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Coexpression cluster:C1085: Difference between revisions

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{{Coexpression_clusters
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0714,0.49649,0.581581,0.212206,2.79508e-06,0.463718,0.531673,0.488584,0.169631,0.4639,0.56248,0.273878,0.00903802,0.500922,0.376098,0.500105,0.389123,0.0993883,0.1667,0.133211,0.116907,0.565967,0.451406,0.683557,0.361689,0.289284,0.241971,0.263726,0.151053,0.477267,0.368791,0.485034,0.43963,0.297904,0.551399,0.625257,0.412086,0.371597,0.547611,0.353179,0.479366,0.297272,0.41916,0.000258646,0.18144,0.000181333,0.554803,0.455388,0.473509,0.0251749,0.335015,0.435559,0.53418,0.28015,0.492484,0.529209,0.397471,0.449258,0.330704,0.443138,0.519779,0.364755,0.312488,0.547073,0.48939,0.395736,0.404755,0.238065,0.12262,0.62882,0.585012,0.481224,0.204547,0.452254,0.259924,0.136638,0.137048,0.353983,0.194753,0.104944,0.136955,0.642324,0.554772,0.469052,0.425619,0.50814,0.429061,0.202353,0.240717,0.162041,0.292976,0.161384,0.255196,0.167238,0.190639,0.307532,0.265287,0.113346,0.168727,0.221472,0.095012,0.320667,0.456504,0.607439,0.5938,0.679098,0.334729,0.557075,0.545435,0.448658,0.497569,0.611294,0.541437,0.406439,0.589165,0.559083,0.313926,0.373141,0.459861,0.447066,0.594101,0.512982,0.649607,0.279812,0.481032,0.0312514,0.278645,0.439191,0.431751,0.586217,0.588503,0.535591,0.381036,0.491941,0.230489,0.653021,0.494548,0.462673,0.23568,0.213047,0.638022,0.394858,0.369527,0.569966,0.178571,0.568909,0.247225,0.48895,0.403105,0.366377,0.476867,0.540268,0.459344,0.697624|tfbs_overrepresentation_for_novel_motifs=0.348717,0.898711,1.62205,0.481684,0.301904,0.480078,1.36559,0.19223,0.190005,0.994235,1.14354,0.597407,4.39499,0.543352,0.300614,0.322799,1.82405,0.250594,1.51831,0.264925,0.341703,0.715078,0.472508,0.29709,0.385586,0.619829,0.833436,1.18607,0.304828,2.49127,0.429397,0.810962,0.220667,0.154814,0.269459,8.24183,0.266487,0.481208,1.96738,5.5951,0.268162,1.87106,0.0547276,0.299183,0.949078,1.72504,0.555735,0.440085,0.0498256,0.304949,0.63387,2.38188,0.0927889,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,3.25048,0.85167,0.558065,1.06063,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,1.03556,0.197328,1.56216,1.03748,0.891424,1.36791,0.127753,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,0.730725,0.0757344,1.81046,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,6.16222,0.239285,0.162291,0.87,0.664183,2.9884,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,1.00159,4.94728,0.352381,0.861701,1.60345,0.459808,1.17281,0.265019,0.826889,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,2.85991,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,2.7654,1.88987,0.410382,0.224241,0.593875,2.70449,0.960402,0.183004,3.44854,1.36372,0.643609,0.288769,0.385642,0.941217,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.0643507|tfbs_overrepresentation_jaspar=MA0003.1;1.66566,MA0004.1;4.06176,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;2.22106,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;1.60389,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;12.4984,MA0056.1;0,MA0057.1;0.0912556,MA0058.1;1.69448,MA0059.1;4.52601,MA0060.1;1.06021,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.326687,MA0074.1;2.33338,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;2.18672,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;2.26508,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;2.64083,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.655057,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;2.10712,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.0613434,MA0146.1;2.05336,MA0147.1;3.60206,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.0817047,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;3.14068,MA0047.2;0.586412,MA0112.2;1.21228,MA0065.2;0.490252,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;2.61329,MA0155.1;0.197713,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;3.19992,MA0163.1;1.42814,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;4.43084,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;3.66727,MA0442.1;0}}
|full_id=C1085_liposarcoma_placenta_Olfactory_amniotic_Hair_mesothelioma_Smooth
|id=C1085
}}

Latest revision as of 11:37, 17 September 2013


Full id: C1085_liposarcoma_placenta_Olfactory_amniotic_Hair_mesothelioma_Smooth



Phase1 CAGE Peaks

Hg19::chr5:95066730..95066782,+p4@RHOBTB3
Hg19::chr5:95066823..95066879,+p2@RHOBTB3
Hg19::chr5:95067004..95067024,+p5@RHOBTB3
Hg19::chr5:95067025..95067058,+p1@RHOBTB3
Hg19::chr5:95067060..95067082,+p3@RHOBTB3
Hg19::chr5:95067089..95067108,+p6@RHOBTB3
Hg19::chr5:95067128..95067139,+p8@RHOBTB3
Hg19::chr5:95067165..95067168,+p12@RHOBTB3


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 structure1.03e-21342
anatomical cluster7.23e-19373
cell layer9.17e-18309
epithelium1.85e-17306
skeletal muscle tissue8.77e-1662
striated muscle tissue8.77e-1662
myotome8.77e-1662
structure with developmental contribution from neural crest1.62e-15132
dense mesenchyme tissue2.20e-1573
muscle tissue2.45e-1564
musculature2.45e-1564
musculature of body2.45e-1564
paraxial mesoderm6.67e-1572
presumptive paraxial mesoderm6.67e-1572
somite1.39e-1471
presomitic mesoderm1.39e-1471
presumptive segmental plate1.39e-1471
dermomyotome1.39e-1471
trunk paraxial mesoderm1.39e-1471
anatomical conduit3.42e-14240
trunk mesenchyme1.53e-13122
epithelial vesicle3.28e-1378
tube4.27e-13192
multi-cellular organism1.22e-12656
mesenchyme1.37e-12160
entire embryonic mesenchyme1.37e-12160
central nervous system5.65e-1281
nervous system8.41e-1289
brain9.04e-1268
future brain9.04e-1268
neural plate5.93e-1182
presumptive neural plate5.93e-1182
ectoderm-derived structure1.00e-10171
ectoderm1.00e-10171
presumptive ectoderm1.00e-10171
organ system subdivision1.28e-10223
multilaminar epithelium1.35e-1083
anatomical system1.67e-10624
organism subdivision1.99e-10264
anatomical group2.36e-10625
neural tube3.47e-1056
neural rod3.47e-1056
future spinal cord3.47e-1056
neural keel3.47e-1056
unilaminar epithelium4.96e-10148
neurectoderm8.48e-1086
regional part of nervous system1.57e-0953
regional part of brain1.57e-0953
germ layer2.90e-09560
germ layer / neural crest2.90e-09560
embryonic tissue2.90e-09560
presumptive structure2.90e-09560
germ layer / neural crest derived structure2.90e-09560
epiblast (generic)2.90e-09560
embryonic structure9.79e-09564
pre-chordal neural plate1.25e-0861
trunk1.29e-08199
regional part of forebrain4.00e-0841
forebrain4.00e-0841
anterior neural tube4.00e-0841
future forebrain4.00e-0841
developing anatomical structure7.11e-08581
organ part1.78e-07218
telencephalon2.49e-0734
splanchnic layer of lateral plate mesoderm2.66e-0783
embryo4.82e-07592
brain grey matter5.04e-0734
gray matter5.04e-0734
ecto-epithelium8.37e-07104
epithelial tube8.75e-07117


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)
MA0003.11.66566
MA0004.14.06176
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.12.22106
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.11.60389
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.112.4984
MA0056.10
MA0057.10.0912556
MA0058.11.69448
MA0059.14.52601
MA0060.11.06021
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.326687
MA0074.12.33338
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.12.18672
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.12.26508
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.12.64083
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.12.10712
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.12.05336
MA0147.13.60206
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0817047
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.23.14068
MA0047.20.586412
MA0112.21.21228
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.12.61329
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.13.19992
MA0163.11.42814
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.24.43084
MA0102.21.46209
MA0258.10.209744
MA0259.13.66727
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
BHLHE40#8553739.26283685360522.13093689260982e-112.55221236384492e-09
CCNT2#90586.336201576962633.84606837428661e-071.87613047614255e-05
CTBP2#1488862.71700033932814.13860279872435e-157.33839622573807e-13
CTCF#1066474.690224326440655.26249365325459e-050.000893819441620193
E2F1#186984.907389214879322.97124777369457e-060.0001015425871194
E2F6#187674.390011265235218.25033297218753e-050.00124032895535093
EBF1#187977.793158490747881.62130676909081e-066.14842620396063e-05
EGR1#195874.364656707958878.58120841941444e-050.00128636834522065
EP300#203386.77394172622322.25366016107097e-071.19114379333042e-05
ETS1#211378.512665806927048.8174082362229e-073.82425788531098e-05
GATA1#2623813.56030814380048.7300552826276e-108.1845443775794e-08
HEY1#2346284.040111043105711.4081650274634e-050.000339177461492736
HMGN3#932488.178547723350594.99020179935884e-083.19541192963359e-06
IRF1#365987.63716375356398.63190100943299e-085.13094541561851e-06
JUNB#3726830.61063265982111.29143502615752e-121.79595449662937e-10
MAX#414975.645986070381231.48396919857828e-050.000351917027997995
MYC#460985.22228187160941.80650725138099e-066.77206786887938e-05
POLR2A#543082.147453176558070.002210725788971910.0127244965926942
RAD21#588579.060654658524295.73112922357867e-072.63912436058789e-05
REST#597856.031267947580010.0005105473532543910.00442976281685929
SIN3A#2594285.408884726815141.36410592556506e-065.35585935188305e-05
SMC3#912659.403083028083036.12099279950925e-050.00100387934514439
SP1#666764.273786033605670.0005904726864288940.00494414951478772
STAT1#6772820.70658749719922.95008695392417e-113.42337923756541e-09
TAF1#687283.343046285745296.40776711117462e-050.00104386334319758
TBP#690883.706770687096392.80450451364125e-050.00059231475611765
TCF12#693879.305156789413124.76792693502233e-072.25014695511431e-05
TCF7L2#6934810.77017656313735.51536816569572e-094.40045481938193e-07
TFAP2A#7020816.5186343730451.79963993911652e-101.88140736337728e-08
TFAP2C#7022810.80922860986025.35792840387033e-094.28794394307903e-07
USF1#739186.361499277207963.72538670743375e-071.83266915844406e-05
ZBTB7A#5134187.35190930787591.17052559937328e-076.76527521156316e-06
ZNF263#1012788.221841637010684.78378813558924e-083.10512149840152e-06



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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