenchymal_small_neuroepithelioma_colon_Adipocyte_neuroectodermal_mature
|id=C2452
|id=C2452

Revision as of 15:11, 12 September 2012


Full id: C2452_Mesenchymal_small_neuroepithelioma_colon_Adipocyte_neuroectodermal_mature



Phase1 CAGE Peaks

Hg19::chr18:10454594..10454645,+p1@APCDD1
Hg19::chr18:10471655..10471667,+p@chr18:10471655..10471667
+
Hg19::chr18:10471813..10471824,+p@chr18:10471813..10471824
+
Hg19::chr18:10471826..10471841,+p@chr18:10471826..10471841
+


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
fat cell2.54e-0715
Uber Anatomy
Ontology termp-valuen
adult organism2.23e-37115
ectoderm3.64e-30173
presumptive ectoderm3.64e-30173
neural tube6.69e-2857
neural rod6.69e-2857
future spinal cord6.69e-2857
neural keel6.69e-2857
ectoderm-derived structure8.45e-28169
neurectoderm1.41e-2790
head9.52e-27123
central nervous system2.16e-2682
anterior region of body3.91e-26129
craniocervical region3.91e-26129
neural plate5.46e-2586
presumptive neural plate5.46e-2586
regional part of brain2.90e-2459
regional part of nervous system3.52e-2494
nervous system3.52e-2494
brain6.80e-2469
future brain6.80e-2469
anterior neural tube7.34e-2142
regional part of forebrain1.53e-2041
forebrain1.53e-2041
future forebrain1.53e-2041
pre-chordal neural plate7.31e-1961
gray matter6.96e-1834
brain grey matter6.96e-1834
telencephalon7.04e-1834
regional part of telencephalon2.04e-1733
cerebral hemisphere8.05e-1732
organ7.13e-16511
multi-cellular organism3.09e-15659
cerebral cortex3.25e-1325
pallium3.25e-1325
organ part9.25e-13219
regional part of cerebral cortex1.64e-1222
organism subdivision1.09e-11365
neocortex1.98e-1120
embryo2.24e-10612
anatomical group4.05e-10626
anatomical system4.74e-10625
multi-tissue structure1.75e-09347
embryonic structure5.28e-09605
developing anatomical structure5.28e-09605
germ layer1.12e-08604
embryonic tissue1.12e-08604
presumptive structure1.12e-08604
epiblast (generic)1.12e-08604
surface structure3.24e-0895
posterior neural tube3.54e-0815
chordal neural plate3.54e-0815
segmental subdivision of nervous system5.36e-0713


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

No analysis results for this cluster

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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