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Coexpression cluster:C1432: Difference between revisions

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|full_id=C1432_mesenchymal_Smooth_Lymphatic_Preadipocyte_Sebocyte_CD14_anaplastic
|full_id=C1432_mesenchymal_Smooth_Lymphatic_Preadipocyte_Sebocyte_CD14_anaplastic
|id=C1432
|id=C1432
|ontology_enrichment_celltype=CL:0000680!4.76e-13!57;CL:0000056!4.76e-13!57;CL:0000355!4.76e-13!57;CL:0000222!1.14e-12!119;CL:0000359!1.90e-12!32;CL:0000187!1.88e-11!54;CL:0000192!3.22e-11!42;CL:0000514!3.22e-11!42;CL:0000183!3.11e-10!59;CL:0000220!4.42e-09!246;CL:0000393!4.53e-09!60;CL:0000211!4.53e-09!60;CL:0002321!1.03e-08!248;CL:0002139!5.09e-08!24;CL:0002539!5.15e-08!10;CL:0000115!9.90e-07!35
|ontology_enrichment_celltype=CL:0000359!3.43e-14!32;CL:0002539!7.90e-14!10;CL:0000680!5.32e-12!58;CL:0000056!5.32e-12!58;CL:0000355!5.32e-12!58;CL:0000192!2.48e-11!43;CL:0000514!2.48e-11!43;CL:0000187!1.50e-09!55;CL:0000183!1.72e-08!59;CL:0000393!5.10e-08!61;CL:0000211!5.10e-08!61;CL:0002321!2.03e-07!250
|ontology_enrichment_disease=DOID:2394!5.08e-07!14
|ontology_enrichment_disease=DOID:2394!9.06e-09!14
|ontology_enrichment_uberon=UBERON:0000055!7.99e-21!69;UBERON:0001637!9.61e-19!42;UBERON:0003509!9.61e-19!42;UBERON:0004572!9.61e-19!42;UBERON:0001981!1.63e-18!60;UBERON:0007500!1.63e-18!60;UBERON:0004537!1.63e-18!60;UBERON:0006965!1.63e-18!60;UBERON:0000486!4.15e-18!82;UBERON:0002049!1.19e-17!79;UBERON:0007798!1.19e-17!79;UBERON:0004872!4.47e-17!84;UBERON:0000119!8.98e-17!312;UBERON:0000483!1.20e-16!309;UBERON:0004573!1.42e-16!33;UBERON:0004571!1.42e-16!33;UBERON:0004290!3.08e-16!70;UBERON:0000914!4.06e-16!83;UBERON:0002329!4.06e-16!83;UBERON:0003077!4.06e-16!83;UBERON:0003059!4.06e-16!83;UBERON:0007282!4.06e-16!83;UBERON:0009618!4.06e-16!83;UBERON:0007285!4.06e-16!83;UBERON:0000467!3.71e-15!625;UBERON:0000480!5.74e-15!626;UBERON:0000923!4.88e-14!604;UBERON:0005291!4.88e-14!604;UBERON:0006598!4.88e-14!604;UBERON:0002532!4.88e-14!604;UBERON:0002050!7.43e-14!605;UBERON:0005423!7.43e-14!605;UBERON:0000468!8.13e-14!659;UBERON:0004111!2.48e-13!241;UBERON:0001009!2.57e-13!113;UBERON:0000922!3.07e-13!612;UBERON:0002385!7.12e-13!63;UBERON:0001015!7.12e-13!63;UBERON:0000383!7.12e-13!63;UBERON:0001134!1.12e-12!61;UBERON:0002036!1.12e-12!61;UBERON:0003082!1.12e-12!61;UBERON:0004535!1.78e-12!110;UBERON:0000477!9.54e-11!286;UBERON:0000025!1.40e-10!194;UBERON:0000481!1.55e-10!347;UBERON:0000490!4.84e-09!138;UBERON:0000947!5.82e-09!21;UBERON:0010191!5.82e-09!21;UBERON:0003914!6.91e-09!118;UBERON:0000475!1.12e-08!365;UBERON:0001135!3.04e-08!15;UBERON:0004237!5.15e-08!10;UBERON:0004695!5.15e-08!10;UBERON:0002111!5.15e-08!10;UBERON:0004178!5.15e-08!10;UBERON:0000926!1.19e-07!448;UBERON:0004120!1.19e-07!448;UBERON:0006603!1.19e-07!448;UBERON:0005256!1.38e-07!143;UBERON:0007023!1.91e-07!115
|ontology_enrichment_uberon=UBERON:0004573!1.20e-16!33;UBERON:0004571!1.20e-16!33;UBERON:0004237!7.90e-14!10;UBERON:0004695!7.90e-14!10;UBERON:0002111!7.90e-14!10;UBERON:0004178!7.90e-14!10;UBERON:0000486!2.02e-13!83;UBERON:0001637!5.34e-13!42;UBERON:0003509!5.34e-13!42;UBERON:0004572!5.34e-13!42;UBERON:0002329!1.99e-12!71;UBERON:0003059!1.99e-12!71;UBERON:0007282!1.99e-12!71;UBERON:0004290!1.99e-12!71;UBERON:0009618!1.99e-12!71;UBERON:0003077!3.89e-12!72;UBERON:0007285!3.89e-12!72;UBERON:0001135!5.09e-12!15;UBERON:0007524!7.43e-12!73;UBERON:0001134!7.79e-12!62;UBERON:0002036!7.79e-12!62;UBERON:0003082!7.79e-12!62;UBERON:0000055!2.62e-11!68;UBERON:0002385!3.14e-11!64;UBERON:0001015!3.14e-11!64;UBERON:0000383!3.14e-11!64;UBERON:0007503!1.45e-10!78;UBERON:0007500!2.09e-09!59;UBERON:0001981!2.09e-09!59;UBERON:0004537!2.09e-09!59;UBERON:0006965!2.09e-09!59;UBERON:0002049!6.89e-09!78;UBERON:0007798!6.89e-09!78;UBERON:0002118!9.30e-09!5;UBERON:0004872!1.97e-08!83;UBERON:0000947!8.39e-08!21;UBERON:0010191!8.39e-08!21;UBERON:0000992!1.05e-07!13;UBERON:0004535!9.49e-07!109
|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380255479471045!STAT3#6774;3:5.25973249857712:0.0137766205807855:0.0484727445620948!TCF7L2#6934;3:5.38508828156867:0.0129048877993104:0.0464093377250155
|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380255479471045!STAT3#6774;3:5.25973249857712:0.0137766205807855:0.0484727445620948!TCF7L2#6934;3:5.38508828156867:0.0129048877993104:0.0464093377250155
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}}
}}

Revision as of 11:16, 19 October 2012


Full id: C1432_mesenchymal_Smooth_Lymphatic_Preadipocyte_Sebocyte_CD14_anaplastic



Phase1 CAGE Peaks

Hg19::chr17:38171624..38171635,+p2@CSF3
Hg19::chr17:38171681..38171699,+p1@CSF3
Hg19::chr17:38171895..38171901,+p4@CSF3
Hg19::chr17:38172763..38172779,+p@chr17:38172763..38172779
+
Hg19::chr17:38172802..38172815,+p@chr17:38172802..38172815
+
Hg19::chr17:38173175..38173226,+p@chr17:38173175..38173226
+


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
systemic artery1.20e-1633
systemic arterial system1.20e-1633
blood vessel smooth muscle7.90e-1410
arterial system smooth muscle7.90e-1410
artery smooth muscle tissue7.90e-1410
aorta smooth muscle tissue7.90e-1410
multilaminar epithelium2.02e-1383
artery5.34e-1342
arterial blood vessel5.34e-1342
arterial system5.34e-1342
somite1.99e-1271
presomitic mesoderm1.99e-1271
presumptive segmental plate1.99e-1271
dermomyotome1.99e-1271
trunk paraxial mesoderm1.99e-1271
paraxial mesoderm3.89e-1272
presumptive paraxial mesoderm3.89e-1272
smooth muscle tissue5.09e-1215
dense mesenchyme tissue7.43e-1273
skeletal muscle tissue7.79e-1262
striated muscle tissue7.79e-1262
myotome7.79e-1262
vessel2.62e-1168
muscle tissue3.14e-1164
musculature3.14e-1164
musculature of body3.14e-1164
epithelial vesicle1.45e-1078
epithelial tube open at both ends2.09e-0959
blood vessel2.09e-0959
blood vasculature2.09e-0959
vascular cord2.09e-0959
vasculature6.89e-0978
vascular system6.89e-0978
right ovary9.30e-095
splanchnic layer of lateral plate mesoderm1.97e-0883
aorta8.39e-0821
aortic system8.39e-0821
female gonad1.05e-0713
cardiovascular system9.49e-07109
Disease
Ontology termp-valuen
ovarian cancer9.06e-0914


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
POLR2A#543062.147453176558070.01019570676818780.0380255479471045
STAT3#677435.259732498577120.01377662058078550.0484727445620948
TCF7L2#693435.385088281568670.01290488779931040.0464093377250155



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.