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Coexpression cluster:C1710: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!6.40e-20!169;UBERON:0000925!6.40e-20!169;UBERON:0006595!6.40e-20!169;UBERON:0001007!1.27e-15!155;UBERON:0001555!1.27e-15!155;UBERON:0007026!1.27e-15!155;UBERON:0000924!2.22e-11!173;UBERON:0006601!2.22e-11!173;UBERON:0004921!3.22e-11!129;UBERON:0004185!3.22e-11!129;UBERON:0001004!1.20e-10!72;UBERON:0004121!4.10e-10!169;UBERON:0000077!8.07e-10!130;UBERON:0000062!2.14e-09!511;UBERON:0000481!2.16e-09!347;UBERON:0007023!2.40e-09!115;UBERON:0000922!6.60e-09!612;UBERON:0000468!7.91e-09!659;UBERON:0000161!2.58e-08!35;UBERON:0005631!2.87e-08!14;UBERON:0000158!2.87e-08!14;UBERON:0005153!9.79e-08!37;UBERON:0005181!1.18e-07!35;UBERON:0000153!1.23e-07!129;UBERON:0007811!1.23e-07!129;UBERON:0005911!1.53e-07!82;UBERON:0002050!1.76e-07!605;UBERON:0005423!1.76e-07!605;UBERON:0005178!2.68e-07!34;UBERON:0002224!2.68e-07!34;UBERON:0000165!2.79e-07!28;UBERON:0000930!2.79e-07!28;UBERON:0005157!3.44e-07!51;UBERON:0000923!3.45e-07!604;UBERON:0005291!3.45e-07!604;UBERON:0006598!3.45e-07!604;UBERON:0002532!3.45e-07!604;UBERON:0000166!3.74e-07!21;UBERON:0000033!3.94e-07!123;UBERON:0000475!6.17e-07!365
|ontology_enrichment_uberon=UBERON:0004119!6.40e-20!169;UBERON:0000925!6.40e-20!169;UBERON:0006595!6.40e-20!169;UBERON:0001007!1.27e-15!155;UBERON:0001555!1.27e-15!155;UBERON:0007026!1.27e-15!155;UBERON:0000924!2.22e-11!173;UBERON:0006601!2.22e-11!173;UBERON:0004921!3.22e-11!129;UBERON:0004185!3.22e-11!129;UBERON:0001004!1.20e-10!72;UBERON:0004121!4.10e-10!169;UBERON:0000077!8.07e-10!130;UBERON:0000062!2.14e-09!511;UBERON:0000481!2.16e-09!347;UBERON:0007023!2.40e-09!115;UBERON:0000922!6.60e-09!612;UBERON:0000468!7.91e-09!659;UBERON:0000161!2.58e-08!35;UBERON:0005631!2.87e-08!14;UBERON:0000158!2.87e-08!14;UBERON:0005153!9.79e-08!37;UBERON:0005181!1.18e-07!35;UBERON:0000153!1.23e-07!129;UBERON:0007811!1.23e-07!129;UBERON:0005911!1.53e-07!82;UBERON:0002050!1.76e-07!605;UBERON:0005423!1.76e-07!605;UBERON:0005178!2.68e-07!34;UBERON:0002224!2.68e-07!34;UBERON:0000165!2.79e-07!28;UBERON:0000930!2.79e-07!28;UBERON:0005157!3.44e-07!51;UBERON:0000923!3.45e-07!604;UBERON:0005291!3.45e-07!604;UBERON:0006598!3.45e-07!604;UBERON:0002532!3.45e-07!604;UBERON:0000166!3.74e-07!21;UBERON:0000033!3.94e-07!123;UBERON:0000475!6.17e-07!365
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249636866660103!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110760266191953!FOXA1#3169;5:11.0814197493855:5.98116883436141e-06:0.000178885249682666!GATA3#2625;5:27.236516357206:6.66232132211975e-08:4.05954595426409e-06!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229400605149419!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.1576523777395e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220322581962201!TRIM28#10155;5:18.5905250452625:4.49912775886781e-07:2.13486780558108e-05
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}}
}}

Revision as of 12:00, 5 September 2012


Full id: C1710_Placental_endometrial_amniotic_smallcell_leiomyoblastoma_pineal_malignant



Phase1 CAGE Peaks

Hg19::chr13:86373423..86373434,-p6@SLITRK6
Hg19::chr13:86373448..86373468,-p3@SLITRK6
Hg19::chr13:86373476..86373501,-p4@SLITRK6
Hg19::chr13:86373510..86373529,-p1@SLITRK6
Hg19::chr13:86373536..86373560,-p2@SLITRK6


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><br>

Cell Type
Ontology termp-valuen
endo-epithelial cell6.96e-1143
endodermal cell5.89e-0859
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.40e-20169
endoderm6.40e-20169
presumptive endoderm6.40e-20169
digestive system1.27e-15155
digestive tract1.27e-15155
primitive gut1.27e-15155
ectoderm2.22e-11173
presumptive ectoderm2.22e-11173
subdivision of digestive tract3.22e-11129
endodermal part of digestive tract3.22e-11129
respiratory system1.20e-1072
ectoderm-derived structure4.10e-10169
mixed endoderm/mesoderm-derived structure8.07e-10130
organ2.14e-09511
multi-tissue structure2.16e-09347
adult organism2.40e-09115
embryo6.60e-09612
multi-cellular organism7.91e-09659
orifice2.58e-0835
extraembryonic membrane2.87e-0814
membranous layer2.87e-0814
epithelial bud9.79e-0837
thoracic segment organ1.18e-0735
anterior region of body1.23e-07129
craniocervical region1.23e-07129
endo-epithelium1.53e-0782
embryonic structure1.76e-07605
developing anatomical structure1.76e-07605
thoracic cavity element2.68e-0734
thoracic cavity2.68e-0734
mouth2.79e-0728
stomodeum2.79e-0728
epithelial fold3.44e-0751
germ layer3.45e-07604
embryonic tissue3.45e-07604
presumptive structure3.45e-07604
epiblast (generic)3.45e-07604
oral opening3.74e-0721
head3.94e-07123
organism subdivision6.17e-07365


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
CTCF#1066455.360256373075030.0002259278299937090.00249636866660103
EP300#203356.77394172622327.00901578206049e-050.00110760266191953
FOXA1#3169511.08141974938555.98116883436141e-060.000178885249682666
GATA3#2625527.2365163572066.66232132211975e-084.05954595426409e-06
RAD21#5885510.35503389545638.39503550283973e-060.000229400605149419
SMC3#9126515.04493284493281.29633924985553e-065.1576523777395e-05
STAT3#6774510.51946499715427.759040745861e-060.000220322581962201
TRIM28#10155518.59052504526254.49912775886781e-072.13486780558108e-05



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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