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Coexpression cluster:C3739: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!2.27e-20!81;UBERON:0001016!3.49e-20!89;UBERON:0004121!9.45e-18!171;UBERON:0000924!9.45e-18!171;UBERON:0006601!9.45e-18!171;UBERON:0010314!2.43e-17!132;UBERON:0003075!2.90e-17!82;UBERON:0007284!2.90e-17!82;UBERON:0000955!7.72e-16!68;UBERON:0006238!7.72e-16!68;UBERON:0002346!2.79e-15!86;UBERON:0010371!1.48e-14!104;UBERON:0003056!2.23e-14!61;UBERON:0000119!1.81e-13!309;UBERON:0001049!2.16e-13!56;UBERON:0005068!2.16e-13!56;UBERON:0006241!2.16e-13!56;UBERON:0007135!2.16e-13!56;UBERON:0000481!2.04e-12!342;UBERON:0000483!2.09e-12!306;UBERON:0000073!2.75e-12!53;UBERON:0002616!2.75e-12!53;UBERON:0002780!7.31e-11!41;UBERON:0001890!7.31e-11!41;UBERON:0003080!7.31e-11!41;UBERON:0006240!7.31e-11!41;UBERON:0011216!1.10e-09!223;UBERON:0003528!2.21e-09!34;UBERON:0002020!2.21e-09!34;UBERON:0001893!3.37e-09!34;UBERON:0000477!3.98e-09!373;UBERON:0001869!6.66e-09!32;UBERON:0002791!8.49e-09!32;UBERON:0000991!3.09e-08!21;UBERON:0009196!3.09e-08!21;UBERON:0009117!3.09e-08!21;UBERON:0005564!3.09e-08!21;UBERON:0000922!8.39e-08!592;UBERON:0000956!1.47e-07!25;UBERON:0000203!1.47e-07!25;UBERON:0004176!1.61e-07!22;UBERON:0005423!1.00e-06!581
|ontology_enrichment_uberon=UBERON:0001017!2.27e-20!81;UBERON:0001016!3.49e-20!89;UBERON:0004121!9.45e-18!171;UBERON:0000924!9.45e-18!171;UBERON:0006601!9.45e-18!171;UBERON:0010314!2.43e-17!132;UBERON:0003075!2.90e-17!82;UBERON:0007284!2.90e-17!82;UBERON:0000955!7.72e-16!68;UBERON:0006238!7.72e-16!68;UBERON:0002346!2.79e-15!86;UBERON:0010371!1.48e-14!104;UBERON:0003056!2.23e-14!61;UBERON:0000119!1.81e-13!309;UBERON:0001049!2.16e-13!56;UBERON:0005068!2.16e-13!56;UBERON:0006241!2.16e-13!56;UBERON:0007135!2.16e-13!56;UBERON:0000481!2.04e-12!342;UBERON:0000483!2.09e-12!306;UBERON:0000073!2.75e-12!53;UBERON:0002616!2.75e-12!53;UBERON:0002780!7.31e-11!41;UBERON:0001890!7.31e-11!41;UBERON:0003080!7.31e-11!41;UBERON:0006240!7.31e-11!41;UBERON:0011216!1.10e-09!223;UBERON:0003528!2.21e-09!34;UBERON:0002020!2.21e-09!34;UBERON:0001893!3.37e-09!34;UBERON:0000477!3.98e-09!373;UBERON:0001869!6.66e-09!32;UBERON:0002791!8.49e-09!32;UBERON:0000991!3.09e-08!21;UBERON:0009196!3.09e-08!21;UBERON:0009117!3.09e-08!21;UBERON:0005564!3.09e-08!21;UBERON:0000922!8.39e-08!592;UBERON:0000956!1.47e-07!25;UBERON:0000203!1.47e-07!25;UBERON:0004176!1.61e-07!22;UBERON:0005423!1.00e-06!581
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}}
}}

Revision as of 16:19, 26 November 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 cell2.58e-10106
neurectodermal cell1.42e-0959
pigment cell2.48e-0814
ectodermal cell2.22e-0772
migratory neural crest cell4.67e-0741
Uber Anatomy
Ontology termp-valuen
central nervous system2.27e-2081
nervous system3.49e-2089
ectoderm-derived structure9.45e-18171
ectoderm9.45e-18171
presumptive ectoderm9.45e-18171
structure with developmental contribution from neural crest2.43e-17132
neural plate2.90e-1782
presumptive neural plate2.90e-1782
brain7.72e-1668
future brain7.72e-1668
neurectoderm2.79e-1586
ecto-epithelium1.48e-14104
pre-chordal neural plate2.23e-1461
cell layer1.81e-13309
neural tube2.16e-1356
neural rod2.16e-1356
future spinal cord2.16e-1356
neural keel2.16e-1356
multi-tissue structure2.04e-12342
epithelium2.09e-12306
regional part of nervous system2.75e-1253
regional part of brain2.75e-1253
regional part of forebrain7.31e-1141
forebrain7.31e-1141
anterior neural tube7.31e-1141
future forebrain7.31e-1141
organ system subdivision1.10e-09223
brain grey matter2.21e-0934
gray matter2.21e-0934
telencephalon3.37e-0934
anatomical cluster3.98e-09373
cerebral hemisphere6.66e-0932
regional part of telencephalon8.49e-0932
gonad3.09e-0821
indifferent external genitalia3.09e-0821
indifferent gonad3.09e-0821
gonad primordium3.09e-0821
embryo8.39e-08592
cerebral cortex1.47e-0725
pallium1.47e-0725
external genitalia1.61e-0722
developing anatomical structure1.00e-06581
Disease
Ontology termp-valuen
ovarian cancer2.82e-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)

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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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