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Coexpression cluster:C1313: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005631!1.73e-25!14;UBERON:0000158!1.73e-25!14;UBERON:0000125!1.85e-22!9;UBERON:0002308!1.85e-22!9;UBERON:0002298!3.42e-18!6;UBERON:0000305!2.30e-16!7;UBERON:0009663!7.79e-15!7;UBERON:0000013!1.63e-14!5;UBERON:0002410!1.63e-14!5;UBERON:0004121!1.86e-14!171;UBERON:0000924!1.86e-14!171;UBERON:0006601!1.86e-14!171;UBERON:0004871!2.77e-14!8;UBERON:0000478!3.67e-14!24;UBERON:0000988!1.04e-13!3;UBERON:0003076!1.91e-13!15;UBERON:0003057!1.91e-13!15;UBERON:0002346!1.92e-13!86;UBERON:0001016!1.76e-12!89;UBERON:0002420!1.72e-11!9;UBERON:0007245!1.72e-11!9;UBERON:0010009!1.72e-11!9;UBERON:0010011!1.72e-11!9;UBERON:0000454!1.72e-11!9;UBERON:0001987!2.25e-11!4;UBERON:0004340!2.25e-11!4;UBERON:0003124!4.54e-11!7;UBERON:0002148!4.81e-10!2;UBERON:0006331!4.81e-10!2;UBERON:0009662!4.81e-10!2;UBERON:0001049!5.62e-10!56;UBERON:0005068!5.62e-10!56;UBERON:0006241!5.62e-10!56;UBERON:0007135!5.62e-10!56;UBERON:0000369!6.27e-10!4;UBERON:0002435!6.27e-10!4;UBERON:0000204!6.27e-10!4;UBERON:0010082!6.27e-10!4;UBERON:0001875!1.66e-09!2;UBERON:0006514!1.66e-09!2;UBERON:0004733!5.73e-09!12;UBERON:0002028!5.73e-09!12;UBERON:0007277!5.73e-09!12;UBERON:0001017!2.69e-08!81;UBERON:0003075!2.80e-08!82;UBERON:0007284!2.80e-08!82;UBERON:0004732!2.96e-08!13;UBERON:0000010!4.27e-08!8;UBERON:0000064!1.35e-07!218;UBERON:0000073!1.81e-07!53;UBERON:0002616!1.81e-07!53;UBERON:0001896!7.17e-07!3;UBERON:0005290!7.17e-07!3;UBERON:0010096!7.17e-07!3;UBERON:0002240!9.33e-07!3;UBERON:0005174!9.33e-07!3;UBERON:0001137!9.33e-07!3
|ontology_enrichment_uberon=UBERON:0005631!1.73e-25!14;UBERON:0000158!1.73e-25!14;UBERON:0000125!1.85e-22!9;UBERON:0002308!1.85e-22!9;UBERON:0002298!3.42e-18!6;UBERON:0000305!2.30e-16!7;UBERON:0009663!7.79e-15!7;UBERON:0000013!1.63e-14!5;UBERON:0002410!1.63e-14!5;UBERON:0004121!1.86e-14!171;UBERON:0000924!1.86e-14!171;UBERON:0006601!1.86e-14!171;UBERON:0004871!2.77e-14!8;UBERON:0000478!3.67e-14!24;UBERON:0000988!1.04e-13!3;UBERON:0003076!1.91e-13!15;UBERON:0003057!1.91e-13!15;UBERON:0002346!1.92e-13!86;UBERON:0001016!1.76e-12!89;UBERON:0002420!1.72e-11!9;UBERON:0007245!1.72e-11!9;UBERON:0010009!1.72e-11!9;UBERON:0010011!1.72e-11!9;UBERON:0000454!1.72e-11!9;UBERON:0001987!2.25e-11!4;UBERON:0004340!2.25e-11!4;UBERON:0003124!4.54e-11!7;UBERON:0002148!4.81e-10!2;UBERON:0006331!4.81e-10!2;UBERON:0009662!4.81e-10!2;UBERON:0001049!5.62e-10!56;UBERON:0005068!5.62e-10!56;UBERON:0006241!5.62e-10!56;UBERON:0007135!5.62e-10!56;UBERON:0000369!6.27e-10!4;UBERON:0002435!6.27e-10!4;UBERON:0000204!6.27e-10!4;UBERON:0010082!6.27e-10!4;UBERON:0001875!1.66e-09!2;UBERON:0006514!1.66e-09!2;UBERON:0004733!5.73e-09!12;UBERON:0002028!5.73e-09!12;UBERON:0007277!5.73e-09!12;UBERON:0001017!2.69e-08!81;UBERON:0003075!2.80e-08!82;UBERON:0007284!2.80e-08!82;UBERON:0004732!2.96e-08!13;UBERON:0000010!4.27e-08!8;UBERON:0000064!1.35e-07!218;UBERON:0000073!1.81e-07!53;UBERON:0002616!1.81e-07!53;UBERON:0001896!7.17e-07!3;UBERON:0005290!7.17e-07!3;UBERON:0010096!7.17e-07!3;UBERON:0002240!9.33e-07!3;UBERON:0005174!9.33e-07!3;UBERON:0001137!9.33e-07!3
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}}
}}

Revision as of 14:49, 26 November 2012


Full id: C1313_Placental_mesothelioma_amniotic_neuroectodermal_renal_chorionic_carcinosarcoma



Phase1 CAGE Peaks

Hg19::chr10:50817847..50817867,+p4@SLC18A3
Hg19::chr10:50818275..50818286,+p6@SLC18A3
Hg19::chr10:50818288..50818298,+p5@SLC18A3
Hg19::chr10:50818343..50818362,+p2@SLC18A3
Hg19::chr10:50818377..50818400,+p1@SLC18A3
Hg19::chr10:50818416..50818427,+p3@SLC18A3


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
extraembryonic cell2.46e-1819
placental epithelial cell5.11e-153
amniotic epithelial cell1.03e-092
amnion mesenchymal stem cell3.33e-095
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane1.73e-2514
membranous layer1.73e-2514
neural nucleus1.85e-229
nucleus of brain1.85e-229
brainstem3.42e-186
amnion2.30e-167
telencephalic nucleus7.79e-157
sympathetic nervous system1.63e-145
autonomic nervous system1.63e-145
ectoderm-derived structure1.86e-14171
ectoderm1.86e-14171
presumptive ectoderm1.86e-14171
somatic layer of lateral plate mesoderm2.77e-148
extraembryonic structure3.67e-1424
pons1.04e-133
posterior neural tube1.91e-1315
chordal neural plate1.91e-1315
neurectoderm1.92e-1386
nervous system1.76e-1289
basal ganglion1.72e-119
nuclear complex of neuraxis1.72e-119
aggregate regional part of brain1.72e-119
collection of basal ganglia1.72e-119
cerebral subcortex1.72e-119
placenta2.25e-114
allantois2.25e-114
chorion4.54e-117
locus ceruleus4.81e-102
brainstem nucleus4.81e-102
hindbrain nucleus4.81e-102
neural tube5.62e-1056
neural rod5.62e-1056
future spinal cord5.62e-1056
neural keel5.62e-1056
corpus striatum6.27e-104
striatum6.27e-104
ventral part of telencephalon6.27e-104
future corpus striatum6.27e-104
globus pallidus1.66e-092
pallidum1.66e-092
segmental subdivision of hindbrain5.73e-0912
hindbrain5.73e-0912
presumptive hindbrain5.73e-0912
central nervous system2.69e-0881
neural plate2.80e-0882
presumptive neural plate2.80e-0882
segmental subdivision of nervous system2.96e-0813
peripheral nervous system4.27e-088
organ part1.35e-07218
regional part of nervous system1.81e-0753
regional part of brain1.81e-0753
medulla oblongata7.17e-073
myelencephalon7.17e-073
future myelencephalon7.17e-073
spinal cord9.33e-073
dorsal region element9.33e-073
dorsum9.33e-073
Disease
Ontology termp-valuen
neuroectodermal tumor2.10e-2710
neuroendocrine tumor4.11e-126
germ cell and embryonal cancer9.43e-1222
germ cell cancer9.43e-1222


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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