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Coexpression cluster:C1037: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0008380!RNA splicing!0.00102948989227113!58517;55119$GO:0006397!mRNA processing!0.00102948989227113!58517;55119$GO:0016071!mRNA metabolic process!0.00107790320168466!58517;55119$GO:0006396!RNA processing!0.0019070019214864!58517;55119$GO:0003729!mRNA binding!0.0128043276729378!58517$GO:0000375!RNA splicing, via transesterification reactions!0.0164674225721434!58517$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0164674225721434!58517$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as nucleophile!0.0164674225721434!58517$GO:0005681!spliceosome!0.0290367588376599!55119$GO:0016070!RNA metabolic process!0.0478583864116401!58517;55119
|gostat_on_coexpression_clusters=GO:0008380!RNA splicing!0.00102948989227113!58517;55119$GO:0006397!mRNA processing!0.00102948989227113!58517;55119$GO:0016071!mRNA metabolic process!0.00107790320168466!58517;55119$GO:0006396!RNA processing!0.0019070019214864!58517;55119$GO:0003729!mRNA binding!0.0128043276729378!58517$GO:0000375!RNA splicing, via transesterification reactions!0.0164674225721434!58517$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0164674225721434!58517$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as nucleophile!0.0164674225721434!58517$GO:0005681!spliceosome!0.0290367588376599!55119$GO:0016070!RNA metabolic process!0.0478583864116401!58517;55119
|id=C1037
|id=C1037
|ontology_enrichment_celltype=CL:0002032!1.08e-10!165;CL:0000837!1.08e-10!165;CL:0000037!5.72e-10!172;CL:0000566!5.72e-10!172;CL:0002087!7.91e-09!119;CL:0000988!2.92e-08!182;CL:0000860!7.33e-08!45;CL:0002031!3.26e-07!124;CL:0000763!4.67e-07!112;CL:0000049!4.67e-07!112;CL:0002057!9.75e-07!42
|ontology_enrichment_celltype=CL:0002032!5.48e-10!161;CL:0000837!5.48e-10!161;CL:0000037!2.41e-09!168;CL:0000566!2.41e-09!168;CL:0002087!1.49e-08!115;CL:0000988!4.93e-08!177;CL:0000860!6.07e-07!42;CL:0002057!6.07e-07!42;CL:0002031!7.88e-07!120
|ontology_enrichment_disease=DOID:162!2.27e-24!235;DOID:14566!1.02e-23!239;DOID:0050687!1.15e-11!143;DOID:0050686!1.37e-11!137;DOID:2531!1.60e-11!51;DOID:0060083!1.60e-11!51;DOID:1240!7.18e-10!39;DOID:305!1.86e-08!106;DOID:8692!4.55e-07!31
|ontology_enrichment_disease=DOID:162!1.22e-23!235;DOID:14566!6.57e-23!239;DOID:0050686!2.34e-11!137;DOID:0050687!2.45e-11!143;DOID:2531!3.37e-11!51;DOID:0060083!3.37e-11!51;DOID:1240!1.32e-09!39;DOID:305!4.62e-08!106;DOID:8692!9.47e-07!31
|ontology_enrichment_uberon=UBERON:0001049!1.04e-07!57;UBERON:0005068!1.04e-07!57;UBERON:0006241!1.04e-07!57;UBERON:0007135!1.04e-07!57;UBERON:0002780!6.22e-07!41;UBERON:0001890!6.22e-07!41;UBERON:0006240!6.22e-07!41
|ontology_enrichment_uberon=UBERON:0001049!2.96e-08!56;UBERON:0005068!2.96e-08!56;UBERON:0006241!2.96e-08!56;UBERON:0007135!2.96e-08!56;UBERON:0000073!2.20e-07!53;UBERON:0002616!2.20e-07!53;UBERON:0002780!3.80e-07!41;UBERON:0001890!3.80e-07!41;UBERON:0003080!3.80e-07!41;UBERON:0006240!3.80e-07!41;UBERON:0001016!9.05e-07!89;UBERON:0003528!9.51e-07!34;UBERON:0002020!9.51e-07!34
|pathway_enrichment=1.99497924496294e-05;0.0126282186206154;2;128;Spliceosome (KEGG):03040
|pathway_enrichment=1.99497924496294e-05;0.0126282186206154;2;128;Spliceosome (KEGG):03040
|tfbs_overrepresentation=0.34609,0.011681,2.68229e-06,0.122235,0.120015,0.229384,0.110615,0.00351867,0.0848916,0.0670884,0.00794804,0.493877,0.427578,0.301671,0.348998,0.15667,0.333184,0.240912,0.000454093,0.262834,0.427322,4.77497e-05,0.203945,0.233475,0.107054,0.476489,0.465564,0.00225045,0.338892,0.0287538,0.457523,0.275959,0.0473641,0.463487,0.000899052,0.209702,0.37685,0.110518,0.289619,0.168138,0.237041,0.0642921,0.331229,0.103294,0.290836,0.093749,0.0981932,0.000232793,0.269921,0.0473291,0.0106348,0.138034,0.176339,0.00242093,0.118949,0.0991916,0.261507,0.471522,0.195469,0.257345,0.0765682,0.350502,0.264034,0.189928,0.138981,0.129036,0.0302497,0.152128,5.43697e-06,0.385796,0.719203,0.17045,0.220164,0.0050472,0.0198121,0.0449986,0.237072,0.112317,0.0962742,0.0192234,0.235123,0.151056,0.109358,0.0427258,5.61967e-07,1.60562e-06,0.162509,3.3328e-07,0.243154,0.158699,0.00190601,0.12683,0.234568,0.00768611,6.9746e-09,0.0428544,1.11685e-12,0.000100355,0.228604,0.0113227,0.0112255,0.0116664,0.335028,0.0958161,6.05929e-06,0.105454,0.168814,0.00096947,0.339859,0.20448,0.101835,0.08811,0.00975188,0.0464689,0.247671,0.0874941,0.00144754,0.144037,0.0613271,0.208244,0.385121,5.90831e-31,0.331405,0.212715,0.250229,0.404991,0.223928,0.0389643,0.209445,0.320588,0.15109,1.74258e-19,0.011123,0.0596149,0.000517545,0.26293,0.163757,1.96018e-05,0.0856983,5.54523e-05,0.059589,0.052178,0.455648,0.0760906,0.435668,0.0161652,0.242306,0.209139,0.100504,0.290656,0.449653,0.0652407,0.412289,0.069324,0.109875,0.00482319,0.187146,0.00551232,0.131992,0.087425,0.497965,0.234343,0.281603,0.347181,0.573425,0.276476,0.103223,0.304631,0.104025,0.0188413,0.00213355,0.326422,0.8104,0.137927,0.199209,0.222543,7.93622e-13,0.414399,0.0976182,0.0922244,0.0786964,0.29418,0.0714241,0.0432422,6.15887e-05,0.0455995,0.416713,0.10358,4.49399e-06,0.398511,0.260822,0.0187303,0.00550021,0.153327,0.272958,0.120656,0.195303,0.152795,0.0154179,0.039134,0.220771,0.0123624,0.0801204,0.153558,0.0592113,0.0475412,0.210133,0.0723592,1.24245e-09,0.407776,9.26544e-06,0.00339971,0.291346,5.09747e-08,0.00365195,0.0139258,0.0014922,0.0333953,0.159292,0.251613,0.000836345,4.31928e-28,0.363941,0.00138088,0.185037,0.0514113,0.328766,0.213152,0.153196,0.151857,0.894484,0.726218,0.10772,0.191224,0.235781,0.229621,0.121035,2.0861e-07,0.378787,0.027778,0.101704,0.681658,0.241356,0.206521,0.280824,0.000723288,0.202866,4.70727e-08,0.711768,0.000388272,0.369936,0.0181213,0.421863,0.240524,0.00283308,0.00133541,0.261035,0.451876,0.174963,2.79438e-08,0.156722,1.63982e-05,0.378539,4.0157e-05,0.0894087,0.201841,0.202064,0.22706,0.0450406,0.0190889,6.81823e-25,0.160003,0.00129376,0.468116,0.214569,0.0982663,1.41121e-07,9.59812e-12,0.120852,0.772492,1.29133e-11,0.890059,9.44053e-10,0.155209,0.663653,0.274443,1.155e-09,0.210551,0.131022,0.627136,4.70804e-07,0.657245,0.0121505,1.88898e-06,9.97763e-06,0.921959,3.08965e-06,0.602042,0.750422,0.0482675,0.205597,0.911491,0.424714,0.699335,0.414206,0.770296,0.267081,0.290524,5.90788e-06,0.187425,0.359502,0.809664,0.149395,0.32438,0.859351,8.47019e-09,0.761328,0.103467,0.541539,0.57865,0.003055,0.256812,0.0199997,0.00506122,0.845203,3.84519e-16,8.23543e-18,0.00378256,0.403575,0.234746,1.22344e-07,0.082836,0.17576,0.236302,0.00860205,3.46147e-05,0.71307,0.403501,3.5693e-12,0.0173425,0.837361,0.989856,0.974624,6.12244e-13,0.162604,2.34944e-05,0.678158,4.16997e-20,1.76756e-09,0.927362,0.845065,1.81986e-08,0.860382,0.533408,2.40959e-23,0.508315,0.378278,0.16896,0.183237,0.0180168,0.0121125,0.00207919,0.410586,0.415009,0.0806852,0.878845,2.15856e-13,0.795,0.482042,0.00366561,0.000458071,0.115811,0.187131,0.500188,0.769073,0.906819,0.285462,0.605844,0.0273552,0.822718,0.231296,0.0909728,0.00436039,0.580536,3.87268e-06,0.775251,0.498619,0.298476,2.08268e-07,0.364444,0.38661,0.767612,0.82753,0.766712,0.85596,0.994589,0.00013952,0.000905829,5.2851e-06,0.142565,0.7159,0.211818,0.227762,0.0439093,0.357127,0.11942,0.0597407,0.550758,0.320286,0.0319169,0.0628286,0.604353,0.590606,0.674753,0.255495,0.622141,0.913966,0.000142532,0.0042216,0.59066,0.195566,0.695117,0.495426,0.0138159,0.176045,0.339358,0.234178,0.0144768,0.000443679,5.81301e-13,1.32327e-09,0.0698224,0.204349,0.0261217,0.362002,0.000307637,0.334789,0.802189,0.859142,0.371064,0.1652,0.711127,0.157469,0.0193774,0.220397,0.151053,5.48868e-12,1.96669e-05,0.679442,0.000301347,0.682813,0.820689,0.402141,0.934803,0.929578,0.63705,0.175401,0.141685,0.434651,0.194711,0.0112567,0.340075,5.82701e-07,0.0238389,1.22899e-08,0.788696,4.85744e-39,0.0406844,0.0140004,0.111931,5.52777e-10,0.302737,0.320418,0.260259,0.0550963,0.158807,0.722166,0.0470509,0.619467,0.583243,0.0113202,0.119202,0.390797,0.0425398,0.000247937,0.0267642,0.214812,0.37149,0.260746,0.112737,0.0103413,0.000482465,0.0533825,3.51601e-07,0.0206292,2.35157e-22,0.127781,0.206068,0.000905883,0.415102,0.269909,0.0295078,0.293328,0.44032,0.314851,0.427434,0.123376,0.448411,0.163866,0.305458,0.0155926,0.419481,0.0885159,0.216979,0.234229,0.0297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344,0.145752,0.260596,6.08564e-13,0.0127838,0.398796,0.333467,0.469524,0.0781888,0.00670663,0.000272676,0.13361,0.464613,0.35815,0.198877,0.000187077,0.372126,0.296436,0.223838,0.141981,0.587588,0.856955,0.325601,0.038461,0.165742,0.133385,0.48542,0.00156075,0.189558,6.73432e-07,3.00229e-05,0.139793,0.19465,0.142897,0.000225368,0.0894806,0.100334,0.543343,0.000168769,4.96761e-15,0.125132,0.401145,0.708839,0.0857811,0.681349,0.48369,0.101821,0.151258,0.765247,0.294186,0.264629,0.267153,0.554314,0.0744668,0.357257,0.340579,0.10027,0.216542,0.140095,7.2581e-05,0.541739,0.00450929,0.10958,0.0549007,0.15125,0.00089885,0.228257,0.190339,0.39643,0.203718,0.416086,0.0248755,3.49311e-07,0.33418,0.386217,0.332439,0.219989,0.627646,0.594435,0.121222,0.233436,0.466178,0.316293,0.0200406,0.00388424,0.307168,0.313275,0.00468733,0.471283,0.132332,0.00294597,0.127929,0.1565,0.188908,0.230656,0.339566,0.0881682,0.18579,3.44934e-07,0.695352,9.65491e-21,0.479647,0.0646306,0.28717,0.0202632,5.01171e-09,0.879571,0.146252,0.12193,0.735829,0.154198,0.401916,0.0719341,0.179067,0.491271,0.600481,0.0920973,0.300879,0.0942623,0.998435,0.999352,0.460251,0.00460229,0.263319,0.169668,0.264355,1.24678e-05,1.58647e-08,0.126607,0.189069,0.117159,9.70532e-07,0.1766,0.495277,0.358721,0.00490333,0.315733,0.00694935,0.13739,0.000352778,0.229078,0.0147452,0.255961,0.487366,0.145278,0.159951,0.190011,0.59406,6.42319e-20,0.0029466,0.0290818,1.21041e-24,2.17822e-24,0.0921742,1.32536e-12,0.354931,0.158525,0.019919,0.348785,0.846337,0.36346,0.180408,0.226687,0.152678,0.340038,0.35297,0.239072,0.0752133,0.39215,0.436719,0.325366,0.498702,0.00806028,0.595929,0.0457329,0.208355,0.658265,0.273994,0.272914,0.423557,1.17513e-06,0.0296333,0.000207073,0.178249,0.00813422,0.24444,0.548105,0.253118,0.273827,0.0667061,0.00163047,0.223866,1.38146e-15,0.385626,0.427353,0.202588,3.90903e-10,3.48393e-18,0.0796865,0.852275,0.149927,0.0415289,0.407834,0.000590709,0.503758,0.752108,0.924193,0.0933565,0.757541,0.0549043,0.111737,0.317827,0.423292,0.707417,0.00585821,0.752206,9.14186e-05,0.349984,0.786493,3.06818e-14,3.52679e-15,0.00128208,2.84675e-06,0.0481292,0.00764599,0.750697,0.721788,0.901346,0.936229,0.778763,0.663186,0.0113159,0.832307,0.552306,0.073583,0.861021,0.99617,0.995774,5.06968e-08,0.580125,0.725822,0.728237,0.225029,0.846474,0.000387035,0.676036,4.64295e-05,0.380163,0.809189,0.595604,0.897663,0.823504,2.45629e-08,0.00768396,0.549112,0.000237235,2.08157e-16,0.908843,0.0453618,0.868268,0.195849,0.375011,0.716143,0.936699,0.113137,0.926969,0.712705,0.915485,0.822762,0.983171,0.305935,0.904104,0.00348761,0.44937,0.458665,0.246976,0.546419,0.772399,0.681923,0.369258,0.364029,0.333879,0.0148865,0.236293,3.93828e-22,0.689159,0.379433,0.502911,0.289349,0.590067,0.889628,0.0815334,0.413633,0.00217632,0.573854,0.922307,0.753368,0.856,0.277896,0.941952,1.22689e-12,0.918981,0.729164,0.860789,0.986712,0.0052382,0.488054,0.000724032,4.76456e-10,0.0868044,0.970896,0.900712,0.457276,4.66882e-05,0.328805,0.798571,0.385504,0.117909,0.207197,0.637438,0.825729,0.401684,0.000132852,0.354359,0.861581,0.753866,0.702714,0.604827,0.380942,0.699838,0.162041,0.45485,0.573299,0.715409,0.79357,0.684354,0.576345,0.507731,0.0174149,0.168342,0.710061,0.62342,0.619131,0.839028,0.728293,0.123891,0.0432865,0.724424,0.48558,0.846436,0.000618635,0.124815,0.442887,0.432731,0.810194,5.51872e-08,0.624396,0.0260605,4.01635e-05,0.890421,0.00816965,1.09742e-14,0.0111854,6.22182e-11,0.0561025,0.141644,0.00208784,3.42601e-05,0.0262578,0.44442,0.917799,0.72892,1.25248e-17,0.865189,0.613531,0.748236,1.9471e-08,0.403985,0.194485,0.214535,0.458152,0.00393548,0.42925,0.55014,0.107704,0.180477,0.559835,6.96793e-07,0.431837,0.0125397,0.483463,0.00380986,0.222529,0.234528,0.383967,0.539263,0.718529,0.544718,0.462199,0.794152,0.409798,0.436622,0.486064,0.489702,0.672033,0.0788555,0.140585,0.445913,0.00248861,0.296003,0.447485,0.00368133,0.0024453,0.000489601,0.410714,0.0053692,0.581581,0.212206,4.51615e-05,0.129563,0.176405,0.488584,0.169631,0.4639,0.0101388,0.273878,0.342908,0.500922,0.376098,0.000753044,0.389123,0.0993883,3.9843e-05,0.133211,0.116907,0.565967,0.451406,0.683557,0.00118502,0.289284,0.00288301,0.00380822,0.151053,0.477267,0.368791,0.00478219,0.43963,0.297904,0.551399,0.625257,0.412086,0.371597,6.23827e-11,0.353179,3.29885e-08,1.98076e-06,0.00235989,0.42109,0.18144,0.54956,0.554803,0.000417751,0.473509,0.128652,0.335015,0.435559,0.00776547,0.28015,0.492484,0.529209,0.00183666,0.00328919,0.330704,3.39469e-05,0.00675792,0.364755,0.312488,0.547073,0.48939,0.395736,0.00020379,0.238065,0.452384,0.0184454,0.0124705,0.481224,9.52235e-05,0.452254,0.259924,0.136638,0.137048,0.353983,0.194753,0.104944,0.136955,0.0207614,0.0487499,0.00405604,0.0188559,0.159135,0.429061,0.0220136,0.240717,0.162041,0.0478574,0.161384,0.255196,0.167238,0.190639,0.307532,0.00388185,0.113346,0.000916259,0.00013408,0.095012,0.00722918,0.0240877,0.607439,0.5938,0.679098,2.40717e-11,0.557075,1.84306e-06,0.448658,0.00542756,0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}}
}}

Revision as of 10:44, 19 October 2012


Full id: C1037_acute_medulloblastoma_Monocytederived_CD4_diffuse_testicular_small



Phase1 CAGE Peaks

Hg19::chr14:73566082..73566112,+p@chr14:73566082..73566112
+
Hg19::chr14:73570051..73570166,+p@chr14:73570051..73570166
+
Hg19::chr14:73572641..73572756,+p4@RBM25
Hg19::chr1:109241850..109241862,+p6@PRPF38B
Hg19::chr1:109241964..109241981,+p2@PRPF38B
Hg19::chr1:109241994..109242012,+p4@PRPF38B
Hg19::chr1:109242036..109242049,+p5@PRPF38B
Hg19::chr1:70710380..70710454,+p@chr1:70710380..70710454
+


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


p.valueFDRnGenesnPathwayName
1.99497924496294e-050.01262821862061542128Spliceosome (KEGG):03040



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


GO IDGO nameFDR corrected p-value
GO:0008380RNA splicing0.00102948989227113
GO:0006397mRNA processing0.00102948989227113
GO:0016071mRNA metabolic process0.00107790320168466
GO:0006396RNA processing0.0019070019214864
GO:0003729mRNA binding0.0128043276729378
GO:0000375RNA splicing, via transesterification reactions0.0164674225721434
GO:0000398nuclear mRNA splicing, via spliceosome0.0164674225721434
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0164674225721434
GO:0005681spliceosome0.0290367588376599
GO:0016070RNA metabolic process0.0478583864116401



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>


Uber Anatomy
Ontology termp-valuen
neural tube2.96e-0856
neural rod2.96e-0856
future spinal cord2.96e-0856
neural keel2.96e-0856
regional part of nervous system2.20e-0753
regional part of brain2.20e-0753
regional part of forebrain3.80e-0741
forebrain3.80e-0741
anterior neural tube3.80e-0741
future forebrain3.80e-0741
nervous system9.05e-0789
brain grey matter9.51e-0734
gray matter9.51e-0734
Disease
Ontology termp-valuen
cancer1.22e-23235
disease of cellular proliferation6.57e-23239
organ system cancer2.34e-11137
cell type cancer2.45e-11143
hematologic cancer3.37e-1151
immune system cancer3.37e-1151
leukemia1.32e-0939
carcinoma4.62e-08106
myeloid leukemia9.47e-0731


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)

{{{tfbs_overrepresentation_jaspar}}}



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


No analysis results for this cluster

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.