Personal tools

Coexpression cluster:C1522: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 6: Line 6:
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.52e-23!115;UBERON:0002390!6.61e-20!102;UBERON:0003061!6.61e-20!102;UBERON:0002193!2.47e-15!112;UBERON:0001049!6.62e-15!57;UBERON:0005068!6.62e-15!57;UBERON:0006241!6.62e-15!57;UBERON:0007135!6.62e-15!57;UBERON:0003080!5.58e-14!42;UBERON:0002780!8.42e-14!41;UBERON:0001890!8.42e-14!41;UBERON:0006240!8.42e-14!41;UBERON:0001893!4.68e-12!34;UBERON:0002020!6.52e-12!34;UBERON:0003528!6.52e-12!34;UBERON:0002791!1.26e-11!33;UBERON:0002616!1.45e-11!59;UBERON:0001869!2.80e-11!32;UBERON:0002371!4.16e-11!80;UBERON:0002619!8.75e-10!22;UBERON:0001017!2.19e-09!82;UBERON:0000955!2.29e-09!69;UBERON:0006238!2.29e-09!69;UBERON:0001474!2.92e-09!86;UBERON:0001950!4.80e-09!20;UBERON:0005743!5.26e-09!86;UBERON:0000956!1.54e-08!25;UBERON:0000203!1.54e-08!25;UBERON:0000178!4.66e-08!15;UBERON:0000179!4.66e-08!15;UBERON:0000463!4.66e-08!15;UBERON:0000073!1.81e-07!94;UBERON:0001016!1.81e-07!94;UBERON:0003075!2.33e-07!86;UBERON:0007284!2.33e-07!86;UBERON:0003056!4.96e-07!61;UBERON:0004765!7.03e-07!101;UBERON:0001434!7.03e-07!101
|ontology_enrichment_uberon=UBERON:0007023!1.52e-23!115;UBERON:0002390!6.61e-20!102;UBERON:0003061!6.61e-20!102;UBERON:0002193!2.47e-15!112;UBERON:0001049!6.62e-15!57;UBERON:0005068!6.62e-15!57;UBERON:0006241!6.62e-15!57;UBERON:0007135!6.62e-15!57;UBERON:0003080!5.58e-14!42;UBERON:0002780!8.42e-14!41;UBERON:0001890!8.42e-14!41;UBERON:0006240!8.42e-14!41;UBERON:0001893!4.68e-12!34;UBERON:0002020!6.52e-12!34;UBERON:0003528!6.52e-12!34;UBERON:0002791!1.26e-11!33;UBERON:0002616!1.45e-11!59;UBERON:0001869!2.80e-11!32;UBERON:0002371!4.16e-11!80;UBERON:0002619!8.75e-10!22;UBERON:0001017!2.19e-09!82;UBERON:0000955!2.29e-09!69;UBERON:0006238!2.29e-09!69;UBERON:0001474!2.92e-09!86;UBERON:0001950!4.80e-09!20;UBERON:0005743!5.26e-09!86;UBERON:0000956!1.54e-08!25;UBERON:0000203!1.54e-08!25;UBERON:0000178!4.66e-08!15;UBERON:0000179!4.66e-08!15;UBERON:0000463!4.66e-08!15;UBERON:0000073!1.81e-07!94;UBERON:0001016!1.81e-07!94;UBERON:0003075!2.33e-07!86;UBERON:0007284!2.33e-07!86;UBERON:0003056!4.96e-07!61;UBERON:0004765!7.03e-07!101;UBERON:0001434!7.03e-07!101
|tfbs_overrepresentation=0.272825,0.113895,0.247595,0.093154,0.359621,0.492787,0.0841651,0.657264,0.0643695,0.0507505,0.259407,0.399944,0.341907,0.236085,0.275252,0.119969,0.262088,0.18676,0.102909,0.204438,0.341686,0.247578,0.157234,0.180791,0.0814159,0.384547,0.37494,0.173212,0.0392706,0.178021,0.3679,0.215086,0.0357376,0.373119,0.128625,0.161809,8.67538e-12,0.0840902,0.226218,0.128959,0.183651,0.0486174,0.260466,0.334176,0.227213,0.0711697,0.074588,0.330075,0.210181,0.227712,0.284405,0.105423,0.135407,0.177342,0.358057,0.0753565,0.203364,0.380173,0.150513,0.199999,0.0579941,0.276509,0.205409,0.146128,0.10616,0.0984283,0.580456,0.116417,0.000849877,0.3062,0.61426,0.130776,0.170145,0.224513,0.0148962,0.0339424,0.183676,0.0854797,0.0731115,0.0144524,0.182113,0.402334,0.0831938,0.216503,0.497782,0.115446,0.124542,0.37437,0.000735703,0.121557,0.164159,0.0967167,0.181667,0.0925031,0.163486,0.216824,0.0334767,0.28366,0.17689,0.473112,0.111667,0.476145,0.263619,0.0727591,0.390176,0.080182,0.12949,0.561883,0.267635,0.466115,0.0624257,0.0668385,0.276738,0.0350582,0.192196,0.0663658,0.0402636,0.1101,0.258716,0.160649,0.305628,0.383317,0.260612,0.164207,0.194257,0.322526,0.173151,0.0293679,0.161604,0.251658,0.115605,0.144069,0.111159,0.045053,0.235761,0.204515,0.125521,0.10761,0.0649881,0.00789487,0.0450332,0.238929,0.366262,0.28766,0.273522,0.133829,0.18788,0.161361,0.0763672,0.227065,0.361034,0.266711,0.328768,0.0524571,0.0835935,0.221281,0.14393,0.40461,0.100724,0.0663128,0.403582,0.181487,0.219679,0.273735,0.134895,0.215506,0.0784618,0.238515,0.0790799,0.526782,0.327089,0.256483,0.712672,0.10534,0.153476,0.172044,0.260974,0.330576,0.325054,0.069998,0.292457,0.229948,0.0540612,0.21779,0.142014,0.223569,0.332561,0.0787371,0.158872,0.317,0.20281,0.339514,0.230757,0.405269,0.212647,0.0919303,0.150381,0.116937,0.130723,0.207318,0.170629,0.117148,0.0607132,0.117534,0.254283,0.451528,0.472314,0.280641,0.370039,0.324906,0.0896296,0.197823,0.22763,0.213053,0.527451,0.309534,0.301442,0.191696,0.122022,0.195373,0.263715,0.606181,0.287766,0.296123,0.142265,0.237192,0.258424,0.164555,0.117251,0.116204,0.000368311,0.62151,0.0819301,0.147153,0.18264,0.177704,0.092224,0.45696,0.30027,0.383466,0.331647,0.212362,0.187116,0.15928,0.219044,0.254951,0.156377,0.21083,0.606625,0.220359,0.292806,0.336043,0.336985,0.186448,0.186558,0.293852,0.202983,0.362971,0.134325,0.521047,0.120009,0.319541,0.300061,0.239783,0.0678354,0.155564,0.15574,0.175654,0.222213,0.145331,0.139451,0.122578,0.444637,0.331554,0.165683,0.0746442,0.243403,0.827706,0.917756,0.952889,0.599514,0.0866987,0.138649,0.0505069,0.558337,0.86274,0.454695,0.693419,0.607724,0.522841,0.741357,0.552041,0.635008,0.55052,0.783515,0.12751,0.469955,0.498953,0.0879932,0.63674,0.825036,0.837729,0.339439,0.593966,0.33041,0.302151,0.207878,0.552298,0.388991,0.671702,0.611777,0.0377326,0.0607298,0.777522,0.0172491,0.604085,0.291623,0.734265,0.442844,0.477024,0.512499,0.378377,0.53335,0.397052,0.753214,0.551491,0.486953,0.530428,0.821632,0.498324,0.695401,0.820775,0.659897,0.499918,0.371535,0.685903,0.607959,0.821595,0.847056,0.331481,0.231872,2.81426e-08,0.0226442,0.474883,0.417024,0.336852,0.572701,0.78433,0.468536,0.860083,0.753048,0.76366,0.771595,0.43545,0.483867,0.138028,0.29984,0.129605,0.140844,0.335439,0.837308,0.325512,0.0998451,0.65524,0.892007,0.0764901,0.798903,0.69534,0.38945,0.527767,0.90708,0.0881806,0.143918,0.405564,0.350549,0.0349719,0.00314529,0.502548,0.568759,0.0428475,0.494769,0.547216,0.0299156,0.47878,0.0196266,0.673583,0.404165,0.559521,0.356202,0.288188,0.236487,0.665296,0.73237,0.664325,0.766191,1.82237e-07,0.557914,0.268648,0.269896,0.0174323,0.610862,0.69455,0.708323,0.440842,0.282051,0.0909735,0.2554,0.451268,0.251408,0.187452,0.468679,0.501137,0.488193,0.0537079,0.519135,0.518055,0.841145,0.407705,0.772364,0.488244,0.456149,0.589702,0.401321,0.647111,0.660192,0.595103,0.713637,0.0652332,0.369917,0.774751,0.878565,0.683229,0.46597,0.563445,0.47744,0.483651,0.263421,0.703388,2.37481e-05,0.293756,0.42025,0.0681131,0.410562,0.343113,0.170331,0.115576,0.774372,0.859607,0.57398,0.78784,0.577344,0.724447,0.645462,0.336246,0.00106255,0.532388,0.134669,0.108266,0.348016,0.149912,0.111821,0.267815,0.396879,0.365836,0.689622,0.113191,0.346776,0.211334,0.494962,0.0851816,0.514659,0.23696,0.251518,0.202355,0.000521833,0.121642,3.90864e-11,0.0354999,0.0372073,0.481305,0.628382,0.0908048,0.310441,0.216037,0.198185,0.171816,0.165877,0.294115,0.202749,0.0858038,0.00776602,0.23191,0.241631,0.376483,0.349839,0.572771,0.0974547,0.15892,0.128942,0.331179,0.210172,0.390637,0.554857,0.352924,0.246924,0.000914409,0.0940377,0.359953,0.0216588,0.239194,0.32067,0.334938,0.309827,0.167604,0.181395,0.0223847,0.395388,0.202628,0.474729,0.00960329,0.317242,0.262323,0.378417,0.0592343,0.245796,0.0870651,0.101982,0.374106,0.282907,0.153213,0.185351,0.29465,0.231794,0.173078,0.108497,0.143495,0.000788187,0.255803,0.0289867,0.127078,0.378656,0.392439,0.153874,0.145835,0.297422,0.349099,0.106792,0.149864,0.109211,0.081783,0.0678906,0.076236,0.444489,0.31161,0.361651,0.0953991,0.319245,0.603631,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.123916,0.0563868,1.78271e-09,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.0806655,0.417985,0.491614,0.146453,0.315229,0.157053,0.332022,1.72402e-08,0.273582,0.262915,0.306556,0.26147,0.170005,0.03931,0.491788,0.092369,0.18076,4.93854e-07,0.248113,0.148878,0.206465,0.240599,0.245625,0.674943,0.696152,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.0018761,0.881177,0.387334,0.000704529,0.224219,0.347904,0.324262,0.000247303,0.111827,0.0929171,0.263641,0.118035,0.319902,0.510835,0.137556,0.397628,8.20602e-05,0.0699003,0.235435,0.31953,3.55118e-06,9.11144e-12,0.370285,0.388777,0.204831,0.130161,0.205669,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.000673612,0.281527,0.35188,0.00165855,0.192889,0.188414,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,2.31601e-06,0.287361,0.138613,0.175356,0.116846,0.267784,0.278571,0.185281,0.286026,0.31159,0.349805,0.035873,0.404239,0.439697,0.0317095,0.223892,0.160738,0.553042,0.213489,0.212611,0.338443,0.319005,0.180695,0.45842,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.173101,0.828194,0.0525138,0.341713,0.156156,0.33569,0.288104,0.00720907,0.0576696,0.114697,0.433479,0.324956,0.388835,0.408751,0.0889679,0.000889813,0.070868,0.0230754,0.245,0.0850317,0.249379,0.661446,0.60218,0.696439,0.0219639,0.409327,0.209927,0.685907,0.603176,0.670776,0.696176,0.355968,0.0824588,0.592254,0.647186,0.0730099,0.82397,0.873099,0.312447,0.922804,0.628346,0.737948,0.750579,0.689958,0.435483,0.129532,5.42051e-10,0.402631,0.768239,0.853963,0.255824,0.488239,0.754734,0.799242,0.2667,0.494578,0.301433,0.711296,0.492887,0.819065,0.0431797,0.559471,0.717449,0.449761,0.6937,0.427531,0.0337266,0.26122,0.0060146,0.00258259,0.297082,0.149532,0.8738,0.746016,0.106636,0.607585,0.0374358,0.72684,0.00434511,0.000573639,6.23633e-05,0.36546,0.360788,0.368898,0.510705,0.447298,0.670481,0.576455,0.619669,0.287839,0.262665,0.654187,0.183051,0.530004,0.583703,0.300816,0.00207686,0.225997,0.487688,0.808511,0.529993,0.329919,0.484887,0.0125264,0.57085,0.650025,0.426477,0.540605,0.00638735,0.563634,0.561918,0.624569,0.772094,0.110095,0.785953,0.394773,0.659669,0.659285,0.711322,2.23376e-05,0.823122,0.367684,0.700165,0.258457,4.24609e-06,0.305952,0.356524,0.159817,0.532764,0.0110025,0.319704,0.555004,0.607569,0.773067,0.0899962,0.0644796,0.198803,0.628973,0.594475,0.416321,0.365565,0.47205,0.610358,0.693748,0.578885,0.474879,0.331214,0.518205,0.424119,0.237985,0.519279,0.515179,0.745866,0.623664,0.757999,0.438945,0.619652,0.706112,0.754688,0.39196,0.172059,0.355152,0.346355,0.712437,0.54954,0.520214,0.00170605,0.486574,0.809543,0.138503,0.639482,0.471879,0.600697,0.474504,0.621275,0.727464,0.589415,0.564042,0.356483,0.120876,0.624316,0.55481,0.0660081,0.509842,0.326636,0.368631,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.450702,0.341084,0.138667,0.459605,0.298707,0.345583,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.00300036,0.246146,0.445744,0.371991,0.0325217,0.326635,0.349721,0.39301,0.396235,0.204251,0.524829,0.388491,0.357781,0.338712,0.231439,0.0739965,0.0641227,0.177916,0.0294624,0.327419,0.402268,0.139798,0.163801,0.245045,0.373321,0.433875,0.395243,0.130132,0.0120485,0.462042,0.213394,0.270174,0.0160499,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.362561,0.213995,0.00495268,0.225945,0.18761,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.121292,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.360691,0.26003,0.35537,0.423126,0.288449,0.244977,0.119936,0.395958,0.314638,0.322324,0.184473,0.363414,0.524458,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.504058,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.0352084,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.544575,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.484083,0.486223,0.437432,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.0177821,0.164471,0.533328,0.313891,0.292462,0.46896,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.441686,0.369492,0.592234
}}
}}

Revision as of 17:23, 8 August 2012


Full id: C1522_CD8_Natural_CD4_Basophils_thymus_Peripheral_CD19



Phase1 CAGE Peaks

Hg19::chr4:36245956..36245972,-p6@ARAP2
Hg19::chr4:36245985..36246005,-p3@ARAP2
Hg19::chr4:36246020..36246034,-p10@ARAP2
Hg19::chr4:36246039..36246051,-p11@ARAP2
Hg19::chr4:36246229..36246251,-p7@ARAP2
Hg19::chr5:49962495..49962577,+p1@PARP8


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


GO IDGO nameFDR corrected p-value
GO:0003950NAD+ ADP-ribosyltransferase activity0.0134228187919463
GO:0016763transferase activity, transferring pentosyl groups0.0141292829388908



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
leukocyte1.04e-44140
nongranular leukocyte2.08e-36119
hematopoietic stem cell4.89e-34172
angioblastic mesenchymal cell4.89e-34172
hematopoietic lineage restricted progenitor cell8.31e-34124
hematopoietic oligopotent progenitor cell1.81e-30165
hematopoietic multipotent progenitor cell1.81e-30165
hematopoietic cell2.40e-30182
lymphocyte2.64e-2253
common lymphoid progenitor2.64e-2253
lymphoid lineage restricted progenitor cell3.96e-2252
myeloid leukocyte1.77e-1676
granulocyte monocyte progenitor cell5.71e-1471
CD14-positive, CD16-negative classical monocyte5.73e-1442
macrophage dendritic cell progenitor1.02e-1365
classical monocyte3.29e-1345
monopoietic cell5.59e-1363
monocyte5.59e-1363
monoblast5.59e-1363
promonocyte5.59e-1363
mature alpha-beta T cell9.47e-1318
alpha-beta T cell9.47e-1318
immature T cell9.47e-1318
mature T cell9.47e-1318
immature alpha-beta T cell9.47e-1318
myeloid lineage restricted progenitor cell4.05e-1270
T cell5.89e-1225
pro-T cell5.89e-1225
myeloid cell4.10e-11112
common myeloid progenitor4.10e-11112
lymphocyte of B lineage1.66e-0924
pro-B cell1.66e-0924
CD8-positive, alpha-beta T cell1.46e-0811
B cell6.76e-0814
Uber Anatomy
Ontology termp-valuen
adult organism1.52e-23115
hematopoietic system6.61e-20102
blood island6.61e-20102
hemolymphoid system2.47e-15112
neural tube6.62e-1557
neural rod6.62e-1557
future spinal cord6.62e-1557
neural keel6.62e-1557
anterior neural tube5.58e-1442
regional part of forebrain8.42e-1441
forebrain8.42e-1441
future forebrain8.42e-1441
telencephalon4.68e-1234
gray matter6.52e-1234
brain grey matter6.52e-1234
regional part of telencephalon1.26e-1133
regional part of brain1.45e-1159
cerebral hemisphere2.80e-1132
bone marrow4.16e-1180
regional part of cerebral cortex8.75e-1022
central nervous system2.19e-0982
brain2.29e-0969
future brain2.29e-0969
bone element2.92e-0986
neocortex4.80e-0920
cerebral cortex1.54e-0825
pallium1.54e-0825
blood4.66e-0815
haemolymphatic fluid4.66e-0815
organism substance4.66e-0815
regional part of nervous system1.81e-0794
nervous system1.81e-0794
neural plate2.33e-0786
presumptive neural plate2.33e-0786
pre-chordal neural plate4.96e-0761
skeletal element7.03e-07101
skeletal system7.03e-07101


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.