Personal tools

Coexpression cluster:C4145: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 5: Line 5:
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.28e-40!115;UBERON:0001049!1.43e-19!57;UBERON:0005068!1.43e-19!57;UBERON:0006241!1.43e-19!57;UBERON:0007135!1.43e-19!57;UBERON:0002616!1.24e-17!59;UBERON:0001017!2.70e-17!82;UBERON:0000955!3.07e-17!69;UBERON:0006238!3.07e-17!69;UBERON:0003080!7.01e-17!42;UBERON:0002780!7.78e-17!41;UBERON:0001890!7.78e-17!41;UBERON:0006240!7.78e-17!41;UBERON:0005743!2.42e-16!86;UBERON:0001893!7.12e-15!34;UBERON:0002020!9.75e-15!34;UBERON:0003528!9.75e-15!34;UBERON:0002791!2.37e-14!33;UBERON:0001869!2.41e-14!32;UBERON:0000073!3.77e-14!94;UBERON:0001016!3.77e-14!94;UBERON:0002619!3.48e-12!22;UBERON:0003075!1.52e-11!86;UBERON:0007284!1.52e-11!86;UBERON:0001950!3.52e-11!20;UBERON:0000956!2.14e-10!25;UBERON:0000203!2.14e-10!25;UBERON:0002346!5.69e-10!90;UBERON:0000153!1.03e-09!129;UBERON:0007811!1.03e-09!129;UBERON:0003056!1.88e-09!61;UBERON:0002390!4.08e-09!102;UBERON:0003061!4.08e-09!102;UBERON:0000033!1.04e-08!123;UBERON:0002193!1.14e-07!112;UBERON:0000178!1.88e-07!15;UBERON:0000179!1.88e-07!15;UBERON:0000463!1.88e-07!15
|ontology_enrichment_uberon=UBERON:0007023!2.28e-40!115;UBERON:0001049!1.43e-19!57;UBERON:0005068!1.43e-19!57;UBERON:0006241!1.43e-19!57;UBERON:0007135!1.43e-19!57;UBERON:0002616!1.24e-17!59;UBERON:0001017!2.70e-17!82;UBERON:0000955!3.07e-17!69;UBERON:0006238!3.07e-17!69;UBERON:0003080!7.01e-17!42;UBERON:0002780!7.78e-17!41;UBERON:0001890!7.78e-17!41;UBERON:0006240!7.78e-17!41;UBERON:0005743!2.42e-16!86;UBERON:0001893!7.12e-15!34;UBERON:0002020!9.75e-15!34;UBERON:0003528!9.75e-15!34;UBERON:0002791!2.37e-14!33;UBERON:0001869!2.41e-14!32;UBERON:0000073!3.77e-14!94;UBERON:0001016!3.77e-14!94;UBERON:0002619!3.48e-12!22;UBERON:0003075!1.52e-11!86;UBERON:0007284!1.52e-11!86;UBERON:0001950!3.52e-11!20;UBERON:0000956!2.14e-10!25;UBERON:0000203!2.14e-10!25;UBERON:0002346!5.69e-10!90;UBERON:0000153!1.03e-09!129;UBERON:0007811!1.03e-09!129;UBERON:0003056!1.88e-09!61;UBERON:0002390!4.08e-09!102;UBERON:0003061!4.08e-09!102;UBERON:0000033!1.04e-08!123;UBERON:0002193!1.14e-07!112;UBERON:0000178!1.88e-07!15;UBERON:0000179!1.88e-07!15;UBERON:0000463!1.88e-07!15
|tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.0275521,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.00920475,0.081977,0.0948982,0.0415721,0.215492,0.0236364,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.113083,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.0244227,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,7.85272e-08,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.0641358,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.00782633,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0413967,0.15185,0.206299,0.0169462,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.00157828,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.0219021,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.355018,0.0691572,0.0821962,0.563047,0.252249,0.228731,0.335423,0.629514,0.261553,0.0222487,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.178727,0.248224,0.271958,0.292154,0.405773,0.39729,0.581713,0.230901,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.213592,0.608919,0.18237,0.126021,0.248484,0.161148,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.258117,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.0138549,0.421596,0.217247,0.412837,0.671377,0.546839,0.0477082,0.448039,0.218623,0.312808,0.032738,0.0451077,0.0747529,0.229003,0.650179,0.061213,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.229008,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.311758,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.166672,0.206222,0.525396,0.0905337,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0129363,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,8.47333e-05,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.0306206,0.000381649,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.0122266,0.288159,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,4.63445e-08,0.00739585,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.000797393,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.0290303,0.0972686,0.00318326,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.276075,0.11074,0.366326,0.390366,0.48809,0.50058,0.443185,0.522904,2.0991e-06,0.0184337,0.227104,0.166658,0.250246,0.38649,0.284625,0.000799065,0.55194,0.375373,0.28907,0.164197,0.462688,0.0461094,0.21103,0.478174,0.00846715,0.468444,0.258219,0.446557,0.243383,0.00448654,0.390974,0.149257,0.029557,0.161598,0.0527155,0.644754,0.496032,0.00613559,0.37357,0.00106614,0.477353,6.7495e-07,0.0508568,0.00415823,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0513026,0.314429,0.181415,0.282286,0.0192486,0.24884,0.408413,0.516511,0.322213,0.0931134,0.33942,0.61031,0.387276,0.522605,1.15611e-06,0.0433137,0.222037,0.416621,0.416292,0.128937,0.0457685,0.0019893,0.0225745,0.452428,0.138871,0.027191,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.0524515,0.0317395,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.125961,0.156714,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.138622,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.0406989,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.0171537,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.0132793,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.00717361,0.261724,0.0240944,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.0352561,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.0342254,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.0164735,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 19:46, 8 August 2012


Full id: C4145_maxillary_gastric_caudate_medulla_Neutrophils_putamen_small



Phase1 CAGE Peaks

Hg19::chr2:175351732..175351743,-p2@GPR155
Hg19::chr2:175351744..175351828,-p1@GPR155
Hg19::chr9:12159267..12159271,+p@chr9:12159267..12159271
+


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
nongranular leukocyte1.13e-16119
leukocyte2.57e-16140
hematopoietic lineage restricted progenitor cell3.39e-13124
CD14-positive, CD16-negative classical monocyte1.30e-0942
mature alpha-beta T cell2.37e-0918
alpha-beta T cell2.37e-0918
immature T cell2.37e-0918
mature T cell2.37e-0918
immature alpha-beta T cell2.37e-0918
T cell2.41e-0925
pro-T cell2.41e-0925
myeloid leukocyte2.91e-0976
monopoietic cell4.93e-0963
monocyte4.93e-0963
monoblast4.93e-0963
promonocyte4.93e-0963
macrophage dendritic cell progenitor1.11e-0865
classical monocyte1.50e-0745
hematopoietic stem cell1.93e-07172
angioblastic mesenchymal cell1.93e-07172
lymphocyte2.08e-0753
common lymphoid progenitor2.08e-0753
lymphoid lineage restricted progenitor cell2.44e-0752
myeloid lineage restricted progenitor cell4.48e-0770
hematopoietic oligopotent progenitor cell5.21e-07165
hematopoietic multipotent progenitor cell5.21e-07165
Uber Anatomy
Ontology termp-valuen
adult organism2.28e-40115
neural tube1.43e-1957
neural rod1.43e-1957
future spinal cord1.43e-1957
neural keel1.43e-1957
regional part of brain1.24e-1759
central nervous system2.70e-1782
brain3.07e-1769
future brain3.07e-1769
anterior neural tube7.01e-1742
regional part of forebrain7.78e-1741
forebrain7.78e-1741
future forebrain7.78e-1741
telencephalon7.12e-1534
gray matter9.75e-1534
brain grey matter9.75e-1534
regional part of telencephalon2.37e-1433
cerebral hemisphere2.41e-1432
regional part of nervous system3.77e-1494
nervous system3.77e-1494
regional part of cerebral cortex3.48e-1222
neural plate1.52e-1186
presumptive neural plate1.52e-1186
neocortex3.52e-1120
cerebral cortex2.14e-1025
pallium2.14e-1025
neurectoderm5.69e-1090
anterior region of body1.03e-09129
craniocervical region1.03e-09129
pre-chordal neural plate1.88e-0961
hematopoietic system4.08e-09102
blood island4.08e-09102
head1.04e-08123
hemolymphoid system1.14e-07112
blood1.88e-0715
haemolymphatic fluid1.88e-0715
organism substance1.88e-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


No analysis results for this cluster

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.