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Coexpression cluster:C2422: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2422_CD14_Mast_Eosinophils_Neutrophils_CD19_Peripheral_Alveolar
|id=C2422
|ontology_enrichment_celltype=CL:0000738!4.06e-40!140;CL:0000037!2.98e-32!172;CL:0000566!2.98e-32!172;CL:0002031!9.30e-32!124;CL:0002032!1.25e-30!165;CL:0000837!1.25e-30!165;CL:0000988!1.43e-30!182;CL:0002087!3.62e-30!119;CL:0002057!6.62e-29!42;CL:0000860!1.89e-28!45;CL:0000766!3.28e-22!76;CL:0000557!7.47e-19!71;CL:0000839!4.69e-18!70;CL:0000763!1.86e-17!112;CL:0000049!1.86e-17!112;CL:0002009!7.93e-17!65;CL:0002194!9.16e-16!63;CL:0000576!9.16e-16!63;CL:0000040!9.16e-16!63;CL:0000559!9.16e-16!63;CL:0000542!1.38e-12!53;CL:0000051!1.38e-12!53;CL:0000838!2.38e-12!52;CL:0000134!3.05e-11!358;CL:0002320!3.35e-10!365;CL:0000219!5.08e-09!390;CL:0000034!2.63e-08!444;CL:0000723!8.26e-08!436;CL:0000048!1.04e-07!430;CL:0002393!3.28e-07!9;CL:0002397!3.28e-07!9;CL:0000945!3.47e-07!24;CL:0000826!3.47e-07!24
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.76e-17!102;UBERON:0003061!2.76e-17!102;UBERON:0002371!4.14e-16!80;UBERON:0001474!1.19e-14!86;UBERON:0002193!2.02e-14!112;UBERON:0004765!4.05e-11!101;UBERON:0001434!4.05e-11!101;UBERON:0002405!1.13e-09!115;UBERON:0002384!4.81e-09!375;UBERON:0003081!5.12e-08!216
|tfbs_overrepresentation=0.191353,0.0774498,0.814139,0.0631091,0.257053,0.363996,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.276459,0.268949,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.00113172,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.439574,0.0792005,0.113084,0.216289,0.470097,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.0469922,0.0562614,0.150119,0.368178,0.320801,0.0848546,0.268505,0.355976,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.327332,0.199405,0.121709,0.347653,0.0759036,0.350158,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.341095,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.233377,0.0352845,0.0565357,0.153577,0.0984158,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.346873,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.179282,0.202544,0.0715212,0.105131,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.329956,0.346995,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.104555,0.476758,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.463127,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.687863,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.324356,0.18736,0.113754,0.0504034,0.169684,0.327364,0.233666,0.333291,0.73998,0.668426,0.407767,0.00738077,0.420045,0.73391,0.332539,0.186966,0.464128,0.389374,0.594055,0.414547,0.146105,0.413223,0.639461,0.720642,0.34505,0.369161,0.500422,0.49089,0.687176,0.702495,0.241524,0.45167,0.234628,0.520726,0.143893,0.41477,0.279946,0.524104,0.467825,0.563725,0.751064,0.632838,0.257158,0.127765,0.511459,0.586668,0.0588752,0.350886,0.380582,0.583749,0.398372,0.286293,0.606558,0.708425,0.359128,0.395864,0.318966,0.368633,0.547291,0.317802,0.162437,0.369971,0.578349,0.537928,0.464342,0.318915,0.356005,0.235444,0.48585,0.0832187,0.114723,0.349116,0.302142,0.239545,0.432689,0.0845186,0.343881,0.145459,0.239383,0.617741,0.626346,0.316925,0.0728506,0.210197,0.211506,0.0883859,0.0962508,0.238465,0.122819,0.571578,0.323783,0.508325,0.436735,0.284591,0.656755,0.188468,0.280307,0.393583,0.469888,0.0596868,0.0984075,0.293026,0.408321,0.0326188,0.605423,0.372182,0.109146,0.214741,0.365653,0.41035,0.784024,0.35234,0.644643,0.525923,0.291917,0.421082,0.25441,0.202782,0.672876,0.517933,0.584705,0.517001,0.620475,0.0497525,0.419676,0.188259,0.189182,0.138387,0.131612,0.546448,0.560187,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.651295,0.370995,0.360161,0.429696,0.386216,0.385297,0.346931,0.606408,0.627185,0.360203,0.333725,0.447838,0.289666,0.500627,0.513045,0.452694,0.565545,0.556975,0.265037,0.629795,0.410093,0.179179,0.341771,0.424526,0.290547,0.356381,0.184395,0.194887,0.624689,0.206945,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.261511,0.376317,0.433821,0.64428,0.436806,0.576549,0.499072,0.396083,0.0115505,0.0922563,0.0919254,0.0735469,0.0336952,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.183047,0.247151,0.146385,0.365815,0.0576261,0.0847761,0.164977,0.175633,0.139918,0.34669,0.0828344,0.135364,0.0238089,0.383126,0.0719157,0.48311,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.243319,0.0637178,0.036377,0.153907,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.0734014,0.0752771,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0922008,0.187953,0.051459,0.00686557,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.0454742,0.173134,0.101893,0.142875,0.167635,0.171311,0.458838,0.189107,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.267945,0.0560157,0.278645,0.0769795,0.155708,0.248017,0.22995,0.285695,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.0464703,0.00147946,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.0756617,0.197817,0.251078,0.279874,0.133127,0.0988568,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.0689994,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.0475113,0.320355,0.0763252,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.00303153,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.140541,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.163504,0.459091,0.54832,0.502211,0.00555197,0.649813,0.181196,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.153911,0.135135,0.0302459,0.0510811,0.529642,0.244786,0.483077,0.590496,0.0671621,0.541914,0.259354,0.0237007,0.0217959,0.290703,0.0757071,0.722684,0.139104,0.360199,0.241059,0.657141,0.253797,0.365494,0.212703,0.201391,0.364079,0.107716,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.0529131,0.142433,0.261345,0.0698158,0.209437,0.11765,0.161672,0.232518,0.0221843,0.464001,0.0572812,0.579004,0.0181398,0.278028,0.0500888,0.261575,0.257956,0.264245,0.379063,0.326516,0.16985,0.113006,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.0215868,0.212239,0.294954,0.156999,0.35974,0.301684,0.39549,0.234254,0.357409,0.146291,0.137737,0.50338,0.620526,0.404625,0.759068,0.424691,0.715362,0.479581,0.259048,0.0230743,0.642173,0.284496,0.512545,0.512178,0.563206,0.260945,0.110875,0.263302,0.552023,0.180735,0.0646927,0.216102,0.254659,0.109605,0.397869,0.217863,0.226491,0.417131,0.463987,0.0782409,0.503881,0.0237654,0.0840572,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.391754,0.385425,0.307816,0.461541,0.386339,0.0849889,0.232374,0.478745,0.24434,0.319747,0.475047,0.557967,0.608127,0.282281,0.245336,0.2536,0.246827,0.564333,0.347466,0.387134,0.559969,0.358813,0.303004,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.106831,0.254628,0.355111,0.479347,0.416962,0.264955,0.378333,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.133173,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.0606443,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.038024,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.0739466,0.335984,0.171704,0.208256,0.265058,0.256405,0.0756763,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
}}

Latest revision as of 12:05, 17 September 2013


Full id: C2422_CD14_Mast_Eosinophils_Neutrophils_CD19_Peripheral_Alveolar



Phase1 CAGE Peaks

Hg19::chr17:49198339..49198357,+p@chr17:49198339..49198357
+
Hg19::chr4:141016098..141016114,-p@chr4:141016098..141016114
-
Hg19::chr5:95296930..95296942,-p@chr5:95296930..95296942
-
Hg19::chr8:103801382..103801405,+p@chr8:103801382..103801405
+


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
classical monocyte1.15e-5442
CD14-positive, CD16-negative classical monocyte1.15e-5442
myeloid leukocyte4.69e-4972
leukocyte1.96e-48136
defensive cell3.69e-4648
phagocyte3.69e-4648
granulocyte monocyte progenitor cell1.83e-4367
myeloid lineage restricted progenitor cell6.57e-4066
macrophage dendritic cell progenitor3.28e-3961
hematopoietic stem cell7.66e-39168
angioblastic mesenchymal cell7.66e-39168
hematopoietic cell2.54e-38177
myeloid cell1.10e-37108
common myeloid progenitor1.10e-37108
hematopoietic lineage restricted progenitor cell2.52e-37120
hematopoietic oligopotent progenitor cell4.64e-37161
hematopoietic multipotent progenitor cell4.64e-37161
monopoietic cell1.61e-3659
monocyte1.61e-3659
monoblast1.61e-3659
promonocyte1.61e-3659
nongranular leukocyte1.50e-34115
stuff accumulating cell8.58e-2487
mesenchymal cell6.58e-13354
intermediate monocyte1.69e-129
CD14-positive, CD16-positive monocyte1.69e-129
connective tissue cell3.06e-12361
motile cell5.81e-11386
granulocyte1.35e-088
multi fate stem cell3.95e-08427
blood cell8.46e-0811
somatic stem cell9.74e-08433
stem cell1.02e-07441
circulating cell3.77e-076
Uber Anatomy
Ontology termp-valuen
bone marrow1.34e-3676
hematopoietic system2.54e-3498
blood island2.54e-3498
bone element7.23e-3382
hemolymphoid system6.51e-31108
skeletal element1.13e-2890
immune system1.42e-2893
skeletal system1.27e-25100
lateral plate mesoderm8.33e-13203
connective tissue7.46e-12371
musculoskeletal system2.47e-11167


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)
MA0003.11.8989
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.12.54366
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.11.9583
MA0101.11.33363
MA0103.10.521546
MA0105.11.22348
MA0106.12.01886
MA0107.12.00595
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.12.78257
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.640035
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.21.6798
MA0102.21.75932
MA0258.11.88931
MA0259.10.471671
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
EBF1#187936.679850134926750.005184294118278910.0240427394946239
THAP1#55145215.68457230142570.005840469678357920.0262466786892437



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.

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