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Coexpression cluster:C1401: Difference between revisions

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|full_id=C1401_Smooth_Fibroblast_leiomyoma_malignant_Small_Skeletal_Preadipocyte
|full_id=C1401_Smooth_Fibroblast_leiomyoma_malignant_Small_Skeletal_Preadipocyte
|id=C1401
|id=C1401
|ontology_enrichment_celltype=CL:0000055!3.00e-10!180;CL:0000680!3.58e-09!57;CL:0000056!3.58e-09!57;CL:0000355!3.58e-09!57;CL:0000393!9.62e-09!60;CL:0000211!9.62e-09!60;CL:0000187!6.30e-08!54;CL:0000183!4.01e-07!59
|ontology_enrichment_celltype=CL:0000680!2.10e-15!58;CL:0000056!2.10e-15!58;CL:0000355!2.10e-15!58;CL:0000187!1.02e-12!55;CL:0000188!1.08e-12!9;CL:0000183!2.02e-12!59;CL:0002570!5.97e-11!8;CL:0000393!8.76e-11!61;CL:0000211!8.76e-11!61;CL:0000048!5.37e-09!427;CL:0000057!6.10e-09!76;CL:0000723!1.39e-08!433;CL:0000034!4.69e-08!441;CL:0002620!7.16e-08!23;CL:0000548!1.28e-07!679;CL:0000255!1.28e-07!679;CL:0002539!1.79e-07!10;CL:0000515!2.10e-07!4;CL:0000192!7.71e-07!43;CL:0000514!7.71e-07!43
|ontology_enrichment_disease=DOID:2394!2.05e-07!14
|ontology_enrichment_disease=DOID:2394!1.34e-15!14;DOID:120!2.99e-09!27;DOID:193!2.27e-08!29;DOID:0060072!5.51e-08!4;DOID:0060084!9.24e-07!3;DOID:127!9.24e-07!3
|ontology_enrichment_uberon=UBERON:0000914!3.34e-12!83;UBERON:0002329!3.34e-12!83;UBERON:0003077!3.34e-12!83;UBERON:0003059!3.34e-12!83;UBERON:0007282!3.34e-12!83;UBERON:0009618!3.34e-12!83;UBERON:0007285!3.34e-12!83;UBERON:0004290!9.37e-11!70;UBERON:0000486!6.75e-10!82;UBERON:0001017!5.45e-09!82;UBERON:0001049!3.16e-08!57;UBERON:0005068!3.16e-08!57;UBERON:0006241!3.16e-08!57;UBERON:0007135!3.16e-08!57;UBERON:0001134!4.15e-08!61;UBERON:0002036!4.15e-08!61;UBERON:0003082!4.15e-08!61;UBERON:0005743!4.37e-08!86;UBERON:0002385!6.09e-08!63;UBERON:0001015!6.09e-08!63;UBERON:0000383!6.09e-08!63;UBERON:0002020!1.17e-07!34;UBERON:0003528!1.17e-07!34;UBERON:0002780!1.26e-07!41;UBERON:0001890!1.26e-07!41;UBERON:0006240!1.26e-07!41;UBERON:0000955!1.32e-07!69;UBERON:0006238!1.32e-07!69;UBERON:0001893!1.39e-07!34;UBERON:0001869!1.51e-07!32;UBERON:0002616!1.55e-07!59;UBERON:0002791!3.13e-07!33;UBERON:0003080!5.13e-07!42
|ontology_enrichment_uberon=UBERON:0002329!9.31e-16!71;UBERON:0003059!9.31e-16!71;UBERON:0007282!9.31e-16!71;UBERON:0004290!9.31e-16!71;UBERON:0009618!9.31e-16!71;UBERON:0003077!2.07e-15!72;UBERON:0007285!2.07e-15!72;UBERON:0000486!2.43e-15!83;UBERON:0007524!4.51e-15!73;UBERON:0001134!6.87e-14!62;UBERON:0002036!6.87e-14!62;UBERON:0003082!6.87e-14!62;UBERON:0007503!1.61e-13!78;UBERON:0002385!3.31e-13!64;UBERON:0001015!3.31e-13!64;UBERON:0000383!3.31e-13!64;UBERON:0003100!2.28e-09!41;UBERON:0000992!2.53e-09!13;UBERON:0001135!3.60e-09!15;UBERON:0005256!7.45e-09!122;UBERON:0003134!2.03e-08!37;UBERON:0000474!2.03e-08!37;UBERON:0002118!3.96e-08!5;UBERON:0002119!6.24e-08!4;UBERON:0005156!1.42e-07!59;UBERON:0000990!1.42e-07!59;UBERON:0004237!1.79e-07!10;UBERON:0004695!1.79e-07!10;UBERON:0002111!1.79e-07!10;UBERON:0004178!1.79e-07!10;UBERON:0001013!1.89e-07!14;UBERON:0000490!5.77e-07!148
|tf_chipseq_enrich=EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.00026944248208358!FOS#2353;5:7.49829609074534:9.22669120642035e-05:0.00134322052259177!STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000766218156511574
|tf_chipseq_enrich=EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.00026944248208358!FOS#2353;5:7.49829609074534:9.22669120642035e-05:0.00134322052259177!STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000766218156511574
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}}
}}

Revision as of 11:14, 19 October 2012


Full id: C1401_Smooth_Fibroblast_leiomyoma_malignant_Small_Skeletal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr14:90863344..90863356,+p11@CALM3
p13@CALM1
p9@CALM2
Hg19::chr4:43341736..43341745,+p@chr4:43341736..43341745
+
Hg19::chr4:43341753..43341762,+p@chr4:43341753..43341762
+
Hg19::chr4:43341772..43341787,+p@chr4:43341772..43341787
+
Hg19::chr4:43341791..43341824,+p@chr4:43341791..43341824
+
Hg19::chr4:43341835..43341849,+p@chr4:43341835..43341849
+


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
somite9.31e-1671
presomitic mesoderm9.31e-1671
presumptive segmental plate9.31e-1671
dermomyotome9.31e-1671
trunk paraxial mesoderm9.31e-1671
paraxial mesoderm2.07e-1572
presumptive paraxial mesoderm2.07e-1572
multilaminar epithelium2.43e-1583
dense mesenchyme tissue4.51e-1573
skeletal muscle tissue6.87e-1462
striated muscle tissue6.87e-1462
myotome6.87e-1462
epithelial vesicle1.61e-1378
muscle tissue3.31e-1364
musculature3.31e-1364
musculature of body3.31e-1364
female organism2.28e-0941
female gonad2.53e-0913
smooth muscle tissue3.60e-0915
trunk mesenchyme7.45e-09122
female reproductive organ2.03e-0837
female reproductive system2.03e-0837
right ovary3.96e-085
left ovary6.24e-084
reproductive structure1.42e-0759
reproductive system1.42e-0759
blood vessel smooth muscle1.79e-0710
arterial system smooth muscle1.79e-0710
artery smooth muscle tissue1.79e-0710
aorta smooth muscle tissue1.79e-0710
adipose tissue1.89e-0714
unilaminar epithelium5.77e-07148
Disease
Ontology termp-valuen
ovarian cancer1.34e-1514
female reproductive organ cancer2.99e-0927
reproductive organ cancer2.27e-0829
benign neoplasm5.51e-084
cell type benign neoplasm9.24e-073
leiomyoma9.24e-073


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
EP300#203366.77394172622321.03454107484288e-050.00026944248208358
FOS#235357.498296090745349.22669120642035e-050.00134322052259177
STAT3#677458.766220830961874.28672496720299e-050.000766218156511574



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.