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Coexpression cluster:C3180: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3180_Adipocyte_Mesenchymal_Hep2_cord_mesenchymal_Smooth_Fibroblast
|id=C3180
}}

Latest revision as of 12:20, 17 September 2013


Full id: C3180_Adipocyte_Mesenchymal_Hep2_cord_mesenchymal_Smooth_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:6340965..6340985,-p3@PRKCDBP
Hg19::chr11:6340994..6341012,-p2@PRKCDBP
Hg19::chr11:6341016..6341030,-p4@PRKCDBP


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>

Cell Type
Ontology termp-valuen
mesodermal cell1.70e-18121
fibroblast2.14e-1776
contractile cell1.07e-1559
muscle precursor cell1.18e-1458
myoblast1.18e-1458
multi-potent skeletal muscle stem cell1.18e-1458
muscle cell8.10e-1455
embryonic cell4.70e-12250
non-terminally differentiated cell5.17e-12106
electrically responsive cell3.49e-1161
electrically active cell3.49e-1161
smooth muscle cell2.75e-1043
smooth muscle myoblast2.75e-1043
fat cell3.20e-0815
animal cell4.96e-08679
eukaryotic cell4.96e-08679
somatic cell1.68e-07588
Uber Anatomy
Ontology termp-valuen
epithelial vesicle5.96e-1878
somite3.77e-1671
presomitic mesoderm3.77e-1671
presumptive segmental plate3.77e-1671
dermomyotome3.77e-1671
trunk paraxial mesoderm3.77e-1671
paraxial mesoderm1.76e-1572
presumptive paraxial mesoderm1.76e-1572
dense mesenchyme tissue3.06e-1573
multilaminar epithelium1.82e-1483
skeletal muscle tissue9.75e-1462
striated muscle tissue9.75e-1462
myotome9.75e-1462
muscle tissue1.33e-1364
musculature1.33e-1364
musculature of body1.33e-1364
trunk mesenchyme2.39e-13122
mesenchyme5.59e-13160
entire embryonic mesenchyme5.59e-13160
splanchnic layer of lateral plate mesoderm7.93e-1383
circulatory system2.00e-12112
vasculature2.47e-1278
vascular system2.47e-1278
cardiovascular system4.66e-12109
organism subdivision7.30e-12264
trunk3.19e-11199
epithelial tube2.82e-10117
unilaminar epithelium3.04e-10148
multi-tissue structure6.94e-09342
vessel8.29e-0968
epithelial tube open at both ends8.65e-0959
blood vessel8.65e-0959
blood vasculature8.65e-0959
vascular cord8.65e-0959
surface structure1.74e-0899
mesoderm5.40e-08315
mesoderm-derived structure5.40e-08315
presumptive mesoderm5.40e-08315
larynx6.68e-089
multi-cellular organism1.79e-07656
integument2.87e-0746
integumental system2.87e-0746
adipose tissue3.32e-0714
cell layer4.74e-07309
artery5.48e-0742
arterial blood vessel5.48e-0742
arterial system5.48e-0742
epithelium7.72e-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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.13.15662
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.12.8848
MA0073.12.26659
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
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.14.18141
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.13.943
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
CTCF#1066435.360256373075030.0064925092527670.0278445784268123
E2F4#1874312.66806031528440.0004917987006298980.00435722467722141
E2F6#187635.017155731697390.00791769806886330.0320609673004813
GTF2F1#2962312.73966087675770.0004835525047438590.00432822592071854
RFX5#5993312.04791082719510.0005717246050312580.00483210698590755
SMARCB1#6598318.25271578115740.000164397760679890.00202614322960196
TCF12#6938310.63446490218640.0008313523990202070.00627897116005723



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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