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Coexpression cluster:C3323: Difference between revisions

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|full_id=C3323_Smooth_Fibroblast_leiomyoma_teratocarcinoma_pagetoid_Chondrocyte_mesenchymal
|full_id=C3323_Smooth_Fibroblast_leiomyoma_teratocarcinoma_pagetoid_Chondrocyte_mesenchymal
|id=C3323
|id=C3323
|ontology_enrichment_celltype=CL:0000055!3.58e-46!180;CL:0000057!3.25e-21!75;CL:0000183!2.36e-17!59;CL:0000680!7.95e-16!57;CL:0000056!7.95e-16!57;CL:0000355!7.95e-16!57;CL:0000187!1.59e-15!54;CL:0000393!4.74e-14!60;CL:0000211!4.74e-14!60;CL:0000192!7.22e-12!42;CL:0000514!7.22e-12!42;CL:0002321!6.30e-11!248;CL:0002620!9.78e-11!23;CL:0000220!1.10e-10!246;CL:0000222!2.82e-10!119;CL:0000359!4.18e-08!32;CL:0000499!1.19e-07!27;CL:0000327!8.04e-07!14
|ontology_enrichment_celltype=CL:0000055!1.07e-21!106;CL:0000057!3.70e-20!76;CL:0000183!1.85e-17!59;CL:0000680!6.69e-16!58;CL:0000056!6.69e-16!58;CL:0000355!6.69e-16!58;CL:0000187!1.46e-15!55;CL:0000393!3.95e-14!61;CL:0000211!3.95e-14!61;CL:0000192!1.04e-11!43;CL:0000514!1.04e-11!43;CL:0002620!1.18e-10!23;CL:0002321!1.84e-10!250;CL:0000222!5.53e-10!121;CL:0000359!1.54e-07!32;CL:0000499!1.54e-07!28;CL:0000327!5.70e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!2.65e-17!83;UBERON:0002329!2.65e-17!83;UBERON:0003077!2.65e-17!83;UBERON:0003059!2.65e-17!83;UBERON:0007282!2.65e-17!83;UBERON:0009618!2.65e-17!83;UBERON:0007285!2.65e-17!83;UBERON:0000486!1.08e-16!82;UBERON:0004290!2.37e-16!70;UBERON:0001134!8.88e-16!61;UBERON:0002036!8.88e-16!61;UBERON:0003082!8.88e-16!61;UBERON:0005256!2.35e-15!143;UBERON:0002385!2.41e-15!63;UBERON:0001015!2.41e-15!63;UBERON:0000383!2.41e-15!63;UBERON:0000475!9.75e-14!365;UBERON:0000119!1.37e-12!312;UBERON:0000483!7.42e-12!309;UBERON:0000481!4.92e-11!347;UBERON:0002100!7.76e-11!216;UBERON:0004872!7.79e-11!84;UBERON:0000490!3.52e-10!138;UBERON:0003914!4.30e-10!118;UBERON:0002049!5.40e-10!79;UBERON:0007798!5.40e-10!79;UBERON:0000468!1.10e-09!659;UBERON:0003104!6.22e-09!238;UBERON:0009142!6.22e-09!238;UBERON:0001981!2.84e-08!60;UBERON:0007500!2.84e-08!60;UBERON:0004537!2.84e-08!60;UBERON:0006965!2.84e-08!60;UBERON:0001637!3.54e-08!42;UBERON:0003509!3.54e-08!42;UBERON:0004572!3.54e-08!42;UBERON:0000055!9.46e-08!69;UBERON:0002199!2.51e-07!45;UBERON:0002416!2.51e-07!45;UBERON:0003102!3.06e-07!95;UBERON:0003103!4.32e-07!69;UBERON:0004573!4.37e-07!33;UBERON:0004571!4.37e-07!33;UBERON:0002097!7.44e-07!40;UBERON:0000467!8.56e-07!625
|ontology_enrichment_uberon=UBERON:0007503!4.00e-18!78;UBERON:0000486!1.30e-17!83;UBERON:0007524!4.85e-17!73;UBERON:0002329!6.60e-17!71;UBERON:0003059!6.60e-17!71;UBERON:0007282!6.60e-17!71;UBERON:0004290!6.60e-17!71;UBERON:0009618!6.60e-17!71;UBERON:0003104!9.69e-17!160;UBERON:0009142!9.69e-17!160;UBERON:0003077!1.43e-16!72;UBERON:0007285!1.43e-16!72;UBERON:0001134!8.69e-16!62;UBERON:0002036!8.69e-16!62;UBERON:0003082!8.69e-16!62;UBERON:0002385!2.16e-15!64;UBERON:0001015!2.16e-15!64;UBERON:0000383!2.16e-15!64;UBERON:0000119!1.84e-13!309;UBERON:0005256!4.15e-13!122;UBERON:0000483!9.76e-13!306;UBERON:0000490!4.62e-11!148;UBERON:0000481!1.19e-10!342;UBERON:0000468!1.92e-10!656;UBERON:0000475!7.05e-10!264;UBERON:0004872!9.29e-10!83;UBERON:0002100!2.45e-09!199;UBERON:0003914!4.62e-09!117;UBERON:0002049!8.77e-09!78;UBERON:0007798!8.77e-09!78;UBERON:0002199!2.56e-08!46;UBERON:0002416!2.56e-08!46;UBERON:0002097!7.22e-08!41;UBERON:0000467!1.31e-07!624;UBERON:0001637!1.32e-07!42;UBERON:0003509!1.32e-07!42;UBERON:0004572!1.32e-07!42;UBERON:0000480!2.05e-07!625;UBERON:0007500!3.82e-07!59;UBERON:0001981!3.82e-07!59;UBERON:0004537!3.82e-07!59;UBERON:0006965!3.82e-07!59;UBERON:0000477!4.37e-07!373;UBERON:0003102!6.78e-07!99;UBERON:0000055!9.27e-07!68
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321020407862888!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000856446799809719!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109067364336318
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321020407862888!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000856446799809719!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109067364336318
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}}
}}

Revision as of 15:00, 19 October 2012


Full id: C3323_Smooth_Fibroblast_leiomyoma_teratocarcinoma_pagetoid_Chondrocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr12:6937349..6937370,+p3@LEPREL2
Hg19::chr12:6937377..6937394,+p2@LEPREL2
Hg19::chr12:6937402..6937414,+p4@LEPREL2


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>


Uber Anatomy
Ontology termp-valuen
epithelial vesicle4.00e-1878
multilaminar epithelium1.30e-1783
dense mesenchyme tissue4.85e-1773
somite6.60e-1771
presomitic mesoderm6.60e-1771
presumptive segmental plate6.60e-1771
dermomyotome6.60e-1771
trunk paraxial mesoderm6.60e-1771
mesenchyme9.69e-17160
entire embryonic mesenchyme9.69e-17160
paraxial mesoderm1.43e-1672
presumptive paraxial mesoderm1.43e-1672
skeletal muscle tissue8.69e-1662
striated muscle tissue8.69e-1662
myotome8.69e-1662
muscle tissue2.16e-1564
musculature2.16e-1564
musculature of body2.16e-1564
cell layer1.84e-13309
trunk mesenchyme4.15e-13122
epithelium9.76e-13306
unilaminar epithelium4.62e-11148
multi-tissue structure1.19e-10342
multi-cellular organism1.92e-10656
organism subdivision7.05e-10264
splanchnic layer of lateral plate mesoderm9.29e-1083
trunk2.45e-09199
epithelial tube4.62e-09117
vasculature8.77e-0978
vascular system8.77e-0978
integument2.56e-0846
integumental system2.56e-0846
skin of body7.22e-0841
anatomical system1.31e-07624
artery1.32e-0742
arterial blood vessel1.32e-0742
arterial system1.32e-0742
anatomical group2.05e-07625
epithelial tube open at both ends3.82e-0759
blood vessel3.82e-0759
blood vasculature3.82e-0759
vascular cord3.82e-0759
anatomical cluster4.37e-07373
surface structure6.78e-0799
vessel9.27e-0768


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
E2F6#187635.017155731697390.00791769806886330.0321020407862888
MAFK#7975327.10073313782995.02195559325033e-050.000856446799809719
ZNF263#1012738.221841637010680.001799043925565870.0109067364336318



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.