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Coexpression cluster:C4344: Difference between revisions

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|full_id=C4344_pleomorphic_Skeletal_Hodgkin_mesenchymal_Osteoblast_Chondrocyte_epithelioid
|full_id=C4344_pleomorphic_Skeletal_Hodgkin_mesenchymal_Osteoblast_Chondrocyte_epithelioid
|id=C4344
|id=C4344
|ontology_enrichment_celltype=CL:0000055!1.61e-33!180;CL:0000183!3.77e-17!59;CL:0000680!1.21e-16!57;CL:0000056!1.21e-16!57;CL:0000355!1.21e-16!57;CL:0000187!1.54e-16!54;CL:0000393!1.05e-14!60;CL:0000211!1.05e-14!60;CL:0000057!7.79e-13!75;CL:0000192!3.25e-12!42;CL:0000514!3.25e-12!42;CL:0000359!1.77e-09!32;CL:0002494!2.47e-08!16
|ontology_enrichment_celltype=CL:0000183!1.60e-18!59;CL:0000055!3.21e-18!106;CL:0000680!7.91e-17!58;CL:0000056!7.91e-17!58;CL:0000355!7.91e-17!58;CL:0000187!1.53e-16!55;CL:0000393!1.09e-14!61;CL:0000211!1.09e-14!61;CL:0000192!5.78e-12!43;CL:0000514!5.78e-12!43;CL:0000057!9.16e-11!76;CL:0002494!4.00e-10!16;CL:0000359!6.25e-10!32;CL:0000499!1.94e-07!28
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!9.11e-21!347;UBERON:0000475!3.71e-20!365;UBERON:0000914!3.96e-17!83;UBERON:0002329!3.96e-17!83;UBERON:0003077!3.96e-17!83;UBERON:0003059!3.96e-17!83;UBERON:0007282!3.96e-17!83;UBERON:0009618!3.96e-17!83;UBERON:0007285!3.96e-17!83;UBERON:0004290!9.72e-17!70;UBERON:0005256!1.48e-16!143;UBERON:0001134!1.58e-16!61;UBERON:0002036!1.58e-16!61;UBERON:0003082!1.58e-16!61;UBERON:0002385!2.62e-16!63;UBERON:0001015!2.62e-16!63;UBERON:0000383!2.62e-16!63;UBERON:0000119!5.21e-15!312;UBERON:0000483!2.10e-14!309;UBERON:0000486!5.89e-14!82;UBERON:0002100!6.07e-14!216;UBERON:0003104!3.99e-12!238;UBERON:0009142!3.99e-12!238;UBERON:0007100!6.27e-11!27;UBERON:0000948!9.86e-11!24;UBERON:0005498!9.86e-11!24;UBERON:0004140!9.86e-11!24;UBERON:0009881!9.86e-11!24;UBERON:0004141!9.86e-11!24;UBERON:0003084!9.86e-11!24;UBERON:0007005!9.86e-11!24;UBERON:0004139!9.86e-11!24;UBERON:0004291!9.86e-11!24;UBERON:0000477!1.14e-10!286;UBERON:0000490!2.04e-09!138;UBERON:0000468!5.10e-09!659;UBERON:0003103!1.26e-08!69;UBERON:0003914!4.13e-08!118;UBERON:0004111!5.83e-08!241;UBERON:0000922!3.02e-07!612;UBERON:0000025!5.19e-07!194;UBERON:0002050!6.80e-07!605;UBERON:0005423!6.80e-07!605;UBERON:0004872!9.27e-07!84;UBERON:0000467!9.40e-07!625;UBERON:0000480!9.90e-07!626
|ontology_enrichment_uberon=UBERON:0001134!2.15e-17!62;UBERON:0002036!2.15e-17!62;UBERON:0003082!2.15e-17!62;UBERON:0002385!9.01e-17!64;UBERON:0001015!9.01e-17!64;UBERON:0000383!9.01e-17!64;UBERON:0007524!1.06e-16!73;UBERON:0002329!2.71e-16!71;UBERON:0003059!2.71e-16!71;UBERON:0007282!2.71e-16!71;UBERON:0004290!2.71e-16!71;UBERON:0009618!2.71e-16!71;UBERON:0003077!2.83e-16!72;UBERON:0007285!2.83e-16!72;UBERON:0003104!3.17e-16!160;UBERON:0009142!3.17e-16!160;UBERON:0005256!1.19e-15!122;UBERON:0007503!1.24e-14!78;UBERON:0000481!3.55e-14!342;UBERON:0000486!2.64e-13!83;UBERON:0000119!1.49e-12!309;UBERON:0000483!6.77e-12!306;UBERON:0000948!8.61e-12!24;UBERON:0005498!8.61e-12!24;UBERON:0004140!8.61e-12!24;UBERON:0009881!8.61e-12!24;UBERON:0004141!8.61e-12!24;UBERON:0003084!8.61e-12!24;UBERON:0007005!8.61e-12!24;UBERON:0004139!8.61e-12!24;UBERON:0004291!8.61e-12!24;UBERON:0007100!4.47e-11!27;UBERON:0000490!4.75e-11!148;UBERON:0000477!8.93e-11!373;UBERON:0002100!2.83e-10!199;UBERON:0000475!4.83e-09!264;UBERON:0003914!8.24e-09!117;UBERON:0004872!1.74e-08!83;UBERON:0001009!6.33e-08!112;UBERON:0004535!6.55e-08!109;UBERON:0010314!3.14e-07!132;UBERON:0004573!3.23e-07!33;UBERON:0004571!3.23e-07!33;UBERON:0000025!8.99e-07!192
|tf_chipseq_enrich=MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295486560953353!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173428173884161!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330515541142353!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109768270457542
|tf_chipseq_enrich=MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295486560953353!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173428173884161!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330515541142353!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109768270457542
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}}
}}

Revision as of 15:52, 19 October 2012


Full id: C4344_pleomorphic_Skeletal_Hodgkin_mesenchymal_Osteoblast_Chondrocyte_epithelioid



Phase1 CAGE Peaks

Hg19::chr3:72937182..72937270,+p1@GXYLT2
Hg19::chr3:72937278..72937291,+p3@GXYLT2
Hg19::chr3:72937303..72937320,+p2@GXYLT2


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
skeletal muscle tissue2.15e-1762
striated muscle tissue2.15e-1762
myotome2.15e-1762
muscle tissue9.01e-1764
musculature9.01e-1764
musculature of body9.01e-1764
dense mesenchyme tissue1.06e-1673
somite2.71e-1671
presomitic mesoderm2.71e-1671
presumptive segmental plate2.71e-1671
dermomyotome2.71e-1671
trunk paraxial mesoderm2.71e-1671
paraxial mesoderm2.83e-1672
presumptive paraxial mesoderm2.83e-1672
mesenchyme3.17e-16160
entire embryonic mesenchyme3.17e-16160
trunk mesenchyme1.19e-15122
epithelial vesicle1.24e-1478
multi-tissue structure3.55e-14342
multilaminar epithelium2.64e-1383
cell layer1.49e-12309
epithelium6.77e-12306
heart8.61e-1224
primitive heart tube8.61e-1224
primary heart field8.61e-1224
anterior lateral plate mesoderm8.61e-1224
heart tube8.61e-1224
heart primordium8.61e-1224
cardiac mesoderm8.61e-1224
cardiogenic plate8.61e-1224
heart rudiment8.61e-1224
primary circulatory organ4.47e-1127
unilaminar epithelium4.75e-11148
anatomical cluster8.93e-11373
trunk2.83e-10199
organism subdivision4.83e-09264
epithelial tube8.24e-09117
splanchnic layer of lateral plate mesoderm1.74e-0883
circulatory system6.33e-08112
cardiovascular system6.55e-08109
structure with developmental contribution from neural crest3.14e-07132
systemic artery3.23e-0733
systemic arterial system3.23e-0733
tube8.99e-07192


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
MYC#460935.22228187160940.007020843755740150.0295486560953353
PAX5#507936.669565531177830.003370290999677260.0173428173884161
YY1#752834.911170749853860.008441455341808260.0330515541142353
ZNF263#1012738.221841637010680.001799043925565870.0109768270457542



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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