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|full_id=C4538_breast_placenta_malignant_choriocarcinoma_Sebocyte_glassy_lung
|full_id=C4538_breast_placenta_malignant_choriocarcinoma_Sebocyte_glassy_lung
|id=C4538
|id=C4538
|ontology_enrichment_celltype=CL:0000066!7.20e-38!254;CL:0002076!7.26e-15!43;CL:0002159!3.74e-13!13;CL:0000223!2.63e-10!59;CL:0002077!5.48e-09!33;CL:0000076!9.57e-09!62;CL:0000240!1.68e-08!6;CL:0000311!1.68e-08!6;CL:0000079!1.68e-08!6;CL:0000237!1.68e-08!6;CL:0000036!1.68e-08!6;CL:0000357!1.68e-08!6;CL:0000114!1.68e-08!6;CL:0002368!1.74e-08!13;CL:0000362!2.37e-08!8;CL:0000312!2.25e-07!5;CL:0002251!9.66e-07!21
|ontology_enrichment_disease=DOID:305!1.01e-22!106;DOID:0050687!1.07e-16!143;DOID:1749!1.41e-12!14;DOID:162!6.87e-07!235
|ontology_enrichment_uberon=UBERON:0001004!1.23e-24!72;UBERON:0000065!8.39e-18!53;UBERON:0004119!6.08e-15!169;UBERON:0000925!6.08e-15!169;UBERON:0006595!6.08e-15!169;UBERON:0000072!1.08e-14!46;UBERON:0008947!3.63e-14!38;UBERON:0003258!3.63e-14!38;UBERON:0000161!4.64e-12!35;UBERON:0000077!1.08e-11!130;UBERON:0000464!5.36e-11!104;UBERON:0000166!1.01e-10!21;UBERON:0005631!1.83e-10!14;UBERON:0000158!1.83e-10!14;UBERON:0001008!6.91e-10!45;UBERON:0005153!1.36e-09!37;UBERON:0001007!1.50e-09!155;UBERON:0001555!1.50e-09!155;UBERON:0007026!1.50e-09!155;UBERON:0001041!1.93e-09!98;UBERON:0006554!2.12e-09!44;UBERON:0004175!2.86e-09!25;UBERON:0000165!5.17e-09!28;UBERON:0000930!5.17e-09!28;UBERON:0001557!7.00e-09!19;UBERON:0004921!1.46e-08!129;UBERON:0004185!1.46e-08!129;UBERON:0001737!1.88e-08!9;UBERON:0005178!2.17e-08!34;UBERON:0002224!2.17e-08!34;UBERON:0005156!2.59e-08!59;UBERON:0000990!2.59e-08!59;UBERON:0005181!5.52e-08!35;UBERON:0003124!6.02e-08!7;UBERON:0003100!1.05e-07!41;UBERON:0005157!1.17e-07!51;UBERON:0000064!1.19e-07!219;UBERON:0003133!1.81e-07!48;UBERON:0000466!1.96e-07!126;UBERON:0001044!4.74e-07!6;UBERON:0003293!4.74e-07!6;UBERON:0003294!4.74e-07!6;UBERON:0010047!4.74e-07!6;UBERON:0000167!4.74e-07!6;UBERON:0000915!5.23e-07!52;UBERON:0005795!5.99e-07!22;UBERON:0003975!6.13e-07!22;UBERON:0004807!7.80e-07!28
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Revision as of 14:49, 21 May 2012


Full id: C4538_breast_placenta_malignant_choriocarcinoma_Sebocyte_glassy_lung



Phase1 CAGE Peaks

Hg19::chr6:10419750..10419757,-p30@TFAP2A
Hg19::chr6:10419768..10419819,-p6@TFAP2A
Hg19::chr6:10419824..10419840,-p9@TFAP2A


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>


Uber Anatomy
Ontology termp-valuen
respiratory system1.23e-2472
respiratory tract8.39e-1853
endoderm-derived structure6.08e-15169
endoderm6.08e-15169
presumptive endoderm6.08e-15169
segment of respiratory tract1.08e-1446
respiratory primordium3.63e-1438
endoderm of foregut3.63e-1438
orifice4.64e-1235
mixed endoderm/mesoderm-derived structure1.08e-11130
anatomical space5.36e-11104
oral opening1.01e-1021
extraembryonic membrane1.83e-1014
membranous layer1.83e-1014
renal system6.91e-1045
epithelial bud1.36e-0937
digestive system1.50e-09155
digestive tract1.50e-09155
primitive gut1.50e-09155
foregut1.93e-0998
urinary system structure2.12e-0944
internal genitalia2.86e-0925
mouth5.17e-0928
stomodeum5.17e-0928
upper respiratory tract7.00e-0919
subdivision of digestive tract1.46e-08129
endodermal part of digestive tract1.46e-08129
larynx1.88e-089
thoracic cavity element2.17e-0834
thoracic cavity2.17e-0834
reproductive structure2.59e-0859
reproductive system2.59e-0859
thoracic segment organ5.52e-0835
chorion6.02e-087
female organism1.05e-0741
epithelial fold1.17e-0751
organ part1.19e-07219
reproductive organ1.81e-0748
immaterial anatomical entity1.96e-07126
saliva-secreting gland4.74e-076
gland of oral region4.74e-076
gland of foregut4.74e-076
oral gland4.74e-076
oral cavity4.74e-076
thoracic segment of trunk5.23e-0752
embryonic uterus5.99e-0722
internal female genitalia6.13e-0722
respiratory system epithelium7.80e-0728
Disease
Ontology termp-valuen
carcinoma1.01e-22106
cell type cancer1.07e-16143
squamous cell carcinoma1.41e-1214
cancer6.87e-07235


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.