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Coexpression cluster:C295: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002204!6.91e-18!167;UBERON:0000486!7.87e-18!83;UBERON:0001134!6.28e-17!62;UBERON:0002036!6.28e-17!62;UBERON:0003082!6.28e-17!62;UBERON:0002329!8.47e-16!71;UBERON:0003059!8.47e-16!71;UBERON:0007282!8.47e-16!71;UBERON:0004290!8.47e-16!71;UBERON:0009618!8.47e-16!71;UBERON:0002385!1.04e-15!64;UBERON:0001015!1.04e-15!64;UBERON:0000383!1.04e-15!64;UBERON:0007524!1.58e-15!73;UBERON:0003077!2.93e-15!72;UBERON:0007285!2.93e-15!72;UBERON:0000926!4.37e-15!315;UBERON:0004120!4.37e-15!315;UBERON:0006603!4.37e-15!315;UBERON:0007503!1.85e-14!78;UBERON:0005256!2.12e-12!122;UBERON:0001637!1.30e-10!42;UBERON:0003509!1.30e-10!42;UBERON:0004572!1.30e-10!42;UBERON:0003104!1.46e-10!160;UBERON:0009142!1.46e-10!160;UBERON:0004573!3.28e-10!33;UBERON:0004571!3.28e-10!33;UBERON:0002384!1.70e-09!371;UBERON:0002100!2.49e-09!199;UBERON:0000490!5.49e-09!148;UBERON:0000468!2.85e-08!656;UBERON:0000475!5.72e-08!264;UBERON:0003081!1.07e-07!203;UBERON:0000467!2.08e-07!624;UBERON:0000480!2.80e-07!625;UBERON:0004872!5.59e-07!83;UBERON:0000479!6.33e-07!773
|ontology_enrichment_uberon=UBERON:0002204!6.91e-18!167;UBERON:0000486!7.87e-18!83;UBERON:0001134!6.28e-17!62;UBERON:0002036!6.28e-17!62;UBERON:0003082!6.28e-17!62;UBERON:0002329!8.47e-16!71;UBERON:0003059!8.47e-16!71;UBERON:0007282!8.47e-16!71;UBERON:0004290!8.47e-16!71;UBERON:0009618!8.47e-16!71;UBERON:0002385!1.04e-15!64;UBERON:0001015!1.04e-15!64;UBERON:0000383!1.04e-15!64;UBERON:0007524!1.58e-15!73;UBERON:0003077!2.93e-15!72;UBERON:0007285!2.93e-15!72;UBERON:0000926!4.37e-15!315;UBERON:0004120!4.37e-15!315;UBERON:0006603!4.37e-15!315;UBERON:0007503!1.85e-14!78;UBERON:0005256!2.12e-12!122;UBERON:0001637!1.30e-10!42;UBERON:0003509!1.30e-10!42;UBERON:0004572!1.30e-10!42;UBERON:0003104!1.46e-10!160;UBERON:0009142!1.46e-10!160;UBERON:0004573!3.28e-10!33;UBERON:0004571!3.28e-10!33;UBERON:0002384!1.70e-09!371;UBERON:0002100!2.49e-09!199;UBERON:0000490!5.49e-09!148;UBERON:0000468!2.85e-08!656;UBERON:0000475!5.72e-08!264;UBERON:0003081!1.07e-07!203;UBERON:0000467!2.08e-07!624;UBERON:0000480!2.80e-07!625;UBERON:0004872!5.59e-07!83;UBERON:0000479!6.33e-07!773
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842e-13,0.0698014,3.52458e-06,7.1184e-05,0.17881,0.987439,0.0117747,0.00571722,3.97477e-07,0.74589,0.602865,0.0245607,2.06621e-12,0.280355,0.868024,0.918756,1.01578e-05,0.000478228,0.712744,0.0436101,0.013076,0.25984,0.279385,6.57512e-06,0.101681,0.0392931,0.0127447,2.90032e-13,0.0243154,0.00117787,0.476142,0.493195,0.755429,0.000836944,0.165278,0.428189,0.764167,0.368842,3.35601e-07,0.506332,0.916207,0.0419446,0.652612,0.300955,0.782693,0.0118284,0.302189,0.0389308,0.862258,0.129917,6.76321e-11,4.3825e-05
|tfbs_overrepresentation_for_novel_motifs=0.0819678,0.552203,0.0771632,1.64462,1.44445,1.16517,0.0822671,1.94418,1.5607,0.355207,0.167007,0.1018,0.320428,0.267003,1.84229,0.0650927,0.584546,2.22266,0.228837,1.64376,0.198198,0.355219,0.0505631,0.0503835,1.15761,0.112829,0.551263,0.186662,0.0111052,0.0601642,0.0371597,0.225942,0.893123,1.48113,0.0368643,1.39091,0.00662732,0.0535421,1.75243,0.15016,0.0362878,0.132827,0.149896,3.83011,0.119613,0.0226632,0.281761,0.0402706,0.505159,0.300024,0.381461,0.0878499,0.556715,0.764443,0.395448,0.0786547,1.91219,0.0656157,1.35483,0.0652342,0.253821,0.0837482,0.488857,0.184561,0.0916505,0.163857,0.467759,0.795125,1.17261,0.646807,0.291014,1.00624,0.000562928,0.39385,0.00434601,0.157335,1.15077,0.995643,1.81872,3.0642,2.36683,0.1839,0.633561,0.0119849,0.353377,3.53851e-05,0.115833,1.58884,0.133659,0.888194,0.547349,0.332662,0.237235,3.30232,0.145317,1.69985,0.22496,0.266743,0.422911,0.0823536,0.0272664,0.233414,0.26281,0.204284,0.157159,0.0421223,0.194232,0.263017,0.495262,0.00882274,0.0845165,0.260865,0.372288,0.176012,1.26237,1.18878,0.00347016,0.145905,0.488841,1.99457,0.38725,0.132357,0.193841,0.0966312,0.602275,0.174728,0.0795824,0.240631,0.42154,0.739349,0.333187,1.38993,1.93786,1.08365,0.558549,0.00016068,0.940149,3.96775,0.521838,1.32718,0.937823,0.49003,0.578841,0.264254,0.158173,0.224168,0.88966,1.17173,5.36125,0.0198308,0.143423,4.08729e-05,0.333478,0.45385,1.48904,0.674386,0.125088,0.458312,0.265771,0.0884499,0.489002,0.85563,0.216412,0.432698,0.5014,0.631854,1.1304,0.278899,0.609765
}}
}}

Revision as of 14:04, 26 November 2012


Full id: C295_Fibroblast_Smooth_Myoblast_Chondrocyte_hepatic_Synoviocyte_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr5:135364668..135364689,+p1@TGFBI
Hg19::chr5:135369443..135369509,+p@chr5:135369443..135369509
+
Hg19::chr5:135369523..135369555,-p@chr5:135369523..135369555
-
Hg19::chr5:135379776..135379798,-p@chr5:135379776..135379798
-
Hg19::chr5:135382010..135382029,+p11@TGFBI
Hg19::chr5:135382052..135382068,+p2@TGFBI
Hg19::chr5:135382086..135382142,-p@chr5:135382086..135382142
-
Hg19::chr5:135382108..135382117,+p15@TGFBI
Hg19::chr5:135382120..135382141,+p4@TGFBI
Hg19::chr5:135382143..135382154,-p@chr5:135382143..135382154
-
Hg19::chr5:135382532..135382588,+p6@TGFBI
Hg19::chr5:135382596..135382676,+p3@TGFBI
Hg19::chr5:135382629..135382709,-p@chr5:135382629..135382709
-
Hg19::chr5:135382957..135382978,+p12@TGFBI
Hg19::chr5:135382982..135383001,-p@chr5:135382982..135383001
-
Hg19::chr5:135382984..135383005,+p14@TGFBI
Hg19::chr5:135383003..135383023,-p@chr5:135383003..135383023
-
Hg19::chr5:135383008..135383051,+p5@TGFBI
Hg19::chr5:135383053..135383075,-p@chr5:135383053..135383075
-
Hg19::chr5:135383091..135383114,-p@chr5:135383091..135383114
-
Hg19::chr5:135385116..135385139,+p9@TGFBI
Hg19::chr5:135385158..135385200,+p7@TGFBI
Hg19::chr5:135385167..135385196,-p@chr5:135385167..135385196
-
Hg19::chr5:135385202..135385212,+p21@TGFBI
Hg19::chr5:135385225..135385241,+p@chr5:135385225..135385241
+
Hg19::chr5:135385228..135385240,-p@chr5:135385228..135385240
-
Hg19::chr5:135388647..135388663,+p@chr5:135388647..135388663
+
Hg19::chr5:135388658..135388689,-p@chr5:135388658..135388689
-
Hg19::chr5:135388671..135388713,+p@chr5:135388671..135388713
+
Hg19::chr5:135388720..135388737,+p@chr5:135388720..135388737
+
Hg19::chr5:135388749..135388800,-p@chr5:135388749..135388800
-
Hg19::chr5:135388762..135388777,+p@chr5:135388762..135388777
+
Hg19::chr5:135389696..135389715,+p@chr5:135389696..135389715
+
Hg19::chr5:135389720..135389746,+p@chr5:135389720..135389746
+
Hg19::chr5:135391432..135391456,+p18@TGFBI
Hg19::chr5:135392372..135392421,+p@chr5:135392372..135392421
+
Hg19::chr5:135394834..135394855,-p@chr5:135394834..135394855
-
Hg19::chr5:135394840..135394872,+p10@TGFBI
Hg19::chr5:135397204..135397221,+p13@TGFBI
Hg19::chr5:135398892..135398970,+p@chr5:135398892..135398970
+
Hg19::chr5:135398904..135398952,-p1@CU674033
p1@CU678833
Hg19::chr5:135399064..135399095,-p2@CU674033
p2@CU678833
Hg19::chr5:135399376..135399482,+p@chr5:135399376..135399482
+


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

GO IDGO nameFDR corrected p-value
GO:0007162negative regulation of cell adhesion0.013879076886848
GO:0005178integrin binding0.013879076886848
GO:0030155regulation of cell adhesion0.0148946190980808
GO:0032403protein complex binding0.0170949605557518
GO:0050953sensory perception of light stimulus0.0251628792338789
GO:0007601visual perception0.0251628792338789
GO:0005578proteinaceous extracellular matrix0.0407184067551429
GO:0005615extracellular space0.0446838572942423
GO:0008283cell proliferation0.0499959242453061
GO:0044421extracellular region part0.0499959242453061
GO:0007600sensory perception0.0499959242453061
GO:0022610biological adhesion0.0499959242453061
GO:0007155cell adhesion0.0499959242453061



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
musculoskeletal system6.91e-18167
multilaminar epithelium7.87e-1883
skeletal muscle tissue6.28e-1762
striated muscle tissue6.28e-1762
myotome6.28e-1762
somite8.47e-1671
presomitic mesoderm8.47e-1671
presumptive segmental plate8.47e-1671
dermomyotome8.47e-1671
trunk paraxial mesoderm8.47e-1671
muscle tissue1.04e-1564
musculature1.04e-1564
musculature of body1.04e-1564
dense mesenchyme tissue1.58e-1573
paraxial mesoderm2.93e-1572
presumptive paraxial mesoderm2.93e-1572
mesoderm4.37e-15315
mesoderm-derived structure4.37e-15315
presumptive mesoderm4.37e-15315
epithelial vesicle1.85e-1478
trunk mesenchyme2.12e-12122
artery1.30e-1042
arterial blood vessel1.30e-1042
arterial system1.30e-1042
mesenchyme1.46e-10160
entire embryonic mesenchyme1.46e-10160
systemic artery3.28e-1033
systemic arterial system3.28e-1033
connective tissue1.70e-09371
trunk2.49e-09199
unilaminar epithelium5.49e-09148
multi-cellular organism2.85e-08656
organism subdivision5.72e-08264
lateral plate mesoderm1.07e-07203
anatomical system2.08e-07624
anatomical group2.80e-07625
splanchnic layer of lateral plate mesoderm5.59e-0783
tissue6.33e-07773


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

No analysis results for this cluster

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

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