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{{Coexpression_clusters
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667,0.39043,0.590546,0.990228,0.906142,0.538136,0.40459,0.963813,0.131986,0.904118,0.956751,0.976001,0.949686,0.908211,0.00928659,0.0336351,0.000805526,0.391072,0.666559,0.546882,0.644656,0.618042,0.918234,0.580926,0.604644,0.138611,0.95413,0.553548,0.708817,0.965361,0.19515,0.705269,0.8715,0.232688,0.633196,0.475837,0.742409,0.26085,0.584857,0.214574,0.464121,0.800313,0.713064,0.874478,0.979461,0.950552,0.851275,0.333061,0.655787,0.975681,0.507187,0.740736,0.810673,0.714194,0.547448,0.592058,0.209014,0.685169,0.928819,0.753711,0.67414,0.903329,0.6603,0.500539,0.746987,0.755386,0.755489,0.785801,0.894642,0.856402,0.889401,0.969474,0.995463,0.82753,0.72662,0.889909,0.63151,0.900517,0.40382,0.47645,0.60752,0.648862,0.168092,0.721476,0.456477,0.456364,0.930277,0.0191781,0.740317,0.941218,0.413885,0.00276793,0.167054,0.393981,0.446275,0.968889,0.823376,0.848082,0.472666,0.893076,0.000170294,0.398826,0.951538,0.658504,0.993329,0.922372,0.575134,0.630428,0.922976,0.464857,0.952055,0.132055,0.730147,0.329488,0.851256,0.620314,0.545054,0.824708,0.873661,0.784671,0.774214,0.151698,0.884449,0.726857,0.986563,0.412766,0.9287,0.938046,0.971865,0.892955,0.830502,0.894806,0.96657,0.831962,0.602204,0.945291,0.786224,0.989285,0.447432,0.77438,0.89562,0.917553,0.971306,0.800018,0.742931,0.433183,0.080186,0.799816,0.213424,0.184185,0.349532,0.767777,0.406941,0.634099,0.711167,0.436818,0.712346,0.82344,0.485495,0.483529,0.50419,0.719644,0.149098,0.0528241,0.873239,0.0252701,0.126783,0.00302938,0.778257,0.825765,0.828983,0.172535,0.926044,0.513368,0.0720592,0.764838,0.23533,0.789306,0.207013,0.49626,0.067396,0.750479,0.834891,0.0822489,0.465333,0.626127,0.805169,0.051871,0.258759,0.386116,0.805343,0.885812,0.568332,0.6679,0.838679,0.00878977,0.837984,0.725761,0.240267,0.38041,0.312897,0.27845,0.0715176,0.793208,0.951216,0.115872,0.0622641,0.516746,0.552309,0.0697343,0.507623,0.340193,0.824846,0.781352,0.604824,0.878064,0.728039,0.406209,0.12477,0.875342,0.681354,0.81974,0.60389,0.759758,0.761849,0.408769,0.876747,0.880478,0.797125,0.814368,0.224022,0.29033,0.777157,0.324782,0.213963,0.531289,0.861588,0.73549,0.791076,0.651463,0.454407,0.854192,0.696107,0.62601,0.614972,0.828709,0.0114041,0.39491,0.510182,0.468821,0.732915,0.0847715,0.513785,0.451581,0.794046,0.546215,0.320004,0.320851,0.318117,0.433678,0.252507,0.320659,0.136918,0.356863,0.810215,0.766708,0.118973,0.183969,0.4476,0.514645,0.371276,0.597501,0.369981,0.538566,0.381461,0.00255018,0.618891,0.554795,0.270785,0.384359,0.481683,0.230538,0.637576,0.798214,0.232751,0.421091,0.798393,0.656939,0.168536,0.873762,0.073787,0.271194,0.0407275,0.870827,0.0503172,0.67716,0.88347,0.628059,0.126191,0.480482,0.460529,0.906223,0.12335,0.0225424,0.57753,0.821251,0.529292,0.0560248,0.780902,0.187057,0.672895,0.90279,0.597596,0.716128,0.830946,0.497294,0.937871,0.833214,0.804171,0.0348164,0.466831,0.930571,0.732468,0.341299,0.0256408,0.403313,0.890164,0.52549,0.525801,0.741933,0.69814,0.81746,0.604691,0.80097,0.956705|tfbs_overrepresentation_for_novel_motifs=0.102469,0.942481,0.0984893,0.18689,0.266493,0.185775,0.239567,1.68754,0.290667,0.0204012,0.165709,0.748251,1.78186,0.231159,0.264653,0.617533,0.416635,0.760183,1.44754,0.28395,0.0985208,0.60723,0.180548,0.259643,0.392149,1.4358,0.864352,0.529528,0.0787487,0.147924,0.151697,0.448071,0.157997,0.21322,0.0614574,0.512406,0.0600845,0.547612,0.0504655,0.104553,0.478015,0.141543,0.181777,0.556551,0.805663,0.115453,0.240368,0.479472,0.278107,0.571352,0.300624,0.249086,1.1366,0.515129,0.653159,1.22705,0.981635,1.13675,0.0544304,0.209089,0.483605,0.679156,0.537605,0.393294,0.255455,0.364726,0.73513,1.08739,0.43915,0.930562,0.824895,0.130122,0.00553467,0.651319,0.0785724,1.63269,0.157868,0.379205,0.436366,0.120546,0.737888,0.392395,0.25519,0.127139,0.604277,0.000162154,0.279364,0.0102959,0.859503,1.18432,0.823081,0.579812,0.462581,0.672886,0.0776122,0.181399,0.229209,0.499768,0.324895,0.00795051,0.0509974,0.45769,1.23849,1.89196,0.355282,0.16277,0.406348,0.228655,0.391767,0.0697646,0.69516,0.492438,1.08687,0.171884,0.777703,0.215264,0.133612,0.460172,0.362802,0.169406,0.64371,0.319278,0.183912,0.263675,0.882719,0.379837,0.234914,2.05092,0.683004,0.182525,0.580435,0.153507,0.696335,0.26116,0.835304,0.130453,0.147939,0.179476,0.795107,1.6331,1.23566,0.759951,0.236178,0.496668,0.356718,0.589128,0.343142,1.4753,0.850664,0.162413,0.173139,0.0328567,0.58078,0.113903,0.241755,0.959994,0.308372,0.247915,0.392237,0.709852,0.758809,0.564094,0.435692,0.354071,0.36994,0.254599,0.0377709,1.93463,0.0277697|tfbs_overrepresentation_jaspar=MA0003.1;0.143293,MA0004.1;0.169125,MA0006.1;1.41774,MA0007.1;0.924144,MA0009.1;0.543169,MA0014.1;0.0126523,MA0017.1;0.657001,MA0019.1;0.275941,MA0024.1;0.450307,MA0025.1;0.665335,MA0027.1;2.11401,MA0028.1;0.0843345,MA0029.1;0.467171,MA0030.1;0.457153,MA0031.1;0.401568,MA0038.1;0.24162,MA0040.1;0.472301,MA0041.1;1.02521,MA0042.1;0.938412,MA0043.1;0.543454,MA0046.1;0.533373,MA0048.1;0.375507,MA0050.1;2.87426,MA0051.1;2.7114,MA0052.1;0.475699,MA0055.1;0.232397,MA0056.1;0,MA0057.1;0.09109,MA0058.1;0.110291,MA0059.1;0.35417,MA0060.1;0.122116,MA0061.1;0.237238,MA0063.1;0,MA0066.1;0.241938,MA0067.1;0.83875,MA0068.1;0.0133711,MA0069.1;0.529912,MA0070.1;0.519883,MA0071.1;0.213282,MA0072.1;0.515863,MA0073.1;0.00057575,MA0074.1;0.23792,MA0076.1;0.379988,MA0077.1;0.508982,MA0078.1;0.31524,MA0081.1;0.354412,MA0083.1;2.32517,MA0084.1;1.01907,MA0087.1;0.513678,MA0088.1;0.933871,MA0089.1;0,MA0090.1;0.800698,MA0091.1;0.509438,MA0092.1;0.146372,MA0093.1;0.268179,MA0095.1;0,MA0098.1;0,MA0100.1;0.252028,MA0101.1;0.0794742,MA0103.1;0.914326,MA0105.1;0.00427625,MA0106.1;1.37512,MA0107.1;0.046982,MA0108.2;0.398967,MA0109.1;0,MA0111.1;0.836455,MA0113.1;0.285689,MA0114.1;1.50951,MA0115.1;0.766188,MA0116.1;0.719614,MA0117.1;0.577217,MA0119.1;0.100647,MA0122.1;0.600851,MA0124.1;0.727093,MA0125.1;0.648747,MA0130.1;0,MA0131.1;0.329895,MA0132.1;0,MA0133.1;0,MA0135.1;0.570637,MA0136.1;0.690268,MA0139.1;1.80516,MA0140.1;0.606998,MA0141.1;1.17568,MA0142.1;0.374765,MA0143.1;0.285827,MA0144.1;0.64066,MA0145.1;1.34665,MA0146.1;0.304434,MA0147.1;1.12418,MA0148.1;0.185927,MA0149.1;0.204488,MA0062.2;0.22708,MA0035.2;0.210872,MA0039.2;0.050501,MA0138.2;0.316226,MA0002.2;1.16349,MA0137.2;1.03083,MA0104.2;0.534714,MA0047.2;0.263601,MA0112.2;0.193034,MA0065.2;0.793594,MA0150.1;0.124469,MA0151.1;0,MA0152.1;0.216094,MA0153.1;0.633172,MA0154.1;0.163016,MA0155.1;0.0886229,MA0156.1;1.03924,MA0157.1;0.352016,MA0158.1;0,MA0159.1;0.734091,MA0160.1;0.571442,MA0161.1;0,MA0162.1;0.783827,MA0163.1;0.188845,MA0164.1;0.295453,MA0080.2;0.959473,MA0018.2;0.274004,MA0099.2;2.5584,MA0079.2;9.9942e-06,MA0102.2;1.05522,MA0258.1;0.0364681,MA0259.1;0.196503,MA0442.1;0}}
|full_id=C461_oral_chorionic_squamous_amniotic_epidermoid_gall_bronchogenic
|id=C461
|ontology_enrichment_celltype=CL:0000548!5.83e-23!679;CL:0000004!5.83e-23!679;CL:0000255!5.83e-23!679;CL:0000012!2.92e-22!682;CL:0000066!8.26e-22!254;CL:0000063!4.13e-16!578;CL:0000003!2.21e-12!722;CL:0000057!5.91e-10!75;CL:0002076!1.49e-09!43;CL:0000223!1.58e-09!59;CL:0002620!2.68e-09!23;CL:0000144!1.16e-08!625;CL:0000055!2.84e-08!180;CL:0002371!5.48e-07!591
|ontology_enrichment_disease=DOID:305!9.25e-17!106;DOID:0050687!1.66e-14!143;DOID:162!3.82e-14!235;DOID:14566!7.44e-14!239;DOID:1749!3.65e-07!14
|ontology_enrichment_uberon=UBERON:0004923!9.57e-11!57;UBERON:0004119!3.94e-09!169;UBERON:0000925!3.94e-09!169;UBERON:0006595!3.94e-09!169;UBERON:0005631!1.15e-08!14;UBERON:0000158!1.15e-08!14;UBERON:0000478!5.43e-07!24
}}

Latest revision as of 11:23, 17 September 2013


Full id: C461_oral_chorionic_squamous_amniotic_epidermoid_gall_bronchogenic



Phase1 CAGE Peaks

Hg19::chr10:128111291..128111299,-p@chr10:128111291..128111299
-
Hg19::chr12:4116249..4116260,+p@chr12:4116249..4116260
+
Hg19::chr12:4121031..4121079,+p@chr12:4121031..4121079
+
Hg19::chr12:4136898..4136917,+p@chr12:4136898..4136917
+
Hg19::chr12:4136920..4136943,+p@chr12:4136920..4136943
+
Hg19::chr12:4140802..4140815,+p@chr12:4140802..4140815
+
Hg19::chr13:114487620..114487623,-p@chr13:114487620..114487623
-
Hg19::chr13:45390377..45390382,+p@chr13:45390377..45390382
+
Hg19::chr14:81036045..81036050,-p@chr14:81036045..81036050
-
Hg19::chr16:50451403..50451407,-p@chr16:50451403..50451407
-
Hg19::chr20:60736437..60736455,-p@chr20:60736437..60736455
-
Hg19::chr2:150999864..150999872,+p@chr2:150999864..150999872
+
Hg19::chr3:52705394..52705398,+p@chr3:52705394..52705398
+
Hg19::chr3:87039544..87039558,-p@chr3:87039544..87039558
-
Hg19::chr3:87039601..87039605,-p@chr3:87039601..87039605
-
Hg19::chr3:87039621..87039638,-p@chr3:87039621..87039638
-
Hg19::chr3:87039662..87039723,-p@chr3:87039662..87039723
-
Hg19::chr6:170533335..170533355,+p@chr6:170533335..170533355
+
Hg19::chr7:106415430..106415437,+p2@ENST00000490162
Hg19::chr7:106415457..106415472,+p1@ENST00000490162
Hg19::chrX:29678307..29678312,+p@chrX:29678307..29678312
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
bladder cell3.30e-401
lower urinary tract cell3.30e-401
epithelial cell of cervix3.81e-212
Disease
Ontology termp-valuen
squamous cell carcinoma2.90e-2614
carcinoma5.66e-10106
cervical cancer2.74e-095
cell type cancer1.55e-07143


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)
MA0003.10.143293
MA0004.10.169125
MA0006.11.41774
MA0007.10.924144
MA0009.10.543169
MA0014.10.0126523
MA0017.10.657001
MA0019.10.275941
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.10.24162
MA0040.10.472301
MA0041.11.02521
MA0042.10.938412
MA0043.10.543454
MA0046.10.533373
MA0048.10.375507
MA0050.12.87426
MA0051.12.7114
MA0052.10.475699
MA0055.10.232397
MA0056.10
MA0057.10.09109
MA0058.10.110291
MA0059.10.35417
MA0060.10.122116
MA0061.10.237238
MA0063.10
MA0066.10.241938
MA0067.10.83875
MA0068.10.0133711
MA0069.10.529912
MA0070.10.519883
MA0071.10.213282
MA0072.10.515863
MA0073.10.00057575
MA0074.10.23792
MA0076.10.379988
MA0077.10.508982
MA0078.10.31524
MA0081.10.354412
MA0083.12.32517
MA0084.11.01907
MA0087.10.513678
MA0088.10.933871
MA0089.10
MA0090.10.800698
MA0091.10.509438
MA0092.10.146372
MA0093.10.268179
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.0794742
MA0103.10.914326
MA0105.10.00427625
MA0106.11.37512
MA0107.10.046982
MA0108.20.398967
MA0109.10
MA0111.10.836455
MA0113.10.285689
MA0114.11.50951
MA0115.10.766188
MA0116.10.719614
MA0117.10.577217
MA0119.10.100647
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.690268
MA0139.11.80516
MA0140.10.606998
MA0141.11.17568
MA0142.10.374765
MA0143.10.285827
MA0144.10.64066
MA0145.11.34665
MA0146.10.304434
MA0147.11.12418
MA0148.10.185927
MA0149.10.204488
MA0062.20.22708
MA0035.20.210872
MA0039.20.050501
MA0138.20.316226
MA0002.21.16349
MA0137.21.03083
MA0104.20.534714
MA0047.20.263601
MA0112.20.193034
MA0065.20.793594
MA0150.10.124469
MA0151.10
MA0152.10.216094
MA0153.10.633172
MA0154.10.163016
MA0155.10.0886229
MA0156.11.03924
MA0157.10.352016
MA0158.10
MA0159.10.734091
MA0160.10.571442
MA0161.10
MA0162.10.783827
MA0163.10.188845
MA0164.10.295453
MA0080.20.959473
MA0018.20.274004
MA0099.22.5584
MA0079.29.9942e-06
MA0102.21.05522
MA0258.10.0364681
MA0259.10.196503
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
EP300#203382.580549229037410.007550248883413940.0311220919262292
FOS#235372.999318436298140.005916791946132820.0265394190887376
JUN#372563.575094054953240.004935274138548950.0230619729644704
JUND#3727113.663871588599114.44264141518177e-050.000787483073252153
SIRT6#51548214.63222895143090.008188652290872860.0323308126646934
SMARCA4#6597214.93008602932270.00787792474235810.03234383922349



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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