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Coexpression cluster:C232: Difference between revisions

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{{Coexpression_clusters
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12584,0.871969,0.500998,0.9933,0.878003,0.778253,0.482699,0.67298,0.985931,0.880248,0.772017,0.511531,0.997394,0.999631,0.737772,0.999747,0.800199,0.999981,0.605411,0.795577,0.969983,0.982354,0.999932,0.784331,0.962971,0.764263,0.213782,0.986375,0.995328,0.999886,0.683983,0.960073,0.806755,0.999992,0.716763,0.988691,0.261461,0.78337,0.954385,0.902107,0.714115,0.609388,0.997355,0.981397,0.994901,0.986998,0.972226,0.43579,0.30985,0.944902,0.887737,0.915369,0.954954,0.651266,0.637986,0.917316,0.978529,0.659443,0.470415,0.938751,0.742941,0.323464,0.773923,0.850783,0.373738,0.967316,0.475319,0.763382,0.880154,0.975601,0.651,0.433961,0.96866,0.960597,0.995158,0.965803,0.905879,0.857763,0.649073,0.891635,0.629607,0.587387,0.780917,0.988645,0.951768,0.887317,0.845868,0.824335,0.966164,0.96985,0.713606,0.967648,0.72997,0.656282,0.686411,0.904374,0.807774,0.959775,0.844901,0.50209,0.926681,0.983952,0.418158,0.780768,0.948568,0.875041,0.803993,0.876198,0.740149,0.949921,0.853287,0.869695,0.975127,0.840473,0.748216,0.554262,0.694941,0.762139,0.764898,0.275921,0.572676,0.963725,0.969905,0.765577,0.735007,0.988914,0.922311,0.931178,0.829073,0.490209,0.863548,0.750078,0.0223445,0.966701,0.897648,0.837764,0.778585,0.514805,0.927682,0.884557,0.757651,0.515278,0.873862,0.229739,0.959318,0.774507,0.0730409,0.89752,0.976671,0.549858,0.404884,0.663808,0.612476,0.987317,0.835009,0.975107,0.855757,0.733349,0.623559,0.677006,0.71311,0.55002,0.680703,0.880341,0.987919,0.932583,0.984244,0.335842,0.769161,0.68692,0.997638,0.963923,0.958787,0.932119,0.918322,0.128891,0.782725,0.725662,0.421053,0.99028,0.540283,0.51098,0.601198,0.810159,0.232321,0.918441,0.414099,0.67925,0.978995,0.831774,0.809873,0.822329,0.65679,0.671654,0.320747,0.939757,0.885499,0.978529,0.755335,0.156319,0.0193143,0.995529,0.505667,0.735558,0.520579,0.989845,0.899253,0.67381,0.674988,0.845205,0.808262,0.570603,0.674722,0.952787,0.737043,0.953335,0.923754,0.905925,0.926531,0.821636,0.620328,0.740239,0.928889,0.387988,0.894241,0.752274,0.800664,0.93932,0.904688,0.600398,0.75563,0.298687,0.532909,0.947564,0.945942,0.973134,0.967307,0.991867,0.816364,0.94675,0.849833,0.940866,0.967155,0.974625,0.707499,0.981264,0.991182,0.59269,0.781042,0.870433,0.948005,0.300138,0.967445,0.640271,0.996971,0.456917,0.959617,0.887593,0.917132,0.987846,0.986561,0.902931,0.905467,0.834738,0.707351,0.412673,0.86436,0.695221,0.594302,0.851304,0.871183,0.545105,0.996225,0.97829,0.144681,0.883575,0.77685,0.618623,0.885298,0.884986,0.903512,0.270652,0.548984,0.542277,0.846607,0.994341|tfbs_overrepresentation_for_novel_motifs=0.0266749,0.0122587,0.0244656,1.04942,0.217865,0.434722,0.14804,0.280266,0.403423,0.0808238,0.612856,0.733315,0.0460563,0.138529,0.550178,0.140411,0.38793,0.222361,0.0272041,0.136639,1.00928,0.0891804,0.21765,0.044678,0.240396,0.20872,0.0593144,0.0849417,0.567815,0.0778901,0.0126847,0.14148,0.0366067,0.35971,0.0303031,0.14844,0.00113983,0.229701,0.208211,0.0349267,0.842936,0.0528835,0.336531,0.212257,0.00578961,0.215107,0.344497,0.175423,0.586629,0.37462,0.223047,0.040951,0.0561057,0.185058,1.42128,0.140925,0.387138,0.277855,0.414934,0.114647,0.492768,0.150961,0.0973898,0.352855,0.0433443,0.642939,0.350587,0.658583,0.422519,0.516982,0.046875,0.439935,0.0529327,0.775783,0.00192709,0.113424,1.18663,0.101246,0.418204,0.404533,0.299524,0.108558,0.377973,1.02009,0.248516,6.61632e-07,0.369965,0.276879,1.36827,0.748573,0.423767,0.230543,0.459241,0.277969,0.367384,0.317637,0.400592,0.174731,0.0733195,0.0859441,0.211212,0.451517,0.171477,0.124329,0.0884977,0.0702504,0.116504,0.318558,0.11431,0.0389709,0.184314,0.97773,0.159822,0.0783143,0.385616,0.259441,0.00987254,0.0603198,0.0924319,0.0936256,0.27828,0.247799,0.428553,0.397442,0.475037,0.333024,0.602081,0.153318,0.308831,0.108185,0.65322,0.165784,1.54318,0.39165,0.434176,0.104498,1.50627,0.215519,0.400154,1.17966,0.796831,0.370915,0.335164,0.989142,0.622722,1.15654,0.280545,1.02612,0.0513238,0.00339876,0.0204391,9.58754e-05,0.231247,0.0418672,0.0382744,1.34113,1.30485,0.191428,0.240497,0.029738,0.369974,0.219209,0.133886,0.198216,0.656164,0.165569,0.939981,0.614907,6.0459e-06|tfbs_overrepresentation_jaspar=MA0003.1;1.15416e-05,MA0004.1;0.195251,MA0006.1;0.00217274,MA0007.1;0.172037,MA0009.1;0.204394,MA0014.1;1.691e-06,MA0017.1;0.072348,MA0019.1;0.191546,MA0024.1;0.142868,MA0025.1;0.294989,MA0027.1;1.65408,MA0028.1;0.0173494,MA0029.1;0.909931,MA0030.1;0.147145,MA0031.1;0.365193,MA0038.1;1.87051,MA0040.1;0.923645,MA0041.1;1.01595,MA0042.1;1.62746,MA0043.1;0.204593,MA0046.1;0.197569,MA0048.1;0.0337299,MA0050.1;0.179546,MA0051.1;0.34028,MA0052.1;0.158952,MA0055.1;0.0504723,MA0056.1;0,MA0057.1;0.00576414,MA0058.1;0.0926466,MA0059.1;0.0915374,MA0060.1;1.22836,MA0061.1;0.0111768,MA0063.1;0,MA0066.1;0.0383404,MA0067.1;0.43712,MA0068.1;1.78606,MA0069.1;0.568357,MA0070.1;0.188293,MA0071.1;0.28527,MA0072.1;0.185556,MA0073.1;0.164074,MA0074.1;0.14616,MA0076.1;0.00696909,MA0077.1;1.02246,MA0078.1;0.242376,MA0081.1;0.564043,MA0083.1;0.601727,MA0084.1;0.596203,MA0087.1;0.184074,MA0088.1;0.00356109,MA0089.1;0,MA0090.1;0.969737,MA0091.1;0.385792,MA0092.1;0.307878,MA0093.1;0.114498,MA0095.1;0,MA0098.1;0,MA0100.1;0.370772,MA0101.1;0.0502056,MA0103.1;0.100367,MA0105.1;0.000323139,MA0106.1;0.0502319,MA0107.1;0.0477538,MA0108.2;1.20021,MA0109.1;0,MA0111.1;0.276587,MA0113.1;0.203809,MA0114.1;0.292682,MA0115.1;0.376065,MA0116.1;0.0502539,MA0117.1;0.22866,MA0119.1;0.0256525,MA0122.1;0.688133,MA0124.1;0.344064,MA0125.1;0.282149,MA0130.1;0,MA0131.1;0.262224,MA0132.1;0,MA0133.1;0,MA0135.1;0.223906,MA0136.1;0.0401427,MA0139.1;0.00825033,MA0140.1;0.117046,MA0141.1;0.557382,MA0142.1;6.01022,MA0143.1;2.80407,MA0144.1;0.0789837,MA0145.1;0.00603849,MA0146.1;0.00658866,MA0147.1;0.0196811,MA0148.1;0.708648,MA0149.1;0.0260116,MA0062.2;0.00057408,MA0035.2;0.280133,MA0039.2;0.00450393,MA0138.2;0.243696,MA0002.2;0.0391724,MA0137.2;0.0604977,MA0104.2;0.00639385,MA0047.2;0.397271,MA0112.2;0.00062245,MA0065.2;0.00101873,MA0150.1;0.115109,MA0151.1;0,MA0152.1;0.85347,MA0153.1;0.270235,MA0154.1;0.53616,MA0155.1;0.0286539,MA0156.1;0.0194723,MA0157.1;0.29301,MA0158.1;0,MA0159.1;0.694377,MA0160.1;0.249928,MA0161.1;0,MA0162.1;9.05541e-06,MA0163.1;0.00342326,MA0164.1;0.472135,MA0080.2;0.114601,MA0018.2;0.0506682,MA0099.2;0.122327,MA0079.2;2.87634e-10,MA0102.2;0.629093,MA0258.1;0.068534,MA0259.1;0.00596409,MA0442.1;0}}
|full_id=C232_teratocarcinoma_HES3GFP_H9_iPS_testicular_neuroblastoma_cerebellum
|id=C232
}}

Latest revision as of 11:02, 17 September 2013


Full id: C232_teratocarcinoma_HES3GFP_H9_iPS_testicular_neuroblastoma_cerebellum



Phase1 CAGE Peaks

Hg19::chr10:98161098..98161100,+p@chr10:98161098..98161100
+
Hg19::chr11:122684227..122684231,+p@chr11:122684227..122684231
+
Hg19::chr11:2022489..2022501,-p37@H19
Hg19::chr11:41327517..41327518,+p@chr11:41327517..41327518
+
Hg19::chr11:92850299..92850305,-p@chr11:92850299..92850305
-
Hg19::chr12:68284590..68284597,-p@chr12:68284590..68284597
-
Hg19::chr12:8034314..8034336,-p@chr12:8034314..8034336
-
Hg19::chr13:102603275..102603278,+p@chr13:102603275..102603278
+
Hg19::chr13:27914684..27914686,-p@chr13:27914684..27914686
-
Hg19::chr13:44925859..44925864,+p@chr13:44925859..44925864
+
Hg19::chr13:51747485..51747488,-p@chr13:51747485..51747488
-
Hg19::chr14:98103699..98103702,-p@chr14:98103699..98103702
-
Hg19::chr15:73150394..73150400,+p@chr15:73150394..73150400
+
Hg19::chr15:79787932..79787937,-p@chr15:79787932..79787937
-
Hg19::chr16:16064786..16064790,-p@chr16:16064786..16064790
-
Hg19::chr1:10875488..10875494,+p@chr1:10875488..10875494
+
Hg19::chr1:146544055..146544062,-p@chr1:146544055..146544062
-
Hg19::chr1:38619558..38619563,+p@chr1:38619558..38619563
+
Hg19::chr1:62661907..62661916,+p@chr1:62661907..62661916
+
Hg19::chr1:62675663..62675671,-p@chr1:62675663..62675671
-
Hg19::chr20:52685670..52685678,+p@chr20:52685670..52685678
+
Hg19::chr2:168243434..168243438,+p@chr2:168243434..168243438
+
Hg19::chr2:169769806..169769861,-p2@SPC25
Hg19::chr2:202835658..202835677,+p@chr2:202835658..202835677
+
Hg19::chr2:48919688..48919703,+p@chr2:48919688..48919703
+
Hg19::chr2:48919725..48919761,+p@chr2:48919725..48919761
+
Hg19::chr3:14658573..14658581,+p@chr3:14658573..14658581
+
Hg19::chr3:186700341..186700345,+p@chr3:186700341..186700345
+
Hg19::chr3:194646645..194646650,-p@chr3:194646645..194646650
-
Hg19::chr3:32455724..32455728,-p@chr3:32455724..32455728
-
Hg19::chr3:32904712..32904715,+p@chr3:32904712..32904715
+
Hg19::chr3:32937906..32937913,+p@chr3:32937906..32937913
+
Hg19::chr3:32938576..32938590,+p@chr3:32938576..32938590
+
Hg19::chr4:113572878..113572895,-p@chr4:113572878..113572895
-
Hg19::chr4:113628003..113628015,-p1@ENST00000505632
Hg19::chr5:116157646..116157650,+p@chr5:116157646..116157650
+
Hg19::chr5:118738398..118738400,+p@chr5:118738398..118738400
+
Hg19::chr5:120034108..120034114,-p@chr5:120034108..120034114
-
Hg19::chr5:122512045..122512049,+p@chr5:122512045..122512049
+
Hg19::chr5:147253888..147253894,-p@chr5:147253888..147253894
-
Hg19::chr5:81591218..81591231,+p@chr5:81591218..81591231
+
Hg19::chr6:10417667..10417676,-p54@TFAP2A
Hg19::chr7:148034419..148034425,+p@chr7:148034419..148034425
+
Hg19::chr7:21120890..21120893,+p@chr7:21120890..21120893
+
Hg19::chr7:24436189..24436212,+p@chr7:24436189..24436212
+
Hg19::chr7:44263545..44263550,-p@chr7:44263545..44263550
-
Hg19::chr7:66858115..66858118,+p@chr7:66858115..66858118
+
Hg19::chr8:101973268..101973275,+p@chr8:101973268..101973275
+
Hg19::chr8:38389009..38389020,+p@chr8:38389009..38389020
+
Hg19::chr9:17536850..17536852,+p@chr9:17536850..17536852
+
Hg19::chr9:5868313..5868316,+p@chr9:5868313..5868316
+
Hg19::chr9:79633621..79633632,+p2@FOXB2
Hg19::chr9:93653244..93653250,-p@chr9:93653244..93653250
-
Hg19::chrX:136646431..136646476,+p@chrX:136646431..136646476
+
Hg19::chrX:136648279..136648295,+p1@ZIC3
Hg19::chrX:136648297..136648319,+p3@ZIC3
Hg19::chrX:136648554..136648576,+p4@ZIC3
Hg19::chrX:136650899..136650918,+p7@ZIC3
Hg19::chrX:36968877..36968881,-p@chrX:36968877..36968881
-
Hg19::chrX:97828862..97828879,+p@chrX:97828862..97828879
+
Hg19::chrX:99848620..99848641,+p5@TNMD


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
embryonic stem cell1.35e-705
germ line cell3.03e-327
germ cell3.03e-327
melanocyte1.99e-1310
melanoblast1.99e-1310
neuron1.73e-106
neuroblast1.73e-106
electrically signaling cell1.73e-106
pigment cell9.24e-1014
neuronal stem cell4.34e-088
neurecto-epithelial cell5.45e-0720
Uber Anatomy
Ontology termp-valuen
testis2.83e-288
male reproductive organ1.11e-2011
gonad1.07e-1621
indifferent external genitalia1.07e-1621
indifferent gonad1.07e-1621
gonad primordium1.07e-1621
external genitalia6.11e-1622
male organism1.66e-1022
male reproductive system1.66e-1022
body cavity1.28e-0746
reproductive organ2.68e-0748
body cavity or lining3.79e-0749
Disease
Ontology termp-valuen
germ cell and embryonal cancer8.31e-2322
germ cell cancer8.31e-2322


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)
MA0003.11.15416e-05
MA0004.10.195251
MA0006.10.00217274
MA0007.10.172037
MA0009.10.204394
MA0014.11.691e-06
MA0017.10.072348
MA0019.10.191546
MA0024.10.142868
MA0025.10.294989
MA0027.11.65408
MA0028.10.0173494
MA0029.10.909931
MA0030.10.147145
MA0031.10.365193
MA0038.11.87051
MA0040.10.923645
MA0041.11.01595
MA0042.11.62746
MA0043.10.204593
MA0046.10.197569
MA0048.10.0337299
MA0050.10.179546
MA0051.10.34028
MA0052.10.158952
MA0055.10.0504723
MA0056.10
MA0057.10.00576414
MA0058.10.0926466
MA0059.10.0915374
MA0060.11.22836
MA0061.10.0111768
MA0063.10
MA0066.10.0383404
MA0067.10.43712
MA0068.11.78606
MA0069.10.568357
MA0070.10.188293
MA0071.10.28527
MA0072.10.185556
MA0073.10.164074
MA0074.10.14616
MA0076.10.00696909
MA0077.11.02246
MA0078.10.242376
MA0081.10.564043
MA0083.10.601727
MA0084.10.596203
MA0087.10.184074
MA0088.10.00356109
MA0089.10
MA0090.10.969737
MA0091.10.385792
MA0092.10.307878
MA0093.10.114498
MA0095.10
MA0098.10
MA0100.10.370772
MA0101.10.0502056
MA0103.10.100367
MA0105.10.000323139
MA0106.10.0502319
MA0107.10.0477538
MA0108.21.20021
MA0109.10
MA0111.10.276587
MA0113.10.203809
MA0114.10.292682
MA0115.10.376065
MA0116.10.0502539
MA0117.10.22866
MA0119.10.0256525
MA0122.10.688133
MA0124.10.344064
MA0125.10.282149
MA0130.10
MA0131.10.262224
MA0132.10
MA0133.10
MA0135.10.223906
MA0136.10.0401427
MA0139.10.00825033
MA0140.10.117046
MA0141.10.557382
MA0142.16.01022
MA0143.12.80407
MA0144.10.0789837
MA0145.10.00603849
MA0146.10.00658866
MA0147.10.0196811
MA0148.10.708648
MA0149.10.0260116
MA0062.20.00057408
MA0035.20.280133
MA0039.20.00450393
MA0138.20.243696
MA0002.20.0391724
MA0137.20.0604977
MA0104.20.00639385
MA0047.20.397271
MA0112.20.00062245
MA0065.20.00101873
MA0150.10.115109
MA0151.10
MA0152.10.85347
MA0153.10.270235
MA0154.10.53616
MA0155.10.0286539
MA0156.10.0194723
MA0157.10.29301
MA0158.10
MA0159.10.694377
MA0160.10.249928
MA0161.10
MA0162.19.05541e-06
MA0163.10.00342326
MA0164.10.472135
MA0080.20.114601
MA0018.20.0506682
MA0099.20.122327
MA0079.22.87634e-10
MA0102.20.629093
MA0258.10.068534
MA0259.10.00596409
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
TAF7#6879203.748547345876691.22287687352815e-077.02895089677525e-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

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