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|full_id=C1313_Placental_mesothelioma_amniotic_neuroectodermal_renal_chorionic_carcinosarcoma
|full_id=C1313_Placental_mesothelioma_amniotic_neuroectodermal_renal_chorionic_carcinosarcoma
|id=C1313
|id=C1313
|ontology_enrichment_celltype=CL:0000349!2.70e-08!3;CL:0002577!2.70e-08!3
|ontology_enrichment_disease=DOID:171!4.04e-14!10
|ontology_enrichment_uberon=UBERON:0005631!2.99e-18!14;UBERON:0000158!2.99e-18!14;UBERON:0002308!7.33e-15!9;UBERON:0000125!7.33e-15!9;UBERON:0002346!4.31e-14!90;UBERON:0000073!1.28e-13!94;UBERON:0001016!1.28e-13!94;UBERON:0001049!3.90e-13!57;UBERON:0005068!3.90e-13!57;UBERON:0006241!3.90e-13!57;UBERON:0007135!3.90e-13!57;UBERON:0000924!1.34e-12!173;UBERON:0006601!1.34e-12!173;UBERON:0003124!2.06e-11!7;UBERON:0007023!3.70e-11!115;UBERON:0005743!4.66e-11!86;UBERON:0002616!4.94e-11!59;UBERON:0001017!7.26e-11!82;UBERON:0009663!7.39e-11!7;UBERON:0000955!1.94e-10!69;UBERON:0006238!1.94e-10!69;UBERON:0003075!2.12e-10!86;UBERON:0007284!2.12e-10!86;UBERON:0001987!5.86e-10!4;UBERON:0004340!5.86e-10!4;UBERON:0004121!8.34e-10!169;UBERON:0002298!9.96e-10!8;UBERON:0000478!1.81e-09!24;UBERON:0000369!4.61e-09!4;UBERON:0002435!4.61e-09!4;UBERON:0000204!4.61e-09!4;UBERON:0010082!4.61e-09!4;UBERON:0000305!1.35e-08!7;UBERON:0003076!2.24e-08!15;UBERON:0003057!2.24e-08!15;UBERON:0002420!2.97e-08!9;UBERON:0007245!2.97e-08!9;UBERON:0010009!2.97e-08!9;UBERON:0010011!2.97e-08!9;UBERON:0000454!2.97e-08!9;UBERON:0000064!4.01e-08!219;UBERON:0000013!7.05e-08!5;UBERON:0002410!7.05e-08!5;UBERON:0000988!1.82e-07!3;UBERON:0001896!1.82e-07!3;UBERON:0005290!1.82e-07!3;UBERON:0010096!1.82e-07!3;UBERON:0004871!1.91e-07!8;UBERON:0002780!1.95e-07!41;UBERON:0001890!1.95e-07!41;UBERON:0006240!1.95e-07!41;UBERON:0005383!2.52e-07!3;UBERON:0005382!2.52e-07!3;UBERON:0003080!3.48e-07!42
}}
}}

Revision as of 14:09, 21 May 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 cell2.70e-083
placental epithelial cell2.70e-083
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane2.99e-1814
membranous layer2.99e-1814
nucleus of brain7.33e-159
neural nucleus7.33e-159
neurectoderm4.31e-1490
regional part of nervous system1.28e-1394
nervous system1.28e-1394
neural tube3.90e-1357
neural rod3.90e-1357
future spinal cord3.90e-1357
neural keel3.90e-1357
ectoderm1.34e-12173
presumptive ectoderm1.34e-12173
chorion2.06e-117
adult organism3.70e-11115
regional part of brain4.94e-1159
central nervous system7.26e-1182
telencephalic nucleus7.39e-117
brain1.94e-1069
future brain1.94e-1069
neural plate2.12e-1086
presumptive neural plate2.12e-1086
placenta5.86e-104
allantois5.86e-104
ectoderm-derived structure8.34e-10169
brainstem9.96e-108
extraembryonic structure1.81e-0924
corpus striatum4.61e-094
striatum4.61e-094
ventral part of telencephalon4.61e-094
future corpus striatum4.61e-094
amnion1.35e-087
posterior neural tube2.24e-0815
chordal neural plate2.24e-0815
basal ganglion2.97e-089
nuclear complex of neuraxis2.97e-089
aggregate regional part of brain2.97e-089
collection of basal ganglia2.97e-089
cerebral subcortex2.97e-089
organ part4.01e-08219
sympathetic nervous system7.05e-085
autonomic nervous system7.05e-085
pons1.82e-073
medulla oblongata1.82e-073
myelencephalon1.82e-073
future myelencephalon1.82e-073
somatic layer of lateral plate mesoderm1.91e-078
regional part of forebrain1.95e-0741
forebrain1.95e-0741
future forebrain1.95e-0741
caudate-putamen2.52e-073
dorsal striatum2.52e-073
anterior neural tube3.48e-0742
Disease
Ontology termp-valuen
neuroectodermal tumor4.04e-1410


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.