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Coexpression cluster:C4232: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0005179!hormone activity!0.0191628399858707!11172$GO:0005102!receptor binding!0.0457877075238432!11172
|gostat_on_coexpression_clusters=GO:0005179!hormone activity!0.0191628399858707!11172$GO:0005102!receptor binding!0.0457877075238432!11172
|id=C4232
|id=C4232
|ontology_enrichment_celltype=CL:0000039!4.00e-28!7;CL:0000586!4.00e-28!7;CL:0002541!3.12e-17!3
|ontology_enrichment_celltype=CL:0002541!2.47e-31!3;CL:0000039!2.32e-24!7;CL:0000586!2.32e-24!7
|ontology_enrichment_disease=DOID:3095!1.46e-08!22;DOID:2994!1.46e-08!22;DOID:1036!5.74e-07!8;DOID:2355!6.60e-07!1
|ontology_enrichment_disease=DOID:1036!1.27e-12!8;DOID:2355!1.32e-11!1;DOID:3095!6.54e-08!22;DOID:2994!6.54e-08!22;DOID:2531!4.82e-07!51;DOID:0060083!4.82e-07!51
|ontology_enrichment_uberon=UBERON:0000473!4.98e-25!8;UBERON:0003135!3.11e-24!11;UBERON:0000476!3.12e-17!3;UBERON:0000920!3.12e-17!3;UBERON:0003101!5.47e-15!22;UBERON:0000079!5.47e-15!22;UBERON:0003124!5.10e-13!7;UBERON:0005631!1.02e-09!14;UBERON:0000158!1.02e-09!14;UBERON:0000991!3.60e-09!21;UBERON:0009196!3.60e-09!21;UBERON:0009117!3.60e-09!21;UBERON:0005564!3.60e-09!21;UBERON:0004176!1.00e-08!22;UBERON:0000988!8.04e-08!3;UBERON:0001301!9.79e-07!1
|ontology_enrichment_uberon=UBERON:0000473!5.66e-33!8;UBERON:0000476!2.47e-31!3;UBERON:0000920!2.47e-31!3;UBERON:0003135!5.38e-24!11;UBERON:0003124!6.84e-24!7;UBERON:0000991!1.50e-12!21;UBERON:0009196!1.50e-12!21;UBERON:0009117!1.50e-12!21;UBERON:0005564!1.50e-12!21;UBERON:0005631!4.29e-12!14;UBERON:0000158!4.29e-12!14;UBERON:0004176!5.62e-12!22;UBERON:0003101!5.62e-12!22;UBERON:0000079!5.62e-12!22;UBERON:0003133!1.47e-07!48;UBERON:0000478!3.91e-07!24
|tf_chipseq_enrich=CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306887543968386
|tf_chipseq_enrich=CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306887543968386
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}}
}}

Revision as of 15:46, 19 October 2012


Full id: C4232_choriocarcinoma_testis_adult_chronic_placenta_testicular_chorionic



Phase1 CAGE Peaks

Hg19::chr2:46656215..46656234,-p@chr2:46656215..46656234
-
Hg19::chr2:46656302..46656326,+p1@LOC388946
Hg19::chr9:5185629..5185643,-p1@INSL6


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


GO IDGO nameFDR corrected p-value
GO:0005179hormone activity0.0191628399858707
GO:0005102receptor binding0.0457877075238432



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
chorionic membrane mesenchymal stem cell2.47e-313
germ line cell2.32e-247
germ cell2.32e-247
Uber Anatomy
Ontology termp-valuen
testis5.66e-338
acellular anatomical structure2.47e-313
egg chorion2.47e-313
male reproductive organ5.38e-2411
chorion6.84e-247
gonad1.50e-1221
indifferent external genitalia1.50e-1221
indifferent gonad1.50e-1221
gonad primordium1.50e-1221
extraembryonic membrane4.29e-1214
membranous layer4.29e-1214
external genitalia5.62e-1222
male organism5.62e-1222
male reproductive system5.62e-1222
reproductive organ1.47e-0748
extraembryonic structure3.91e-0724
Disease
Ontology termp-valuen
chronic leukemia1.27e-128
anemia1.32e-111
germ cell and embryonal cancer6.54e-0822
germ cell cancer6.54e-0822
hematologic cancer4.82e-0751
immune system cancer4.82e-0751


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCFL#140690213.16431623931620.007433367036996010.0306887543968386



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.