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{{Coexpression_clusters
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|full_id=C2836_Fibroblast_Endothelial_mature_Cardiac_Smooth_mesenchymal_Adipocyte
|id=C2836
|ontology_enrichment_celltype=CL:0000055!7.15e-30!180;CL:0000222!1.16e-24!119;CL:0000057!2.16e-17!75;CL:0000187!1.11e-15!54;CL:0000680!2.73e-15!57;CL:0000056!2.73e-15!57;CL:0000355!2.73e-15!57;CL:0000183!4.35e-15!59;CL:0000393!1.12e-13!60;CL:0000211!1.12e-13!60;CL:0002139!2.26e-13!24;CL:0000192!3.75e-12!42;CL:0000514!3.75e-12!42;CL:0000213!7.81e-11!57;CL:0000215!7.81e-11!57;CL:0000115!3.28e-10!35;CL:0000071!3.57e-10!18;CL:0002546!3.57e-10!18;CL:0000359!1.00e-09!32;CL:0002620!4.27e-09!23;CL:0002078!5.47e-09!44;CL:0000220!2.02e-08!246;CL:0002321!3.20e-08!248;CL:0000136!7.02e-08!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!5.60e-26!79;UBERON:0007798!5.60e-26!79;UBERON:0000055!9.42e-23!69;UBERON:0004872!7.01e-22!84;UBERON:0001981!2.11e-20!60;UBERON:0007500!2.11e-20!60;UBERON:0004537!2.11e-20!60;UBERON:0006965!2.11e-20!60;UBERON:0001009!1.51e-19!113;UBERON:0004535!1.97e-19!110;UBERON:0000475!2.97e-17!365;UBERON:0000914!3.39e-17!83;UBERON:0002329!3.39e-17!83;UBERON:0003077!3.39e-17!83;UBERON:0003059!3.39e-17!83;UBERON:0007282!3.39e-17!83;UBERON:0009618!3.39e-17!83;UBERON:0007285!3.39e-17!83;UBERON:0004290!3.81e-17!70;UBERON:0000477!6.36e-17!286;UBERON:0004111!2.00e-16!241;UBERON:0000119!2.11e-16!312;UBERON:0003914!3.81e-16!118;UBERON:0002385!5.18e-16!63;UBERON:0001015!5.18e-16!63;UBERON:0000383!5.18e-16!63;UBERON:0000483!1.07e-15!309;UBERON:0001637!1.40e-15!42;UBERON:0003509!1.40e-15!42;UBERON:0004572!1.40e-15!42;UBERON:0001134!1.52e-15!61;UBERON:0002036!1.52e-15!61;UBERON:0003082!1.52e-15!61;UBERON:0000490!7.93e-15!138;UBERON:0004573!3.73e-14!33;UBERON:0004571!3.73e-14!33;UBERON:0000486!5.06e-14!82;UBERON:0005256!5.06e-13!143;UBERON:0000468!6.78e-13!659;UBERON:0000025!8.46e-13!194;UBERON:0000481!6.27e-12!347;UBERON:0002100!3.92e-11!216;UBERON:0000467!5.51e-11!625;UBERON:0000480!9.35e-11!626;UBERON:0001986!3.57e-10!18;UBERON:0004638!3.57e-10!18;UBERON:0004852!3.57e-10!18;UBERON:0000947!1.92e-09!21;UBERON:0010191!1.92e-09!21;UBERON:0006914!9.44e-09!25;UBERON:0000487!1.93e-08!22;UBERON:0003102!1.04e-07!95;UBERON:0002199!1.21e-07!45;UBERON:0002416!1.21e-07!45;UBERON:0003104!1.60e-07!238;UBERON:0009142!1.60e-07!238;UBERON:0000948!3.25e-07!24;UBERON:0005498!3.25e-07!24;UBERON:0004140!3.25e-07!24;UBERON:0009881!3.25e-07!24;UBERON:0004141!3.25e-07!24;UBERON:0003084!3.25e-07!24;UBERON:0007005!3.25e-07!24;UBERON:0004139!3.25e-07!24;UBERON:0004291!3.25e-07!24;UBERON:0007100!3.61e-07!27
}}

Latest revision as of 12:14, 17 September 2013


Full id: C2836_Fibroblast_Endothelial_mature_Cardiac_Smooth_mesenchymal_Adipocyte



Phase1 CAGE Peaks

Hg19::chr6:112575490..112575527,-p3@LAMA4
Hg19::chr6:112575733..112575755,-p2@LAMA4
Hg19::chr6:112575758..112575776,-p1@LAMA4
Hg19::chr6:112575838..112575847,-p6@LAMA4


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
vasculature1.25e-2478
vascular system1.25e-2478
vessel1.40e-2168
splanchnic layer of lateral plate mesoderm1.50e-2083
epithelial tube open at both ends3.98e-1959
blood vessel3.98e-1959
blood vasculature3.98e-1959
vascular cord3.98e-1959
circulatory system2.75e-18112
cardiovascular system3.58e-18109
dense mesenchyme tissue1.44e-1773
somite2.14e-1771
presomitic mesoderm2.14e-1771
presumptive segmental plate2.14e-1771
dermomyotome2.14e-1771
trunk paraxial mesoderm2.14e-1771
paraxial mesoderm3.37e-1772
presumptive paraxial mesoderm3.37e-1772
epithelial vesicle3.62e-1778
cell layer1.65e-16309
unilaminar epithelium1.90e-16148
muscle tissue2.71e-1664
musculature2.71e-1664
musculature of body2.71e-1664
anatomical cluster4.37e-16373
anatomical conduit5.51e-16240
epithelium7.55e-16306
skeletal muscle tissue8.51e-1662
striated muscle tissue8.51e-1662
myotome8.51e-1662
epithelial tube6.49e-15117
artery8.92e-1542
arterial blood vessel8.92e-1542
arterial system8.92e-1542
multilaminar epithelium2.23e-1483
multi-cellular organism5.93e-14656
trunk mesenchyme9.72e-14122
systemic artery1.46e-1333
systemic arterial system1.46e-1333
mesenchyme3.71e-13160
entire embryonic mesenchyme3.71e-13160
anatomical system2.25e-12624
anatomical group3.93e-12625
tube8.64e-12192
multi-tissue structure1.19e-11342
organism subdivision1.06e-10264
trunk6.10e-10199
blood vessel endothelium1.65e-0918
endothelium1.65e-0918
cardiovascular system endothelium1.65e-0918
aorta3.47e-0921
aortic system3.47e-0921
squamous epithelium1.87e-0825
integument3.57e-0846
integumental system3.57e-0846
simple squamous epithelium4.86e-0822
surface structure1.49e-0799
heart4.75e-0724
primitive heart tube4.75e-0724
primary heart field4.75e-0724
anterior lateral plate mesoderm4.75e-0724
heart tube4.75e-0724
heart primordium4.75e-0724
cardiac mesoderm4.75e-0724
cardiogenic plate4.75e-0724
heart rudiment4.75e-0724
primary circulatory organ5.27e-0727


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.12.5647
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.11.75269
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.22.1393
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.23.29861
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.11.84959
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



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
CTBP2#1488462.71700033932816.45042639894877e-083.96746809587639e-06
GATA2#262439.55869880016550.001818151618357440.0109067166496056
ZNF263#1012736.166381227758010.006539814347975980.0279911344079449



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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