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Coexpression cluster:C3380: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!3.57e-21!102;UBERON:0003061!3.57e-21!102;UBERON:0002193!6.53e-18!112;UBERON:0002371!1.02e-15!80;UBERON:0001474!5.54e-14!86;UBERON:0003081!9.40e-13!216;UBERON:0004765!1.12e-09!101;UBERON:0001434!1.12e-09!101;UBERON:0002405!2.63e-09!115;UBERON:0002384!2.77e-07!375;UBERON:0000178!7.40e-07!15;UBERON:0000179!7.40e-07!15;UBERON:0000463!7.40e-07!15
|ontology_enrichment_uberon=UBERON:0002390!3.57e-21!102;UBERON:0003061!3.57e-21!102;UBERON:0002193!6.53e-18!112;UBERON:0002371!1.02e-15!80;UBERON:0001474!5.54e-14!86;UBERON:0003081!9.40e-13!216;UBERON:0004765!1.12e-09!101;UBERON:0001434!1.12e-09!101;UBERON:0002405!2.63e-09!115;UBERON:0002384!2.77e-07!375;UBERON:0000178!7.40e-07!15;UBERON:0000179!7.40e-07!15;UBERON:0000463!7.40e-07!15
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296131261672702!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032421825304727!EBF1#1879;3:8.906466846569:0.0014152328356098:0.0091333808390442!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319648810766322!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460860927978019!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376617946443044!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015380276376548!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127784512065288!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018981998754969
|tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.0275521,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.0226057,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.0308399,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.0244227,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0124566,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.00954291,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.00243119,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.0216297,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.0413643,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.0101199,0.085973,0.060453,0.059896,0.569726,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.01843,0.00497001,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.00029312,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.0429376,0.063292,0.254773,0.119261,0.0865903,0.0380459,0.130174,0.219944,0.131316,0.00485874,0.635872,0.563047,0.0319444,0.00690237,0.335423,0.0790073,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.0914012,0.329568,0.178727,0.248224,0.271958,0.292154,0.405773,0.39729,0.217139,0.0643874,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.107929,0.376924,0.463191,0.0883629,0.528324,0.168255,0.370782,0.415647,0.484505,0.0352744,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.0669244,0.283727,0.314747,0.21363,0.291709,0.448095,0.576651,0.416816,0.292835,0.137839,0.439556,0.373868,0.056723,0.608919,0.18237,0.0359955,0.00847576,0.161148,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.0772647,0.155555,0.0367769,0.169228,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.176034,0.581837,0.412837,0.305671,0.546839,0.551561,0.120021,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.229003,0.0897888,0.061213,0.0338328,0.294698,0.0671437,0.477304,0.289204,0.327108,0.109738,0.278044,0.085507,0.108847,0.228096,0.336314,0.19763,0.15631,0.20495,0.104858,0.48267,0.420626,0.516462,0.000957476,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.306556,0.305777,0.2348,0.155572,0.0391885,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.130283,0.0538047,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.192529,0.281425,0.141758,0.124432,0.168058,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.257493,0.347298,0.539392,0.34988,0.475069,0.404569,0.0204872,0.0186811,0.316179,0.0697683,0.0556835,0.0198561,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0129363,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.026047,0.332809,0.19559,0.132201,0.0190418,0.0481795,0.199971,0.00202975,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.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0558058,0.0443426,0.00662343,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.00956472,0.02609,0.0394698,0.0596469,0.0178982,0.122476,0.108872,0.11002,0.26144,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.0538132,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,0.288159,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,1.70007e-06,3.18684e-05,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.0457643,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.0116284,0.0058211,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.0346616,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.188651,0.0813902,0.184948,0.156261,0.0065917,0.0362615,0.0590944,0.0334734,0.178389,0.218229,0.231073,0.000211542,6.78596e-05,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.418146,0.36927,0.120614,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.0966095,0.381071,0.580441,0.0863135,0.11074,0.138468,0.390366,0.48809,0.0334527,0.443185,0.522904,0.000322406,0.000283689,0.227104,0.166658,0.250246,0.38649,0.284625,0.00583062,0.04783,0.375373,0.28907,0.164197,0.128922,0.287881,0.0556235,0.478174,0.336276,0.0263888,0.258219,0.446557,0.243383,0.0186777,0.390974,0.0458848,0.319063,0.161598,0.0527155,0.0868402,0.150692,0.00613559,0.37357,0.0203982,0.138234,0.000195013,0.0508568,0.000852086,0.20342,0.200493,0.20558,0.300504,0.25656,0.0189087,0.0696455,0.383291,0.156104,0.141318,0.0997241,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0101317,0.00677385,0.181415,0.282286,0.0674279,0.0727621,0.408413,0.0374737,0.322213,0.0931134,0.33942,0.61031,0.387276,0.0391112,0.000283063,0.537348,0.222037,0.416621,0.416292,0.128937,0.0115406,0.057399,0.204817,0.452428,0.138871,0.00105709,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.170369,0.408861,0.0111982,0.534741,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.0344603,0.220231,0.0355483,0.196976,0.191517,0.129584,0.0663581,0.307334,0.459728,0.283463,0.563586,0.135386,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.0153645,0.387069,0.332774,0.173874,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.0358457,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.0211771,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.0204324,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.0269005,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.00717361,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.0352561,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 13:22, 5 September 2012


Full id: C3380_Eosinophils_CD14_Mast_Neutrophils_CD19_CD14CD16_CD34



Phase1 CAGE Peaks

Hg19::chr13:50698820..50698842,+p@chr13:50698820..50698842
+
Hg19::chr6:32163757..32163854,+p@chr6:32163757..32163854
+
Hg19::chr8:12613275..12613329,+p@chr8:12613275..12613329
+


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
leukocyte1.41e-39140
hematopoietic cell2.35e-34182
hematopoietic stem cell1.01e-33172
angioblastic mesenchymal cell1.01e-33172
hematopoietic oligopotent progenitor cell2.42e-30165
hematopoietic multipotent progenitor cell2.42e-30165
hematopoietic lineage restricted progenitor cell6.13e-30124
nongranular leukocyte6.20e-30119
CD14-positive, CD16-negative classical monocyte1.14e-2042
myeloid leukocyte9.49e-1976
classical monocyte8.81e-1845
lymphocyte2.93e-1653
common lymphoid progenitor2.93e-1653
lymphoid lineage restricted progenitor cell3.97e-1652
granulocyte monocyte progenitor cell1.43e-1571
myeloid cell1.87e-14112
common myeloid progenitor1.87e-14112
myeloid lineage restricted progenitor cell3.25e-1370
macrophage dendritic cell progenitor3.95e-1365
monopoietic cell2.36e-1263
monocyte2.36e-1263
monoblast2.36e-1263
promonocyte2.36e-1263
lymphocyte of B lineage6.08e-0924
pro-B cell6.08e-0924
mature alpha-beta T cell2.43e-0818
alpha-beta T cell2.43e-0818
immature T cell2.43e-0818
mature T cell2.43e-0818
immature alpha-beta T cell2.43e-0818
connective tissue cell2.51e-08365
motile cell2.93e-08390
mesenchymal cell4.09e-08358
B cell4.22e-0814
intermediate monocyte2.02e-079
CD14-positive, CD16-positive monocyte2.02e-079
multi fate stem cell4.10e-07430
stem cell4.91e-07444
T cell5.74e-0725
pro-T cell5.74e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.57e-21102
blood island3.57e-21102
hemolymphoid system6.53e-18112
bone marrow1.02e-1580
bone element5.54e-1486
lateral plate mesoderm9.40e-13216
skeletal element1.12e-09101
skeletal system1.12e-09101
immune system2.63e-09115
connective tissue2.77e-07375
blood7.40e-0715
haemolymphatic fluid7.40e-0715
organism substance7.40e-0715


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
BRCA1#672213.45615376214920.007119807716084560.0296131261672702
E2F1#186934.907389214879320.008460985347239390.032421825304727
EBF1#187938.9064668465690.00141523283560980.0091333808390442
EGR1#195834.988179094810140.008056488137383440.0319648810766322
ELF1#199734.258097958807540.01295179875054610.0460860927978019
FOSL2#2355211.28680040304110.0100534586973120.0376617946443044
GABPB1#255337.067683836182170.002832212825417420.015380276376548
IRF1#365937.63716375356390.002244692747297240.0127784512065288
USF1#739136.361499277207960.00388404057290560.018981998754969



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.