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Coexpression cluster:C2907: Difference between revisions

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{{Coexpression_clusters
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0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.80003,1.44778,0.706765,0.867962,1.62243,0.809319,0.532789,0.559384,1.05593,0.471262,1.67497,0.635753,0.581762,2.21632,0.731221,1.3102,0.632849,0.892087,2.33254,0.728867,0.537869,2.23762,1.63433,1.09415,0.433165,0.344471,2.14358,0.285913,0.491074,0.740899,2.0411,0.371755,1.23481,0.66492,1.63146,1.31558,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,3.55571,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.823598,2.3052,1.08,0.62601,0.95118,1.02594,0.844168,1.03184,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,2.78853,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,1.88833,1.52945,0.516141,1.44917,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,1.99225,1.57854,1.0102,0.814847,1.11673,1.36323,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,2.73245,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,1.58968,1.24902,0.383416,0.824835,1.65997,2.11789,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.00378|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.34758,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.709734,MA0050.1;1.66718,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.214613,MA0074.1;0.819248,MA0076.1;1.51122,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;2.9994,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;2.17614,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.08195,MA0146.1;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.533581,MA0156.1;1.37856,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.640035,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;1.85039,MA0079.2;0.0270533,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2907_mesenchymal_myxofibrosarcoma_serous_Smooth_Endothelial_leiomyoma_Fibroblast
|id=C2907
}}

Latest revision as of 12:15, 17 September 2013


Full id: C2907_mesenchymal_myxofibrosarcoma_serous_Smooth_Endothelial_leiomyoma_Fibroblast



Phase1 CAGE Peaks

Hg19::chr7:93551154..93551186,+p4@GNG11
Hg19::chr7:93551194..93551205,+p9@GNG11
Hg19::chr7:93551224..93551235,+p8@GNG11
Hg19::chr7:93551243..93551254,+p10@GNG11


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
cardiovascular system2.42e-35109
circulatory system1.24e-34112
vasculature1.59e-3378
vascular system1.59e-3378
vessel5.89e-2868
epithelial tube open at both ends7.34e-2659
blood vessel7.34e-2659
blood vasculature7.34e-2659
vascular cord7.34e-2659
splanchnic layer of lateral plate mesoderm7.49e-2683
epithelial vesicle2.68e-2378
epithelial tube1.16e-22117
paraxial mesoderm6.03e-2272
presumptive paraxial mesoderm6.03e-2272
somite6.67e-2271
presomitic mesoderm6.67e-2271
presumptive segmental plate6.67e-2271
dermomyotome6.67e-2271
trunk paraxial mesoderm6.67e-2271
dense mesenchyme tissue6.73e-2273
cell layer8.84e-21309
artery9.67e-2142
arterial blood vessel9.67e-2142
arterial system9.67e-2142
anatomical cluster1.11e-20373
unilaminar epithelium1.44e-19148
epithelium1.99e-19306
skeletal muscle tissue2.04e-1962
striated muscle tissue2.04e-1962
myotome2.04e-1962
muscle tissue2.62e-1964
musculature2.62e-1964
musculature of body2.62e-1964
anatomical conduit7.76e-18240
tube8.22e-18192
systemic artery2.43e-1633
systemic arterial system2.43e-1633
multilaminar epithelium5.23e-1683
trunk mesenchyme1.17e-15122
mesenchyme2.88e-15160
entire embryonic mesenchyme2.88e-15160
multi-tissue structure6.10e-15342
multi-cellular organism4.32e-14656
anatomical system6.91e-14624
anatomical group1.25e-13625
simple squamous epithelium2.11e-1122
blood vessel endothelium2.53e-1118
endothelium2.53e-1118
cardiovascular system endothelium2.53e-1118
trunk4.04e-11199
organism subdivision1.36e-10264
squamous epithelium1.94e-1025
structure with developmental contribution from neural crest5.07e-10132
aorta1.68e-0921
aortic system1.68e-0921
mesoderm1.95e-09315
mesoderm-derived structure1.95e-09315
presumptive mesoderm1.95e-09315
embryo1.54e-08592
developing anatomical structure6.30e-08581
germ layer7.14e-08560
germ layer / neural crest7.14e-08560
embryonic tissue7.14e-08560
presumptive structure7.14e-08560
germ layer / neural crest derived structure7.14e-08560
epiblast (generic)7.14e-08560
embryonic structure1.88e-07564
heart8.14e-0724
primitive heart tube8.14e-0724
primary heart field8.14e-0724
anterior lateral plate mesoderm8.14e-0724
heart tube8.14e-0724
heart primordium8.14e-0724
cardiac mesoderm8.14e-0724
cardiogenic plate8.14e-0724
heart rudiment8.14e-0724


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
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
MA0048.10.709734
MA0050.11.66718
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
MA0073.10.214613
MA0074.10.819248
MA0076.11.51122
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
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.9994
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
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
MA0145.11.08195
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.20.0270533
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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#1066445.360256373075030.001211145381643620.00820090848764771
EBF1#187948.9064668465690.00015887907472010.00200183033956962
FOS#235348.99795530889440.0001525147711168630.00195513565492501
GATA2#2624412.7449317335543.78864877853583e-050.000724826323102224
NR3C1#2908414.9730233311731.98868032687801e-050.000444744720896814
RAD21#588537.766275421592250.0033411193858720.0172786911384544
REST#597849.650028716128020.0001152825614219170.00157570938782144
SMARCB1#6598418.25271578115749.00423392720929e-060.000242306927885548
TFAP2A#7020416.5186343730451.34240829060362e-050.000327493061112711
TFAP2C#7022410.80922860986027.32289634782688e-050.00114920506637219



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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