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Coexpression cluster:C288: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004872!1.37e-23!83;UBERON:0002049!2.95e-22!78;UBERON:0007798!2.95e-22!78;UBERON:0001009!1.12e-20!112;UBERON:0000055!1.43e-20!68;UBERON:0007500!3.59e-20!59;UBERON:0001981!3.59e-20!59;UBERON:0004537!3.59e-20!59;UBERON:0006965!3.59e-20!59;UBERON:0004535!8.47e-20!109;UBERON:0001637!2.39e-19!42;UBERON:0003509!2.39e-19!42;UBERON:0004572!2.39e-19!42;UBERON:0004573!1.07e-15!33;UBERON:0004571!1.07e-15!33;UBERON:0003914!1.33e-15!117;UBERON:0002385!3.86e-13!64;UBERON:0001015!3.86e-13!64;UBERON:0000383!3.86e-13!64;UBERON:0001134!6.21e-13!62;UBERON:0002036!6.21e-13!62;UBERON:0003082!6.21e-13!62;UBERON:0007524!2.69e-11!73;UBERON:0007100!3.89e-11!27;UBERON:0007503!4.98e-11!78;UBERON:0003077!8.24e-11!72;UBERON:0007285!8.24e-11!72;UBERON:0004111!8.88e-11!240;UBERON:0002329!1.24e-10!71;UBERON:0003059!1.24e-10!71;UBERON:0007282!1.24e-10!71;UBERON:0004290!1.24e-10!71;UBERON:0009618!1.24e-10!71;UBERON:0000948!2.41e-10!24;UBERON:0005498!2.41e-10!24;UBERON:0004140!2.41e-10!24;UBERON:0009881!2.41e-10!24;UBERON:0004141!2.41e-10!24;UBERON:0003084!2.41e-10!24;UBERON:0007005!2.41e-10!24;UBERON:0004139!2.41e-10!24;UBERON:0004291!2.41e-10!24;UBERON:0000025!2.76e-10!192;UBERON:0000947!1.57e-09!21;UBERON:0010191!1.57e-09!21;UBERON:0000486!3.15e-08!83;UBERON:0003104!5.06e-08!160;UBERON:0009142!5.06e-08!160;UBERON:0005256!6.09e-08!122;UBERON:0000119!9.92e-08!309;UBERON:0000490!3.91e-07!148;UBERON:0000477!4.20e-07!373;UBERON:0000483!5.75e-07!306
|ontology_enrichment_uberon=UBERON:0004872!1.37e-23!83;UBERON:0002049!2.95e-22!78;UBERON:0007798!2.95e-22!78;UBERON:0001009!1.12e-20!112;UBERON:0000055!1.43e-20!68;UBERON:0007500!3.59e-20!59;UBERON:0001981!3.59e-20!59;UBERON:0004537!3.59e-20!59;UBERON:0006965!3.59e-20!59;UBERON:0004535!8.47e-20!109;UBERON:0001637!2.39e-19!42;UBERON:0003509!2.39e-19!42;UBERON:0004572!2.39e-19!42;UBERON:0004573!1.07e-15!33;UBERON:0004571!1.07e-15!33;UBERON:0003914!1.33e-15!117;UBERON:0002385!3.86e-13!64;UBERON:0001015!3.86e-13!64;UBERON:0000383!3.86e-13!64;UBERON:0001134!6.21e-13!62;UBERON:0002036!6.21e-13!62;UBERON:0003082!6.21e-13!62;UBERON:0007524!2.69e-11!73;UBERON:0007100!3.89e-11!27;UBERON:0007503!4.98e-11!78;UBERON:0003077!8.24e-11!72;UBERON:0007285!8.24e-11!72;UBERON:0004111!8.88e-11!240;UBERON:0002329!1.24e-10!71;UBERON:0003059!1.24e-10!71;UBERON:0007282!1.24e-10!71;UBERON:0004290!1.24e-10!71;UBERON:0009618!1.24e-10!71;UBERON:0000948!2.41e-10!24;UBERON:0005498!2.41e-10!24;UBERON:0004140!2.41e-10!24;UBERON:0009881!2.41e-10!24;UBERON:0004141!2.41e-10!24;UBERON:0003084!2.41e-10!24;UBERON:0007005!2.41e-10!24;UBERON:0004139!2.41e-10!24;UBERON:0004291!2.41e-10!24;UBERON:0000025!2.76e-10!192;UBERON:0000947!1.57e-09!21;UBERON:0010191!1.57e-09!21;UBERON:0000486!3.15e-08!83;UBERON:0003104!5.06e-08!160;UBERON:0009142!5.06e-08!160;UBERON:0005256!6.09e-08!122;UBERON:0000119!9.92e-08!309;UBERON:0000490!3.91e-07!148;UBERON:0000477!4.20e-07!373;UBERON:0000483!5.75e-07!306
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59066e-09,0.770935,0.0190757,0.0169194,0.678034,6.36729e-14,0.740157,0.996707,0.536578,0.00527163,0.00129042,0.669282,0.052053,0.797586,0.00555874,0.78582,0.923211,0.973867,0.987365,1.58742e-07,0.99075
|tfbs_overrepresentation_for_novel_motifs=0.187734,2.92497,1.22809,0.0482979,0.127862,0.0477764,2.53978,1.80574,0.631287,1.17757,0.0387673,0.093817,0.27968,0.90421,0.00884225,0.523756,0.557188,1.68783,3.35225,4.1674,0.0679789,3.84161,0.692796,0.0434843,0.740332,1.68402,2.03416,1.50405,0.00933964,4.1103,0.572243,0.613044,2.1502,2.75662,0.568643,0.0578036,0.00544639,0.048143,0.969575,1.27968,0.0308254,1.22057,0.496642,0.987991,2.88851,1.01671,0.0756589,0.0357945,0.153161,0.466455,0.111246,0.978976,0.236885,0.265995,0.380448,0.0717921,0.734811,1.23781,2.86095,1.72382,0.241178,0.560338,0.868795,0.516202,0.0841366,0.153548,0.451923,0.777092,0.207217,0.629532,0.796113,0.00150464,0.043542,0.37887,0.00331585,0.0692471,0.609549,0.491685,4.14193,0.0213533,0.116078,0.172987,0.0839853,0.00141861,0.338961,0.0398999,1.22007,0.724704,0.124382,0.869816,1.31498,0.318564,0.224958,0.12955,0.00907508,0.0652883,0.0496878,0.70632,0.126778,1.25856,0.476151,0.221225,0.249978,0.192812,0.882901,0.0375094,0.183029,0.522762,0.0225263,0.233904,0.192854,0.248074,3.01557,0.160677,1.22775,1.10144,0.0231409,0.311454,0.152221,1.49603,0.372357,2.49633,0.177649,0.0888831,0.585292,0.953974,0.253564,0.228277,0.406216,0.0209528,0.319081,0.0336539,0.417824,0.0874218,0.541892,2.29147,0.128182,0.0448706,0.505486,1.30792,0.919291,0.473972,0.0733598,1.29526,0.148046,0.0564945,0.429776,1.15268,8.16353,0.00263474,0.0665746,1.83927e-06,0.319367,0.255637,0.076425,6.57392,0.748034,2.04624,0.241999,0.0172189,0.472954,0.305602,0.20463,0.0177723,0.157161,0.0836473,0.0456429,0.0746798,1.35651
}}
}}

Revision as of 14:03, 26 November 2012


Full id: C288_Chondrocyte_Renal_Pericytes_Fibroblast_aorta_Smooth_Meningeal



Phase1 CAGE Peaks

Hg19::chrX:152760428..152760447,+p1@BGN
Hg19::chrX:152770059..152770066,+p33@BGN
Hg19::chrX:152770101..152770112,+p23@BGN
Hg19::chrX:152770151..152770173,+p11@BGN
Hg19::chrX:152770174..152770191,+p27@BGN
Hg19::chrX:152770200..152770258,+p4@BGN
Hg19::chrX:152770207..152770220,-p@chrX:152770207..152770220
-
Hg19::chrX:152770262..152770308,-p@chrX:152770262..152770308
-
Hg19::chrX:152770265..152770294,+p15@BGN
Hg19::chrX:152770299..152770310,+p13@BGN
Hg19::chrX:152770690..152770747,+p@chrX:152770690..152770747
+
Hg19::chrX:152770747..152770793,-p@chrX:152770747..152770793
-
Hg19::chrX:152771310..152771324,+p22@BGN
Hg19::chrX:152771355..152771373,+p17@BGN
Hg19::chrX:152771357..152771376,-p@chrX:152771357..152771376
-
Hg19::chrX:152771377..152771404,+p14@BGN
Hg19::chrX:152771413..152771438,+p6@BGN
Hg19::chrX:152771423..152771451,-p@chrX:152771423..152771451
-
Hg19::chrX:152771450..152771463,+p19@BGN
Hg19::chrX:152771465..152771514,-p@chrX:152771465..152771514
-
Hg19::chrX:152771488..152771513,+p21@BGN
Hg19::chrX:152771988..152772002,+p@chrX:152771988..152772002
+
Hg19::chrX:152772003..152772056,+p@chrX:152772003..152772056
+
Hg19::chrX:152772015..152772028,-p@chrX:152772015..152772028
-
Hg19::chrX:152772068..152772079,+p@chrX:152772068..152772079
+
Hg19::chrX:152772312..152772340,-p@chrX:152772312..152772340
-
Hg19::chrX:152772329..152772363,+p@chrX:152772329..152772363
+
Hg19::chrX:152772356..152772373,-p@chrX:152772356..152772373
-
Hg19::chrX:152772503..152772517,+p@chrX:152772503..152772517
+
Hg19::chrX:152772540..152772564,+p@chrX:152772540..152772564
+
Hg19::chrX:152772571..152772585,+p@chrX:152772571..152772585
+
Hg19::chrX:152772597..152772622,+p@chrX:152772597..152772622
+
Hg19::chrX:152773690..152773718,+p10@BGN
Hg19::chrX:152773762..152773796,+p9@BGN
Hg19::chrX:152773830..152773842,+p25@BGN
Hg19::chrX:152773922..152773952,+p16@BGN
Hg19::chrX:152773994..152774035,+p7@BGN
Hg19::chrX:152774081..152774113,+p5@BGN
Hg19::chrX:152774119..152774158,+p12@BGN
Hg19::chrX:152774177..152774196,-p5@CU678629
Hg19::chrX:152774185..152774199,+p8@BGN
Hg19::chrX:152774275..152774309,+p3@BGN
Hg19::chrX:152774321..152774336,+p26@BGN
Hg19::chrX:152774348..152774479,+p2@BGN
Hg19::chrX:152774354..152774382,-p1@CU678629


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:0030133transport vesicle0.032585658777817
GO:0005201extracellular matrix structural constituent0.032585658777817
GO:0016023cytoplasmic membrane-bound vesicle0.032699197658576
GO:0031988membrane-bound vesicle0.032699197658576
GO:0005578proteinaceous extracellular matrix0.032699197658576
GO:0031410cytoplasmic vesicle0.032699197658576
GO:0031982vesicle0.032699197658576



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
splanchnic layer of lateral plate mesoderm1.37e-2383
vasculature2.95e-2278
vascular system2.95e-2278
circulatory system1.12e-20112
vessel1.43e-2068
epithelial tube open at both ends3.59e-2059
blood vessel3.59e-2059
blood vasculature3.59e-2059
vascular cord3.59e-2059
cardiovascular system8.47e-20109
artery2.39e-1942
arterial blood vessel2.39e-1942
arterial system2.39e-1942
systemic artery1.07e-1533
systemic arterial system1.07e-1533
epithelial tube1.33e-15117
muscle tissue3.86e-1364
musculature3.86e-1364
musculature of body3.86e-1364
skeletal muscle tissue6.21e-1362
striated muscle tissue6.21e-1362
myotome6.21e-1362
dense mesenchyme tissue2.69e-1173
primary circulatory organ3.89e-1127
epithelial vesicle4.98e-1178
paraxial mesoderm8.24e-1172
presumptive paraxial mesoderm8.24e-1172
anatomical conduit8.88e-11240
somite1.24e-1071
presomitic mesoderm1.24e-1071
presumptive segmental plate1.24e-1071
dermomyotome1.24e-1071
trunk paraxial mesoderm1.24e-1071
heart2.41e-1024
primitive heart tube2.41e-1024
primary heart field2.41e-1024
anterior lateral plate mesoderm2.41e-1024
heart tube2.41e-1024
heart primordium2.41e-1024
cardiac mesoderm2.41e-1024
cardiogenic plate2.41e-1024
heart rudiment2.41e-1024
tube2.76e-10192
aorta1.57e-0921
aortic system1.57e-0921
multilaminar epithelium3.15e-0883
mesenchyme5.06e-08160
entire embryonic mesenchyme5.06e-08160
trunk mesenchyme6.09e-08122
cell layer9.92e-08309
unilaminar epithelium3.91e-07148
anatomical cluster4.20e-07373
epithelium5.75e-07306


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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