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Coexpression cluster:C3966: Difference between revisions

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|full_id=C3966_CD14_CD19_Basophils_Mast_Peripheral_Neutrophils_CD34
|full_id=C3966_CD14_CD19_Basophils_Mast_Peripheral_Neutrophils_CD34
|id=C3966
|id=C3966
|ontology_enrichment_celltype=CL:0000738!1.59e-44!140;CL:0000037!1.54e-37!172;CL:0000566!1.54e-37!172;CL:0002031!4.38e-36!124;CL:0000988!8.80e-36!182;CL:0002032!1.52e-33!165;CL:0000837!1.52e-33!165;CL:0002087!2.07e-33!119;CL:0002057!1.10e-27!42;CL:0000860!4.85e-25!45;CL:0000766!4.44e-21!76;CL:0000839!3.40e-18!70;CL:0000557!9.11e-18!71;CL:0000763!6.47e-17!112;CL:0000049!6.47e-17!112;CL:0000542!2.14e-16!53;CL:0000051!2.14e-16!53;CL:0000838!3.17e-16!52;CL:0002009!5.43e-16!65;CL:0002194!6.08e-15!63;CL:0000576!6.08e-15!63;CL:0000040!6.08e-15!63;CL:0000559!6.08e-15!63;CL:0000945!2.68e-10!24;CL:0000826!2.68e-10!24;CL:0000791!3.53e-09!18;CL:0000789!3.53e-09!18;CL:0002420!3.53e-09!18;CL:0002419!3.53e-09!18;CL:0000790!3.53e-09!18;CL:0000236!8.08e-09!14;CL:0002393!4.79e-08!9;CL:0002397!4.79e-08!9
|ontology_enrichment_celltype=CL:0000738!1.35e-69!136;CL:0000037!5.51e-55!168;CL:0000566!5.51e-55!168;CL:0002031!4.26e-51!120;CL:0000988!5.58e-51!177;CL:0002087!1.20e-50!115;CL:0002032!1.76e-49!161;CL:0000837!1.76e-49!161;CL:0000860!9.84e-46!42;CL:0002057!9.84e-46!42;CL:0000766!3.82e-42!72;CL:0000473!1.57e-38!48;CL:0000234!1.57e-38!48;CL:0000557!1.23e-36!67;CL:0000839!1.96e-33!66;CL:0002009!6.12e-33!61;CL:0000763!2.09e-31!108;CL:0000049!2.09e-31!108;CL:0002194!1.77e-30!59;CL:0000576!1.77e-30!59;CL:0000040!1.77e-30!59;CL:0000559!1.77e-30!59;CL:0000236!7.77e-19!14;CL:0000945!1.41e-18!24;CL:0000826!1.41e-18!24;CL:0002393!2.58e-17!9;CL:0002397!2.58e-17!9;CL:0000325!2.91e-16!87;CL:0000134!6.40e-16!354;CL:0000542!8.21e-16!53;CL:0000051!8.21e-16!53;CL:0002320!3.56e-15!361;CL:0002242!5.87e-15!55;CL:0000838!6.65e-15!52;CL:0000219!3.86e-13!386;CL:0000034!1.27e-11!441;CL:0000048!6.15e-11!427;CL:0000723!1.76e-10!433;CL:0000094!1.10e-08!8;CL:0000767!4.54e-07!3;CL:0000451!7.93e-07!10;CL:0000226!9.72e-07!3;CL:0000842!9.72e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!7.31e-17!102;UBERON:0003061!7.31e-17!102;UBERON:0002193!1.57e-15!112;UBERON:0002371!6.64e-15!80;UBERON:0001474!2.26e-13!86;UBERON:0002405!3.30e-13!115;UBERON:0004765!5.35e-11!101;UBERON:0001434!5.35e-11!101
|ontology_enrichment_uberon=UBERON:0002390!7.70e-31!98;UBERON:0003061!7.70e-31!98;UBERON:0002371!9.26e-31!76;UBERON:0001474!1.45e-27!82;UBERON:0002405!1.13e-26!93;UBERON:0002193!1.30e-26!108;UBERON:0004765!5.55e-24!90;UBERON:0001434!2.49e-20!100;UBERON:0002384!3.65e-14!371;UBERON:0003081!1.09e-10!203;UBERON:0002204!3.69e-08!167
|tf_chipseq_enrich=PBX3#5090;2:14.6096751244961:0.00605612247321789:0.026840457245084
|tf_chipseq_enrich=PBX3#5090;2:14.6096751244961:0.00605612247321789:0.026840457245084
|tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.0460856,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.010441,0.0982016,0.0528514,0.108057,0.188635,0.00920475,0.081977,0.0948982,0.0415721,0.00198832,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.0308399,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.00719677,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.0413643,0.114283,0.0400322,0.127369,0.0403542,0.0547453,0.179689,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.0169462,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0108418,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.0183114,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.000828043,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.0223286,0.0865903,0.0380459,0.130174,0.584917,0.0381789,0.451377,0.268011,0.051522,0.0986134,0.0853552,0.0638737,0.261644,0.261553,0.118991,0.373681,0.309233,0.147559,0.330703,0.0914012,0.329568,0.53472,0.248224,0.271958,0.292154,0.0964816,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.129235,0.0883629,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.0270783,0.155672,0.236436,0.0447111,0.314747,0.0567394,0.0474194,0.448095,0.212757,0.416816,0.0478086,0.476744,0.439556,0.0807167,0.213592,0.0694028,0.18237,0.0359955,0.0310069,0.0512465,0.275351,0.0304678,0.185661,0.346319,0.0427964,0.270984,0.0772647,0.155555,0.163222,0.169228,0.0338468,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.0138549,0.176034,0.581837,0.1002,0.671377,0.546839,0.551561,0.120021,0.218623,0.312808,0.333034,0.0451077,0.0747529,0.229003,0.0222308,0.0129683,0.154921,0.294698,0.34331,0.477304,0.289204,0.327108,0.0295492,0.278044,0.229008,0.108847,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,0.0150702,0.335105,0.144809,0.145539,0.08628,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.306556,0.0524121,0.2348,0.503082,0.169823,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.0760312,0.464871,1.63525e-05,0.206222,0.171685,0.284166,0.113671,0.269226,0.339277,0.192529,0.281425,0.141758,0.455379,0.168058,0.159617,0.238587,0.0119179,0.232251,0.189515,0.0891382,0.0595618,0.171389,0.0769581,0.0688327,0.539392,0.34988,0.475069,0.404569,0.6408,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.116981,0.441735,0.191777,0.111931,0.046606,0.0435386,0.303336,0.126478,0.134852,0.10689,0.0413156,0.0627924,0.381386,0.0179103,0.0517437,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.0238665,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.0190418,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.0235128,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.09064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75,0.0558058,0.28262,0.0377931,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.0376172,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.0306378,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.0538132,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.00864322,0.131452,0.323837,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.0425274,0.0122266,0.288159,0.21727,0.289306,0.00740669,0.192475,0.177967,0.188967,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.00352878,0.000141874,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.0266106,0.057168,0.000171101,0.0759837,0.286863,0.152372,0.0203723,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0362615,0.0590944,0.247324,0.178389,0.0257622,0.0290303,0.0972686,0.0170505,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.103051,0.36927,0.120614,0.407369,0.231447,0.18653,0.43956,0.37006,0.10748,0.120472,0.197484,0.396996,0.36145,0.0966095,0.381071,0.580441,0.0863135,0.432035,0.366326,0.390366,0.48809,0.0334527,0.443185,0.522904,0.0608227,0.0184337,0.227104,0.166658,0.0734371,0.0867545,0.284625,0.504757,0.55194,0.0437169,0.28907,0.164197,0.0252589,0.287881,0.0556235,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.0186777,0.390974,0.00247135,0.109758,0.161598,0.013901,0.0868402,0.496032,0.0795555,0.37357,0.00500957,0.477353,0.0201095,0.0132585,0.0629574,0.20342,0.0215953,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.446891,0.616388,0.408413,0.516511,0.322213,0.28903,0.33942,0.61031,0.0871388,0.169614,0.0816402,0.537348,0.222037,0.416621,0.416292,0.462712,0.0115406,0.579431,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.373557,0.523625,0.408861,0.0111982,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.0123025,0.4466,0.351067,0.275347,0.637444,0.305885,0.0317395,0.371414,0.30666,0.303709,0.0323359,0.386538,0.508064,0.00324315,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.0663581,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.0780405,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.24107,0.387069,0.332774,0.52832,0.299887,0.0193657,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.222977,0.0664606,0.310674,0.21801,0.198614,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.0267847,0.0673329,0.20847,0.0391817,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.0229018,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.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}}
}}

Revision as of 15:33, 19 October 2012


Full id: C3966_CD14_CD19_Basophils_Mast_Peripheral_Neutrophils_CD34



Phase1 CAGE Peaks

Hg19::chr1:31227530..31227577,-p@chr1:31227530..31227577
-
Hg19::chr4:141677365..141677402,+p@chr4:141677365..141677402
+
Hg19::chr4:78741511..78741543,+p@chr4:78741511..78741543
+


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
leukocyte1.35e-69136
hematopoietic stem cell5.51e-55168
angioblastic mesenchymal cell5.51e-55168
hematopoietic lineage restricted progenitor cell4.26e-51120
hematopoietic cell5.58e-51177
nongranular leukocyte1.20e-50115
hematopoietic oligopotent progenitor cell1.76e-49161
hematopoietic multipotent progenitor cell1.76e-49161
classical monocyte9.84e-4642
CD14-positive, CD16-negative classical monocyte9.84e-4642
myeloid leukocyte3.82e-4272
defensive cell1.57e-3848
phagocyte1.57e-3848
granulocyte monocyte progenitor cell1.23e-3667
myeloid lineage restricted progenitor cell1.96e-3366
macrophage dendritic cell progenitor6.12e-3361
myeloid cell2.09e-31108
common myeloid progenitor2.09e-31108
monopoietic cell1.77e-3059
monocyte1.77e-3059
monoblast1.77e-3059
promonocyte1.77e-3059
B cell7.77e-1914
lymphocyte of B lineage1.41e-1824
pro-B cell1.41e-1824
intermediate monocyte2.58e-179
CD14-positive, CD16-positive monocyte2.58e-179
stuff accumulating cell2.91e-1687
mesenchymal cell6.40e-16354
lymphocyte8.21e-1653
common lymphoid progenitor8.21e-1653
connective tissue cell3.56e-15361
nucleate cell5.87e-1555
lymphoid lineage restricted progenitor cell6.65e-1552
motile cell3.86e-13386
stem cell1.27e-11441
multi fate stem cell6.15e-11427
somatic stem cell1.76e-10433
granulocyte1.10e-088
basophil4.54e-073
dendritic cell7.93e-0710
single nucleate cell9.72e-073
mononuclear cell9.72e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.70e-3198
blood island7.70e-3198
bone marrow9.26e-3176
bone element1.45e-2782
immune system1.13e-2693
hemolymphoid system1.30e-26108
skeletal element5.55e-2490
skeletal system2.49e-20100
connective tissue3.65e-14371
lateral plate mesoderm1.09e-10203
musculoskeletal system3.69e-08167


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
PBX3#5090214.60967512449610.006056122473217890.026840457245084



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.