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Coexpression cluster:C4105: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;1.93041,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;4.13609,MA0059.1;4.12962,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;4.54482,MA0074.1;2.15449,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;2.626,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;1.52002,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;1.31729,MA0145.1;2.11725,MA0146.1;1.16674,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.757898,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;5.75024,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;1.51687,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;3.48527,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.09178,MA0102.2;1.88331,MA0258.1;1.29138,MA0259.1;1.40979,MA0442.1;0
}}
}}

Revision as of 21:50, 22 January 2013


Full id: C4105_Mesenchymal_Adipocyte_Preadipocyte_leiomyoma_Osteoblast_breast_Renal



Phase1 CAGE Peaks

Hg19::chr22:43015363..43015380,-p@chr22:43015363..43015380
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Hg19::chr22:43015486..43015596,-p@chr22:43015486..43015596
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Hg19::chr22:43015698..43015781,-p2@CYB5R3


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
fibroblast3.28e-1276
mesodermal cell1.16e-09121
fat cell8.22e-0815
preadipocyte1.30e-0712
contractile cell2.57e-0759
Uber Anatomy
Ontology termp-valuen
multi-cellular organism8.98e-15656
mesenchyme5.08e-13160
entire embryonic mesenchyme5.08e-13160
epithelial tube7.54e-12117
splanchnic layer of lateral plate mesoderm1.22e-1183
trunk mesenchyme1.40e-11122
anatomical system1.56e-11624
anatomical group2.15e-11625
vasculature4.57e-1178
vascular system4.57e-1178
vessel6.78e-1168
mesoderm1.88e-10315
mesoderm-derived structure1.88e-10315
presumptive mesoderm1.88e-10315
epithelial vesicle4.85e-1078
epithelial tube open at both ends5.66e-1059
blood vessel5.66e-1059
blood vasculature5.66e-1059
vascular cord5.66e-1059
surface structure5.39e-0999
dense mesenchyme tissue1.83e-0873
cell layer2.23e-08309
paraxial mesoderm2.44e-0872
presumptive paraxial mesoderm2.44e-0872
multilaminar epithelium2.51e-0883
artery2.81e-0842
arterial blood vessel2.81e-0842
arterial system2.81e-0842
trunk3.02e-08199
organism subdivision3.08e-08264
somite3.75e-0871
presomitic mesoderm3.75e-0871
presumptive segmental plate3.75e-0871
dermomyotome3.75e-0871
trunk paraxial mesoderm3.75e-0871
epithelium4.42e-08306
developing anatomical structure5.14e-08581
anatomical conduit5.36e-08240
unilaminar epithelium8.04e-08148
circulatory system9.74e-08112
muscle tissue1.28e-0764
musculature1.28e-0764
musculature of body1.28e-0764
integument1.42e-0746
integumental system1.42e-0746
germ layer1.87e-07560
germ layer / neural crest1.87e-07560
embryonic tissue1.87e-07560
presumptive structure1.87e-07560
germ layer / neural crest derived structure1.87e-07560
epiblast (generic)1.87e-07560
embryonic structure1.89e-07564
cardiovascular system2.09e-07109
embryo2.95e-07592
skeletal muscle tissue3.62e-0762
striated muscle tissue3.62e-0762
myotome3.62e-0762
tissue4.69e-07773
compound organ7.45e-0768
anatomical cluster9.39e-07373
multi-tissue structure9.62e-07342


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)
MA0003.10.401049
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.14.13609
MA0059.14.12962
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
MA0073.14.54482
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
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
MA0116.10.560723
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.12.11725
MA0146.11.16674
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.25.75024
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.13.48527
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.11.29138
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

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

This analysis result is provided for C0 - C305 clusters.

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