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Coexpression cluster:C2570: Difference between revisions

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{{Coexpression_clusters
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974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=1.44014,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.151681,1.68405,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,2.21632,5.59024,0.528529,0.632849,4.87831,0.316693,0.728867,2.28567,0.806311,0.682839,1.09415,0.433165,0.911389,0.49475,0.0842336,5.45699,1.75478,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,3.70541,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,1.82985,0.297448,0.776148,2.56328,4.59898,0.393426,2.3411,3.26261,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,7.68184,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,3.8242,0.844168,0.399165,1.27559,4.5493,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,1.66879,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,2.59267,4.4082,1.44917,1.14697,0.575476,0.717043,1.46636,0.489254,7.52185,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,2.76338,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.91548,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,1.4628,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,12.6294|tfbs_overrepresentation_jaspar=MA0003.1;5.41581,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;2.78189,MA0009.1;1.20602,MA0014.1;3.08565,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;5.64565,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,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;0.00636811,MA0074.1;4.57331,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;1.02755,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;0.656404,MA0106.1;3.33935,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;1.57689,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;1.43218,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;1.63368,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;6.62067,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;1.5472,MA0138.2;0.928035,MA0002.2;0.98779,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;1.05083,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;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0021048,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2570_mesenchymal_leiomyoma_Fibroblast_CD14_Mesothelial_Gingival_meningioma
|id=C2570
}}

Latest revision as of 12:08, 17 September 2013


Full id: C2570_mesenchymal_leiomyoma_Fibroblast_CD14_Mesothelial_Gingival_meningioma



Phase1 CAGE Peaks

Hg19::chr1:223900193..223900249,+p1@CAPN2
Hg19::chr1:223900250..223900274,+p3@CAPN2
Hg19::chr1:223900286..223900299,+p4@CAPN2
Hg19::chr1:223900302..223900328,+p2@CAPN2


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
animal cell5.31e-22679
eukaryotic cell5.31e-22679
somatic cell1.45e-21588
mesodermal cell6.67e-17121
native cell1.10e-15722
fibroblast5.95e-1476
classical monocyte2.15e-1342
CD14-positive, CD16-negative classical monocyte2.15e-1342
muscle precursor cell3.31e-1358
myoblast3.31e-1358
multi-potent skeletal muscle stem cell3.31e-1358
vascular associated smooth muscle cell7.65e-1332
muscle cell5.51e-1255
embryonic cell6.36e-12250
smooth muscle cell6.79e-1243
smooth muscle myoblast6.79e-1243
contractile cell4.49e-1159
defensive cell1.92e-0948
phagocyte1.92e-0948
electrically responsive cell1.53e-0861
electrically active cell1.53e-0861
multi fate stem cell5.47e-07427
non-terminally differentiated cell6.09e-07106
somatic stem cell6.19e-07433
squamous epithelial cell6.65e-0763
stuff accumulating cell7.30e-0787
Uber Anatomy
Ontology termp-valuen
mesoderm2.44e-20315
mesoderm-derived structure2.44e-20315
presumptive mesoderm2.44e-20315
multilaminar epithelium6.02e-1683
musculoskeletal system9.40e-16167
somite5.21e-1571
presomitic mesoderm5.21e-1571
presumptive segmental plate5.21e-1571
dermomyotome5.21e-1571
trunk paraxial mesoderm5.21e-1571
artery1.10e-1442
arterial blood vessel1.10e-1442
arterial system1.10e-1442
epithelial vesicle1.34e-1478
paraxial mesoderm2.12e-1472
presumptive paraxial mesoderm2.12e-1472
vasculature2.49e-1478
vascular system2.49e-1478
dense mesenchyme tissue2.54e-1473
anatomical group4.50e-14625
anatomical system5.22e-14624
epithelial tube open at both ends1.00e-1359
blood vessel1.00e-1359
blood vasculature1.00e-1359
vascular cord1.00e-1359
unilaminar epithelium1.27e-12148
splanchnic layer of lateral plate mesoderm2.15e-1283
vessel2.41e-1268
lateral plate mesoderm3.03e-12203
multi-cellular organism6.68e-12656
skeletal muscle tissue7.98e-1262
striated muscle tissue7.98e-1262
myotome7.98e-1262
systemic artery3.07e-1133
systemic arterial system3.07e-1133
surface structure3.63e-1199
muscle tissue3.86e-1164
musculature3.86e-1164
musculature of body3.86e-1164
organism subdivision1.88e-10264
cardiovascular system5.16e-10109
circulatory system1.45e-09112
trunk mesenchyme3.41e-09122
epithelial tube1.54e-08117
developing anatomical structure1.67e-08581
embryonic structure2.48e-08564
trunk5.23e-08199
germ layer1.03e-07560
germ layer / neural crest1.03e-07560
embryonic tissue1.03e-07560
presumptive structure1.03e-07560
germ layer / neural crest derived structure1.03e-07560
epiblast (generic)1.03e-07560
aorta1.19e-0721
aortic system1.19e-0721
mesenchyme1.37e-07160
entire embryonic mesenchyme1.37e-07160
embryo1.77e-07592
organ component layer4.27e-0766


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)
MA0003.15.41581
MA0004.10.71247
MA0006.10.532262
MA0007.12.78189
MA0009.11.20602
MA0014.13.08565
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
MA0048.15.64565
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
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
MA0074.14.57331
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
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
MA0106.13.33935
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.16.62067
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
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
MA0079.20.0021048
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
CCNT2#90546.336201576962630.0006203100587215640.00512495548001119
CTCF#1066445.360256373075030.001211145381643620.00817758032799834
E2F1#186944.907389214879320.001724022357361790.0106547825895324
ELF1#199744.258097958807540.003041525565781240.0160984131646375
FOS#235348.99795530889440.0001525147711168630.0019501089839219
FOSL2#2355416.93020060456171.2165416097647e-050.00030410337286313
GATA1#2623413.56030814380042.95627390049268e-050.0006140618335194
HEY1#2346244.040111043105710.00375304636917980.0186197524939798
HMGN3#932448.178547723350590.0002234570284440470.002482198318833
JUN#3725412.51282919233634.07770316866756e-050.000743749984688214
JUND#372746.994663941871030.000417684217818580.00391936406332028
RAD21#5885410.35503389545638.6948481184721e-050.00129485418885656
SIN3A#2594245.408884726815140.001168172384885160.00796830747208026
SMC3#9126415.04493284493281.95092670935632e-050.000438272391048537
TAF1#687243.343046285745290.008005664898701650.0322458882469629
TBP#690843.706770687096390.005296377814784350.0244453068144892
YY1#752844.911170749853860.00171871838055440.0106915974118007
ZNF263#1012748.221841637010680.0002187871180958320.00249099616557403



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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