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Coexpression cluster:C4799: Difference between revisions

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|ontology_enrichment_disease=DOID:8692!1.88e-08!31;DOID:1240!8.51e-07!39
|ontology_enrichment_disease=DOID:8692!1.88e-08!31;DOID:1240!8.51e-07!39
|ontology_enrichment_uberon=UBERON:0002371!1.03e-29!80;UBERON:0001474!1.13e-28!86;UBERON:0002390!1.31e-27!102;UBERON:0003061!1.31e-27!102;UBERON:0002193!5.84e-25!112;UBERON:0004765!5.25e-23!101;UBERON:0001434!5.25e-23!101;UBERON:0002405!4.83e-22!115;UBERON:0007023!1.20e-10!115;UBERON:0002204!5.05e-10!167;UBERON:0005743!7.19e-10!86;UBERON:0001049!5.55e-09!57;UBERON:0005068!5.55e-09!57;UBERON:0006241!5.55e-09!57;UBERON:0007135!5.55e-09!57;UBERON:0003075!2.80e-08!86;UBERON:0007284!2.80e-08!86;UBERON:0001017!3.18e-08!82;UBERON:0002616!8.01e-08!59;UBERON:0000955!1.10e-07!69;UBERON:0006238!1.10e-07!69;UBERON:0000073!1.42e-07!94;UBERON:0001016!1.42e-07!94;UBERON:0002346!2.57e-07!90;UBERON:0001893!2.65e-07!34;UBERON:0002791!6.29e-07!33;UBERON:0002020!6.32e-07!34;UBERON:0003528!6.32e-07!34;UBERON:0002780!7.81e-07!41;UBERON:0001890!7.81e-07!41;UBERON:0006240!7.81e-07!41
|ontology_enrichment_uberon=UBERON:0002371!1.03e-29!80;UBERON:0001474!1.13e-28!86;UBERON:0002390!1.31e-27!102;UBERON:0003061!1.31e-27!102;UBERON:0002193!5.84e-25!112;UBERON:0004765!5.25e-23!101;UBERON:0001434!5.25e-23!101;UBERON:0002405!4.83e-22!115;UBERON:0007023!1.20e-10!115;UBERON:0002204!5.05e-10!167;UBERON:0005743!7.19e-10!86;UBERON:0001049!5.55e-09!57;UBERON:0005068!5.55e-09!57;UBERON:0006241!5.55e-09!57;UBERON:0007135!5.55e-09!57;UBERON:0003075!2.80e-08!86;UBERON:0007284!2.80e-08!86;UBERON:0001017!3.18e-08!82;UBERON:0002616!8.01e-08!59;UBERON:0000955!1.10e-07!69;UBERON:0006238!1.10e-07!69;UBERON:0000073!1.42e-07!94;UBERON:0001016!1.42e-07!94;UBERON:0002346!2.57e-07!90;UBERON:0001893!2.65e-07!34;UBERON:0002791!6.29e-07!33;UBERON:0002020!6.32e-07!34;UBERON:0003528!6.32e-07!34;UBERON:0002780!7.81e-07!41;UBERON:0001890!7.81e-07!41;UBERON:0006240!7.81e-07!41
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00919588764501041!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465299752230155!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187575620777327!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195516492304938!MEF2C#4208;3:41.3113544926241:1.41744912101957e-05:0.000340863386484372!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270980650845052!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173770646581405!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00632424890387292
|tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,0.0172144,0.03272,0.0257057,0.139423,0.0275521,0.00130551,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.000105295,0.0907212,0.143747,0.0933697,0.0226057,0.000270306,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.00481151,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,2.85767e-05,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.00378698,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.00442705,0.141874,0.0370665,0.219088,0.0409286,0.00229559,0.00862108,0.144217,0.0400492,0.182599,0.0339971,0.0117862,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.0128549,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.00239446,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.0176328,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.037005,0.27358,0.15185,0.206299,0.0010913,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0108418,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.0124596,0.355018,0.0691572,0.635872,0.563047,0.00879988,0.228731,0.0083957,0.629514,0.00370732,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.248224,0.271958,0.292154,0.405773,0.0921263,0.0121013,0.0139202,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.0190732,0.376924,0.463191,0.647576,0.0407001,0.168255,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.00194826,0.291709,0.448095,0.000269721,0.416816,0.0478086,0.0280875,0.439556,0.373868,0.57762,0.0694028,0.18237,0.706298,0.821217,0.400457,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.0772647,0.155555,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.0158541,0.581837,0.412837,0.0267008,0.188159,0.551561,0.448039,0.218623,0.00665903,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.0263998,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.104399,0.0374607,0.311758,0.0637439,0.144809,0.145539,0.0134194,0.0123475,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.284593,0.0673219,0.306556,0.0524121,0.06617,0.503082,0.522888,0.284629,0.262537,0.0741332,0.226257,0.0965765,0.41707,0.363685,0.464871,0.753577,0.206222,0.525396,0.000779217,0.113671,0.269226,0.339277,0.552319,0.281425,0.141758,0.124432,0.168058,0.0134764,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.171389,0.0033863,0.347298,0.539392,0.34988,0.475069,0.0158269,0.6408,0.630264,0.000642687,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.11631,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.00643465,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.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123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.0154037,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.000234172,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.0254773,0.190048,0.131088,0.394069,4.32932e-07,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.0105143,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.696435,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.0266106,0.057168,0.234298,0.00296278,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.00435853,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.00806892,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.0182671,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.0290303,0.407281,0.619906,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,1.81847e-06,0.43956,0.37006,0.42622,0.448797,0.197484,1.51104e-05,0.36145,0.0160226,0.381071,0.580441,0.276075,0.432035,0.138468,0.390366,0.48809,0.153829,2.81064e-06,0.0391928,0.158867,0.151996,0.00235168,0.166658,0.617852,0.38649,0.284625,0.504757,0.55194,0.375373,0.28907,0.164197,0.462688,0.287881,0.0556235,0.138768,0.0642229,0.468444,0.258219,0.446557,0.243383,0.442897,0.0889613,0.00247135,0.683217,0.161598,0.164332,0.0868402,0.150692,0.21803,0.0805771,0.454657,0.000560517,0.069689,0.399222,0.771991,0.20342,0.200493,0.20558,0.300504,0.25656,0.0189087,0.0696455,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.00677385,0.181415,0.00475227,0.78,6.39688e-05,0.408413,0.0374737,0.322213,0.656109,0.00873429,0.61031,0.387276,0.00694606,0.802166,0.537348,0.222037,0.416621,0.0174635,0.000461257,0.382478,0.215157,0.204817,0.0233392,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.0111982,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.0704514,0.275347,0.00388821,0.305885,0.241132,0.00133934,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,8.67098e-07,0.196976,0.191517,0.129584,0.601877,0.307334,0.459728,0.283463,0.0102434,0.472935,0.399569,0.273281,0.368095,0.275089,0.0858306,0.47795,0.0740334,0.00876091,0.197805,0.0690807,0.387069,0.332774,0.52832,0.299887,0.266492,0.0227114,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.0192444,0.036838,0.188263,0.0719199,0.264884,0.0139948,0.19104,0.163057,0.219428,0.208013,0.0900729,0.00469907,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.0171537,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.00155473,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.00899848,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.00080862,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.00972162,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.0132793,0.220319,0.195218,0.124213,0.259632,0.0532009,0.0173907,0.159884,0.0363723,0.0119784,0.0254879,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.0339803,0.115972,0.224568,0.246105,0.173026,0.200432,0.000508432,0.197112,0.240478,0.156465,0.13108,0.256963,0.000137586,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.0359756,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.000416169,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.0203812,0.190993,0.0440463,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.158847,0.271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}}
}}

Revision as of 13:53, 5 September 2012


Full id: C4799_Mast_acute_Monocytederived_xeroderma_plasma_b_migratory



Phase1 CAGE Peaks

Hg19::chr9:127054217..127054252,+p7@NEK6
Hg19::chr9:127054254..127054276,+p5@NEK6
Hg19::chr9:127054288..127054311,+p8@NEK6


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>disease_data<br>


Cell Type
Ontology termp-valuen
myeloid cell9.32e-39112
common myeloid progenitor9.32e-39112
hematopoietic cell1.61e-33182
granulocyte monocyte progenitor cell4.99e-3271
hematopoietic stem cell7.25e-32172
angioblastic mesenchymal cell7.25e-32172
myeloid lineage restricted progenitor cell2.18e-3070
hematopoietic oligopotent progenitor cell2.84e-29165
hematopoietic multipotent progenitor cell2.84e-29165
myeloid leukocyte1.40e-2776
macrophage dendritic cell progenitor7.45e-2765
monopoietic cell2.71e-2563
monocyte2.71e-2563
monoblast2.71e-2563
promonocyte2.71e-2563
leukocyte3.39e-23140
hematopoietic lineage restricted progenitor cell1.91e-20124
CD14-positive, CD16-negative classical monocyte4.69e-1842
nongranular leukocyte7.67e-17119
classical monocyte6.69e-1645
dendritic cell3.61e-1010
conventional dendritic cell1.14e-088
mesenchymal cell9.59e-07358
Uber Anatomy
Ontology termp-valuen
bone marrow1.03e-2980
bone element1.13e-2886
hematopoietic system1.31e-27102
blood island1.31e-27102
hemolymphoid system5.84e-25112
skeletal element5.25e-23101
skeletal system5.25e-23101
immune system4.83e-22115
adult organism1.20e-10115
musculoskeletal system5.05e-10167
neural tube5.55e-0957
neural rod5.55e-0957
future spinal cord5.55e-0957
neural keel5.55e-0957
neural plate2.80e-0886
presumptive neural plate2.80e-0886
central nervous system3.18e-0882
regional part of brain8.01e-0859
brain1.10e-0769
future brain1.10e-0769
regional part of nervous system1.42e-0794
nervous system1.42e-0794
neurectoderm2.57e-0790
telencephalon2.65e-0734
regional part of telencephalon6.29e-0733
gray matter6.32e-0734
brain grey matter6.32e-0734
regional part of forebrain7.81e-0741
forebrain7.81e-0741
future forebrain7.81e-0741
Disease
Ontology termp-valuen
myeloid leukemia1.88e-0831
leukemia8.51e-0739


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
EBF1#187938.9064668465690.00141523283560980.00919588764501041
ELF1#199734.258097958807540.01295179875054610.0465299752230155
MAX#414936.452555509007120.003721913834265510.0187575620777327
MEF2A#4205318.74323090964410.0001518243905622470.00195516492304938
MEF2C#4208341.31135449262411.41744912101957e-050.000340863386484372
NFKB1#479035.488063424193840.006049381815655430.0270980650845052
PAX5#507936.669565531177830.003370290999677260.0173770646581405
TCF12#6938310.63446490218640.0008313523990202070.00632424890387292



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.