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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3739_choriocarcinoma_large_melanoma_pancreatic_mesenchymal_Meningeal_Melanocyte
|full_id=C3739_choriocarcinoma_large_melanoma_pancreatic_mesenchymal_Meningeal_Melanocyte
|id=C3739
|id=C3739

Revision as of 16:42, 12 September 2012


Full id: C3739_choriocarcinoma_large_melanoma_pancreatic_mesenchymal_Meningeal_Melanocyte



Phase1 CAGE Peaks

Hg19::chr18:7117741..7117752,-p3@LAMA1
Hg19::chr18:7117785..7117811,-p1@LAMA1
Hg19::chr18:7117813..7117843,-p2@LAMA1


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
non-terminally differentiated cell6.58e-15180
neurectodermal cell1.53e-0859
ectodermal cell2.06e-0871
pigment cell4.45e-0814
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.89e-2294
nervous system3.89e-2294
ectoderm-derived structure6.04e-22169
central nervous system5.87e-2182
ectoderm8.01e-21173
presumptive ectoderm8.01e-21173
head1.06e-20123
organism subdivision5.71e-20365
anterior region of body2.91e-19129
craniocervical region2.91e-19129
neural plate3.59e-1786
presumptive neural plate3.59e-1786
brain1.23e-1669
future brain1.23e-1669
regional part of brain9.01e-1659
neurectoderm1.09e-1590
cell layer1.66e-14312
pre-chordal neural plate2.19e-1461
neural tube2.48e-1457
neural rod2.48e-1457
future spinal cord2.48e-1457
neural keel2.48e-1457
epithelium2.04e-13309
multi-tissue structure5.68e-13347
anterior neural tube5.33e-1142
regional part of forebrain6.30e-1141
forebrain6.30e-1141
future forebrain6.30e-1141
gray matter2.73e-0934
brain grey matter2.73e-0934
embryo3.28e-09612
telencephalon3.63e-0934
regional part of telencephalon4.67e-0933
cerebral hemisphere1.39e-0832
gonad7.24e-0821
indifferent external genitalia7.24e-0821
indifferent gonad7.24e-0821
gonad primordium7.24e-0821
multi-cellular organism1.26e-07659
embryonic structure1.41e-07605
developing anatomical structure1.41e-07605
germ layer2.15e-07604
embryonic tissue2.15e-07604
presumptive structure2.15e-07604
epiblast (generic)2.15e-07604
external genitalia4.26e-0722
cerebral cortex5.59e-0725
pallium5.59e-0725
Disease
Ontology termp-valuen
ovarian cancer7.47e-0814


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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