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Coexpression cluster:C3330: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3330_Hepatocyte_liver_Mesenchymal_tenocyte_Synoviocyte_Fibroblast_Nucleus
|id=C3330
|ontology_enrichment_celltype=CL:0000055!1.43e-24!180;CL:0000057!3.00e-14!75;CL:0000183!5.07e-10!59;CL:0000680!6.08e-10!57;CL:0000056!6.08e-10!57;CL:0000355!6.08e-10!57;CL:0000187!2.82e-09!54;CL:0000393!9.50e-08!60;CL:0000211!9.50e-08!60
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.72e-21!365;UBERON:0000481!7.40e-20!347;UBERON:0005256!8.59e-13!143;UBERON:0000477!2.62e-12!286;UBERON:0003104!7.92e-12!238;UBERON:0009142!7.92e-12!238;UBERON:0000468!1.01e-11!659;UBERON:0002100!4.52e-11!216;UBERON:0002385!1.28e-10!63;UBERON:0001015!1.28e-10!63;UBERON:0000383!1.28e-10!63;UBERON:0000119!1.82e-10!312;UBERON:0000483!2.10e-10!309;UBERON:0000914!2.16e-10!83;UBERON:0002329!2.16e-10!83;UBERON:0003077!2.16e-10!83;UBERON:0003059!2.16e-10!83;UBERON:0007282!2.16e-10!83;UBERON:0009618!2.16e-10!83;UBERON:0007285!2.16e-10!83;UBERON:0001134!3.18e-10!61;UBERON:0002036!3.18e-10!61;UBERON:0003082!3.18e-10!61;UBERON:0004290!2.92e-09!70;UBERON:0000486!5.26e-09!82;UBERON:0000467!3.43e-08!625;UBERON:0003102!4.03e-08!95;UBERON:0000480!4.23e-08!626;UBERON:0004111!5.35e-08!241;UBERON:0000490!2.42e-07!138;UBERON:0007100!4.90e-07!27;UBERON:0001048!5.93e-07!168
}}

Latest revision as of 12:23, 17 September 2013


Full id: C3330_Hepatocyte_liver_Mesenchymal_tenocyte_Synoviocyte_Fibroblast_Nucleus



Phase1 CAGE Peaks

Hg19::chr12:7245125..7245138,-p3@C1R
Hg19::chr12:7245139..7245150,-p4@C1R
Hg19::chr12:7245152..7245169,-p5@C1R


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
multi-tissue structure3.08e-19342
anatomical cluster6.54e-14373
mesenchyme1.91e-13160
entire embryonic mesenchyme1.91e-13160
trunk mesenchyme2.50e-12122
organism subdivision7.86e-12264
multi-cellular organism1.40e-11656
muscle tissue1.74e-1064
musculature1.74e-1064
musculature of body1.74e-1064
skeletal muscle tissue5.12e-1062
striated muscle tissue5.12e-1062
myotome5.12e-1062
dense mesenchyme tissue2.07e-0973
primordium2.66e-09160
paraxial mesoderm4.01e-0972
presumptive paraxial mesoderm4.01e-0972
somite5.26e-0971
presomitic mesoderm5.26e-0971
presumptive segmental plate5.26e-0971
dermomyotome5.26e-0971
trunk paraxial mesoderm5.26e-0971
cell layer1.72e-08309
epithelium1.79e-08306
anatomical system2.16e-08624
anatomical group2.75e-08625
multilaminar epithelium2.96e-0883
epithelial vesicle5.76e-0878
trunk1.43e-07199
primary circulatory organ2.57e-0727
digestive system3.07e-07145
digestive tract3.07e-07145
primitive gut3.07e-07145
surface structure4.67e-0799
heart6.01e-0724
primitive heart tube6.01e-0724
primary heart field6.01e-0724
anterior lateral plate mesoderm6.01e-0724
heart tube6.01e-0724
heart primordium6.01e-0724
cardiac mesoderm6.01e-0724
cardiogenic plate6.01e-0724
heart rudiment6.01e-0724
organ system subdivision8.45e-07223
unilaminar epithelium8.56e-07148


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.12.60497
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.12.97077
MA0091.10.829044
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.12.53618
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.12.47657
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CEBPB#105137.971147625824820.001974187055288560.0115031311017229
CTCF#1066435.360256373075030.0064925092527670.0278697564262118
CTCFL#140690319.74647435897440.0001298372005551160.00171386089342465
POU2F2#545239.106124057742520.001324165192682130.00880520110521641
RAD21#5885310.35503389545630.0009004912073565420.00662485215589672
SMC3#9126315.04493284493280.0002935825420371870.00308403410861212
STAT3#6774310.51946499715420.0008589184530415310.00641663693256112
YY1#752834.911170749853860.008441455341808260.0328373493162661
ZNF143#7702313.50087655222790.0004062804962997170.00388176093248981



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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