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Difference between revisions of "Coexpression cluster:C3053"

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|ontology_enrichment_disease=DOID:2531!8.01e-07!51;DOID:0060083!8.01e-07!51
 
|ontology_enrichment_disease=DOID:2531!8.01e-07!51;DOID:0060083!8.01e-07!51
 
|ontology_enrichment_uberon=UBERON:0002390!1.81e-31!102;UBERON:0003061!1.81e-31!102;UBERON:0002193!2.91e-28!112;UBERON:0001474!4.45e-23!86;UBERON:0002371!4.94e-23!80;UBERON:0002405!1.90e-20!115;UBERON:0004765!1.04e-15!101;UBERON:0001434!1.04e-15!101;UBERON:0000178!7.56e-07!15;UBERON:0000179!7.56e-07!15;UBERON:0000463!7.56e-07!15
 
|ontology_enrichment_uberon=UBERON:0002390!1.81e-31!102;UBERON:0003061!1.81e-31!102;UBERON:0002193!2.91e-28!112;UBERON:0001474!4.45e-23!86;UBERON:0002371!4.94e-23!80;UBERON:0002405!1.90e-20!115;UBERON:0004765!1.04e-15!101;UBERON:0001434!1.04e-15!101;UBERON:0000178!7.56e-07!15;UBERON:0000179!7.56e-07!15;UBERON:0000463!7.56e-07!15
 +
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296084095747454!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00658250686855356!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323494233665374!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435242475172324!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0459967665161957!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00759724348023499!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089466016422402!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108275752508615!IRF3#3661;2:31.3213014743264:0.00133951467332011:0.00887449714329355!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185676120820088!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00717983904428403!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029317096517762!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00198983874941111!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024491152201759!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469315163958541!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172231649320005!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268063307895912!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245395217446027!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203069847885504!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189474199352463!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327848408182333!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00387573335340209!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0108928255865369
 
|tfbs_overrepresentation=0.147255,0.0586687,0.00192761,0.0477154,0.199763,0.0460856,0.0430074,0.0022397,0.03272,0.0257057,0.139423,0.00229455,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,9.60364e-05,0.114046,0.0180314,0.0233668,0.0665252,0.0844722,0.000210711,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.0102981,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.00149495,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.0244227,0.0783235,0.105572,0.0294301,0.0117644,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.00183766,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,5.63916e-05,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.0649715,0.144217,0.00407722,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,5.19942e-06,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.0223702,0.0128549,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.00995227,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.000154392,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0413967,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.0142864,0.100942,0.062995,0.00549554,0.14193,0.00135672,0.15606,0.161026,0.0738599,0.126611,0.000497929,0.085973,0.060453,0.059896,0.0538541,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.0381183,0.163502,0.214803,0.182472,6.0212e-06,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.00647842,0.00136269,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.00161471,0.0695832,0.0121776,0.0619218,0.00102968,0.0141386,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.00292601,0.0429376,0.063292,0.0356268,2.21349e-07,0.0865903,0.0380459,0.130174,0.219944,0.131316,0.451377,0.0821962,0.051522,0.0319444,0.00690237,0.0638737,0.0185583,0.261553,0.446302,0.0806291,0.309233,0.147559,0.330703,0.0146881,0.00791734,0.042539,0.0164332,0.271958,0.292154,0.0964816,0.0921263,0.0582602,0.0643874,0.187251,0.362792,0.181715,0.10624,0.109988,0.330894,0.218329,0.107929,0.376924,0.025356,0.000737505,0.00734087,0.168255,0.370782,0.101703,0.0297533,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.0340949,0.0146955,0.283727,0.0557438,0.0567394,0.00529148,0.00324826,0.0115542,0.416816,0.00535876,0.476744,0.115044,0.0120909,0.056723,0.0154652,0.18237,0.0359955,0.0310069,1.43819e-05,0.275351,0.236471,0.185661,0.000971103,0.00787142,0.270984,0.0772647,0.155555,0.0367769,0.00691094,0.248634,0.281576,0.000524881,0.163244,0.0670502,0.0730934,0.184794,0.0641718,0.0582356,0.0583074,0.0169683,0.102184,0.546839,0.0477082,0.120021,0.218623,0.312808,0.00142673,0.0451077,0.0747529,0.229003,0.0222308,0.00223439,0.154921,0.0484563,0.0671437,0.138202,0.289204,0.0605279,0.0295492,0.278044,0.0015747,0.108847,0.228096,0.336314,0.19763,0.15631,0.0106166,0.104858,0.141711,0.420626,0.516462,0.00404127,0.0637439,0.144809,0.145539,0.08628,0.0123475,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.2348,0.155572,0.0391885,0.284629,0.0379506,0.359455,0.0277799,0.0965765,0.102469,0.0760312,0.0256829,0.40841,0.206222,0.00713629,0.000779217,0.437176,0.269226,0.339277,0.0479524,0.0439467,0.141758,0.124432,0.000974263,0.159617,0.238587,0.0119179,0.0293409,0.189515,0.0891382,0.0595618,0.00710886,0.257493,0.347298,0.539392,0.34988,0.00431743,0.0958562,0.0204872,0.000578907,0.316179,0.0697683,0.0556835,0.0198561,0.0779981,0.0575676,0.144322,0.0270501,0.203656,3.38013e-05,0.11631,0.0196924,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.0413156,0.0627924,0.0842821,0.0179103,0.0517437,0.279795,0.0886747,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.00184145,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.0205132,0.132201,0.188694,0.0481795,0.199971,0.00202975,0.127758,0.0164446,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.0419304,0.0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0481323,0.173708,0.0104618,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.0235128,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.000389382,0.000941007,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.00132287,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.0178982,0.122476,0.108872,0.11002,0.26144,0.0286025,2.02725e-05,0.144567,0.038848,0.00394051,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.00176415,0.237101,1.5582e-06,0.0761239,0.172491,0.0818785,0.0178107,0.0637246,0.011488,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.28711,0.0473033,0.094881,0.118532,0.000434303,0.0774373,0.109194,0.128564,0.00904548,0.00681584,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.0122266,0.0232393,0.21727,0.00514993,0.119215,0.192475,0.0168693,0.0088427,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.00352878,0.00217769,0.206454,0.0257531,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.0227848,0.0755808,0.045654,0.110216,0.070276,0.00232088,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.000415994,0.000665506,0.194941,0.00207136,0.101607,0.000748789,0.172982,0.00886538,0.151597,0.0626744,0.191335,0.148574,0.0058211,0.0128248,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.0126914,0.170295,0.193653,0.137219,0.228144,0.251466,0.0461822,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.0186145,0.00102368,0.0948451,0.0384217,0.249049,0.140533,0.0997756,0.00352872,0.103667,0.113069,0.025556,0.16791,0.09066,0.0125264,0.166967,0.188651,0.00340589,0.184948,0.000720136,0.311847,0.161789,0.0590944,0.0334734,0.178389,0.0257622,0.231073,0.0972686,0.00318326,0.0360851,0.000227331,0.131093,0.0434602,0.133616,0.0177337,0.36927,0.449036,0.407369,0.231447,0.00858901,0.00296095,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.276075,0.432035,0.0411943,0.0886602,0.145312,0.50058,0.443185,0.00696618,0.616975,5.69054e-05,0.227104,0.166658,0.0167433,0.38649,0.284625,0.156746,0.0091887,0.0437169,0.28907,0.164197,0.462688,0.287881,0.0113427,0.478174,0.336276,0.132529,0.258219,0.0222932,0.243383,0.191695,0.390974,0.00247135,0.00650842,0.161598,0.013901,0.021206,0.0323708,0.00613559,0.37357,0.200632,0.477353,0.0201095,0.000558506,0.00415823,0.20342,0.200493,0.20558,0.300504,0.00348292,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.00677445,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.0556238,0.181415,0.282286,0.0674279,0.616388,0.408413,0.165147,0.322213,0.0234043,0.33942,0.00285083,0.387276,0.522605,0.221908,0.0433137,0.222037,0.416621,0.416292,0.462712,0.00246111,0.215157,0.204817,0.122646,0.138871,2.27405e-05,0.166905,0.19783,0.0833851,0.316453,0.0289164,0.175199,0.332919,0.373557,0.0393909,0.000216517,0.0768488,0.534741,0.0889149,0.0758087,0.236011,0.00165643,0.0413386,0.0123025,0.4466,0.351067,0.275347,0.019895,0.0524515,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.125961,0.156714,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.127092,0.283463,0.201728,0.0272975,0.399569,0.273281,0.368095,0.275089,0.384593,0.138622,0.359231,0.339729,0.197805,0.24107,0.0136044,0.332774,0.173874,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.000350724,0.0172483,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.0701861,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.0262794,0.0204324,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.0223377,0.21382,0.0232077,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.0215816,0.0102599,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.00162178,0.310405,0.280943,0.0257454,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.187731,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.0224775,0.0488311,0.286691,0.0687209,0.141729,0.263159,0.255956,0.200105,0.227491,0.0497481,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.0597546,0.115817,0.218052,0.0271615,0.11528,0.194982,0.190993,0.281727,0.283218,0.0342254,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.0406636,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
 
}}
 
}}

Revision as of 05:25, 5 September 2012


Full id: C3053_Eosinophils_Neutrophils_CD14_granulocyte_immature_CD8_Basophils



Phase1 CAGE Peaks

  Short description
Hg19::chr10:88281494..88281570,- p1@WAPAL
Hg19::chr16:75498553..75498621,- p1@TMEM170A
Hg19::chr5:139781445..139781487,+ p2@ANKHD1-EIF4EBP3
p2@ANKHD1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
hematopoietic stem cell3.92e-56172
angioblastic mesenchymal cell3.92e-56172
hematopoietic oligopotent progenitor cell1.48e-52165
hematopoietic multipotent progenitor cell1.48e-52165
leukocyte2.94e-51140
hematopoietic cell3.90e-50182
hematopoietic lineage restricted progenitor cell4.91e-42124
nongranular leukocyte4.58e-41119
myeloid cell9.88e-38112
common myeloid progenitor9.88e-38112
myeloid leukocyte1.49e-3376
granulocyte monocyte progenitor cell3.66e-3071
myeloid lineage restricted progenitor cell2.61e-2870
macrophage dendritic cell progenitor7.63e-2865
monopoietic cell1.12e-2663
monocyte1.12e-2663
monoblast1.12e-2663
promonocyte1.12e-2663
classical monocyte9.02e-2545
CD14-positive, CD16-negative classical monocyte4.80e-2442
lymphocyte9.04e-1353
common lymphoid progenitor9.04e-1353
lymphoid lineage restricted progenitor cell2.12e-1252
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.81e-31102
blood island1.81e-31102
hemolymphoid system2.91e-28112
bone element4.45e-2386
bone marrow4.94e-2380
immune system1.90e-20115
skeletal element1.04e-15101
skeletal system1.04e-15101
blood7.56e-0715
haemolymphatic fluid7.56e-0715
organism substance7.56e-0715
Disease
Ontology termp-valuen
hematologic cancer8.01e-0751
immune system cancer8.01e-0751


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


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

TF#promotersEnrichmentp-valueq-value
BRCA1#672213.45615376214920.007119807716084560.0296084095747454
CHD2#1106310.34402283411690.0009033701102746880.00658250686855356
E2F1#186934.907389214879320.008460985347239390.0323494233665374
E2F4#1874312.66806031528440.0004917987006298980.00435242475172324
ELF1#199734.258097958807540.01295179875054610.0459967665161957
ETS1#211339.728760922202340.001085840092584840.00759724348023499
FOS#235338.99795530889440.001372499272417130.0089466016422402
HMGN3#932438.178547723350590.001827766942164210.0108275752508615
IRF3#3661231.32130147432640.001339514673320110.00887449714329355
MAX#414936.452555509007120.003721913834265510.0185676120820088
MXI1#460139.96157162875930.001011470541259020.00717983904428403
MYC#460935.22228187160940.007020843755740150.029317096517762
NFYA#4800318.42558069983050.0001598135507814160.00198983874941111
NFYB#4801316.75979325353650.0002123649923296180.0024491152201759
NRF1#4899312.21027944771090.0005492172401020010.00469315163958541
PAX5#507936.669565531177830.003370290999677260.0172231649320005
PBX3#5090214.60967512449610.006056122473217890.0268063307895912
SP1#666735.69838137814090.005403962701712170.0245395217446027
SP2#6668217.43568699589640.004273568481769740.0203069847885504
USF1#739136.361499277207960.00388404057290560.0189474199352463
YY1#752834.911170749853860.008441455341808260.0327848408182333
ZNF143#7702313.50087655222790.0004062804962997170.00387573335340209
ZNF263#1012738.221841637010680.001799043925565870.0108928255865369



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.