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Coexpression cluster:C1132: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:3.82875455219645:0.00338737119268134:0.0172909902244598!FOXA1#3169;4:6.33223985679169:0.00185468101692017:0.0109429428126165!GATA3#2625;3:11.6727927245169:0.00154910869847361:0.0098440744362571!RAD21#5885;5:7.3964527824688:0.000149101450522837:0.00192318221454299
|tf_chipseq_enrich=CTCF#10664;5:3.82875455219645:0.00338737119268134:0.0172909902244598!FOXA1#3169;4:6.33223985679169:0.00185468101692017:0.0109429428126165!GATA3#2625;3:11.6727927245169:0.00154910869847361:0.0098440744362571!RAD21#5885;5:7.3964527824688:0.000149101450522837:0.00192318221454299
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216,0.0947479,0.0787488,0.0883646,0.496336,0.353144,0.0974692,0.11039,0.361507,0.660283,0.0754745,0.632378,0.439214,0.0896836,0.133679,0.361823,0.262768,0.235824,0.23812,0.506939,0.0654706,0.844302,0.305348,0.0883079,0.192275,0.123717,0.0519109,0.494788,0.435034,0.388488,0.27954,0.689314,0.468189,0.0458919,0.168686,0.35711,0.180717,0.375467,0.614081,0.311267,0.299453,0.347601,0.297851,0.195385,0.578705,0.546003,0.106912,0.207535,0.747423,0.283013,0.17144,0.236468,0.274647,0.280244,0.933654,0.750867,0.1168,0.216736,0.112879,0.138362,0.1674,0.205022,0.304414,0.0775871,0.1646,0.530976,0.956744,0.452369,0.435374,0.54926,0.25636,0.392755,0.366993,0.843094,0.12921,0.107541,0.688004,0.136306,0.362226,0.565792,0.158567,0.446426,0.551931,0.0810658,0.268889,0.361819,0.996492,0.998378,0.417001,0.436925,0.234633,0.150144,0.235575,0.111506,0.209512,0.415762,0.167545,0.1033,0.238509,0.156356,0.450242,0.00733677,0.0857464,0.282499,0.101873,0.121306,0.246526,0.203595,0.356991,0.227948,0.44271,0.128341,0.129502,0.168391,0.545636,0.320047,0.397073,0.437057,0.221207,0.603174,0.358,0.621995,0.318595,0.140173,0.0888517,0.312917,0.805801,0.326484,0.15977,0.201434,0.134947,0.304849,0.316782,0.212636,0.325012,0.353123,0.394821,0.291345,0.453507,0.491263,0.547467,0.255995,0.184894,0.609179,0.244347,0.243363,0.382464,0.361244,0.207462,0.51104,0.487422,0.29768,0.217499,0.500934,0.225368,0.244195,0.0586175,0.348776,0.198885,0.001299,0.347052,0.386025,0.1797,0.379465,0.327304,0.581915,0.812383,0.132491,0.48467,0.367752,0.436987,0.458334,0.704893,0.895348,0.0821811,0.71056,0.279549,0.0984834,0.284421,0.71736,0.658832,0.405011,0.704995,0.458949,0.840587,0.741039,0.0241698,0.14201,0.40466,0.401507,0.692805,0.0890752,0.703424,0.673541,0.86822,0.0361807,0.732853,0.35015,0.00662952,0.790371,0.802111,0.744931,2.11364e-06,0.99232,0.991631,0.451787,0.818359,0.0270901,0.315577,0.542303,0.0843722,0.558605,0.0888143,0.00893069,0.341975,0.765292,0.547149,0.863925,0.780774,0.615729,0.433619,0.501908,0.161783,0.478352,0.969954,0.32181,0.37458,0.502019,0.337191,0.834663,0.910621,0.797881,0.976385,0.297799,0.972335,0.779967,0.971958,0.829635,0.96824,0.411785,0.40673,0.101625,0.565657,0.0331465,0.371455,0.265079,0.311148,0.00771497,0.299176,0.129041,0.210121,0.585578,0.640275,0.0662996,0.12574,0.258349,0.541728,0.574271,0.585566,0.373172,0.538803,0.280793,0.893074,0.0359672,0.505417,0.596462,0.240432,0.0744189,0.377003,0.316667,0.249468,0.977195,0.834451,0.443364,0.358039,0.132914,0.765316,0.597705,0.32901,0.41419,0.7547,0.294507,0.926591,0.346938,0.0945861,0.183851,0.588416,0.198404,0.362009,0.611179,0.664218,0.250792,0.706724,0.654039,0.0024572,0.321679,0.651111,0.466416,0.0168358,0.525367,0.667,9.69089e-05,0.0819628,0.0407023,0.0337416,0.573415,0.474724,0.661532,0.574524,0.207335,0.00132736,0.68023,0.0003257,0.490466,0.676249,0.173467,0.487711,0.440345,0.232264,1.61415e-05,0.391073,0.426674,0.170712,0.575489,0.420733,0.540565,0.576036,0.775603,0.695855,0.525188,0.657348,0.52794,0.67786,0.195343,0.646027,0.0746134,0.0945637,0.887664,0.680876,0.243699,0.101338,0.564763,0.000169342,0.415214,0.364157,0.172412,0.175623,0.415017,0.0769041,0.387804,0.502902,0.385339,0.159832,0.0363719,0.338978,0.390233,0.0657095,0.438999,0.41967,0.197678,0.208523,0.34551,0.0315271,0.304359,0.151812,0.103429,0.749185,0.369586,0.394729,0.441472,0.444932,0.0758483,0.580249,0.436618,0.403472,0.0849422,0.264429,0.404954,0.0744027,0.204325,0.265849,0.370442,0.451398,0.0421649,0.188364,0.279598,0.420279,0.485091,0.443868,0.150111,0.104304,0.00644063,0.00297106,0.307495,0.455626,0.3382,0.124108,0.350305,0.0875262,0.147486,0.117583,0.103076,0.518238,0.40865,0.019407,0.324846,0.25829,0.215261,0.235004,0.133496,0.433115,0.331422,0.440492,0.397558,0.266168,0.00079261,0.0562494,0.371725,0.334024,0.500457,0.0565897,0.435107,0.26559,0.378345,0.380153,0.160696,0.502341,0.15862,0.00218511,0.00265168,0.418893,0.300222,0.393729,0.487504,0.249956,0.447581,0.141745,0.35808,0.406625,0.296254,0.400859,0.473667,0.327684,0.279523,0.00555762,0.444635,0.356463,0.364875,0.0241877,0.409573,0.579867,0.536787,0.436872,0.181464,0.40945,0.231548,0.120636,0.121001,0.317719,0.172653,0.0924531,0.120918,0.593272,0.158598,0.425328,0.384398,0.462521,0.387627,0.179489,0.214126,0.143317,0.261663,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.558766,0.545381,0.630108,0.299959,0.0356876,0.0329198,0.406059,0.023339,0.56256,0.494497,0.366448,0.540845,0.511559,0.280842,0.335456,0.00229313,0.404559,0.545676,0.467154,0.600528,0.249647,0.43669,0.446356,0.248584,0.397145,0.390152,0.537963,0.540199,0.000651537,0.342785,0.119442,0.20487,0.23711,0.449548,0.41929,0.209566,0.189123,0.22355,0.355645,0.332105,0.522124,0.158122,0.521096,0.220023,0.0218866,0.363335,0.329186,0.432735,0.493369,0.416144,0.281368
|tfbs_overrepresentation_for_novel_motifs=1.01633,3.00841,0.384703,0.529489,2.46184,1.30874,1.47005,0.643217,0.637583,0.773341,2.1529,0.647852,0.541517,0.592674,0.341795,0.365029,0.827563,0.28906,4.04242,0.0986842,0.384762,2.36891,0.520063,1.60954,0.430372,0.670692,0.164928,0.517892,0.346214,0.459534,0.475674,0.864517,0.257226,1.04347,0.309012,1.05693,0.305874,0.529001,0.282922,0.207499,0.307642,1.16235,0.541549,0.340293,0.265117,0.415364,0.60533,0.486696,0.237549,0.346342,0.684981,1.49721,1.23204,0.941629,1.09491,0.595623,0.350547,0.562713,0.459282,0.561701,0.905643,0.60771,0.224801,1.87621,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,0.744055,1.0929,0.179863,0.168304,0.921933,0.782748,0.850825,1.0864,0.200147,0.798651,0.625403,0.229431,1.04131,0.131619,0.322252,1.41581,0.711163,1.65172,1.27705,1.01423,0.881388,2.06836,0.343884,0.759662,0.566252,0.924148,0.715799,1.92468,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,2.38505,1.81048,0.915771,0.379203,0.507004,1.22894,0.821533,0.039977,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,1.53117,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,2.98295,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.619774,0.607223,1.42052,0.694887,0.877715,0.430431,0.401655,1.2088,0.996724,4.70253,0.404861,0.7715,1.51278,0.24928,0.602897,0.00626991
}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1132_thymus_CD4_CD8_Natural_chronic_acute_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:118175596..118175612,+p3@CD3E
Hg19::chr11:118186215..118186232,+p@chr11:118186215..118186232
+
Hg19::chr11:118186261..118186272,+p@chr11:118186261..118186272
+
Hg19::chr11:118186324..118186363,+p@chr11:118186324..118186363
+
Hg19::chr11:118186366..118186415,+p@chr11:118186366..118186415
+
Hg19::chr11:118186552..118186562,+p@chr11:118186552..118186562
+
Hg19::chr11:60780935..60780941,+p@chr11:60780935..60780941
+


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
T cell1.30e-4525
pro-T cell1.30e-4525
mature alpha-beta T cell1.25e-4318
alpha-beta T cell1.25e-4318
immature T cell1.25e-4318
mature T cell1.25e-4318
immature alpha-beta T cell1.25e-4318
CD8-positive, alpha-beta T cell1.90e-2711
lymphoid lineage restricted progenitor cell4.58e-2552
lymphocyte1.87e-2453
common lymphoid progenitor1.87e-2453
nucleate cell2.66e-2355
CD4-positive, alpha-beta T cell1.44e-156
nongranular leukocyte3.47e-14115
leukocyte1.33e-13136
hematopoietic lineage restricted progenitor cell3.42e-10120
hematopoietic stem cell2.35e-09168
angioblastic mesenchymal cell2.35e-09168
natural killer cell5.38e-093
pro-NK cell5.38e-093
single nucleate cell1.48e-083
mononuclear cell1.48e-083
hematopoietic cell1.86e-08177
naive T cell3.51e-083
hematopoietic oligopotent progenitor cell4.46e-07161
hematopoietic multipotent progenitor cell4.46e-07161
Uber Anatomy
Ontology termp-valuen
blood3.95e-1515
haemolymphatic fluid3.95e-1515
organism substance3.95e-1515
hemopoietic organ2.08e-127
immune organ2.08e-127
thymus9.92e-114
hemolymphoid system gland9.92e-114
thymic region9.92e-114
pharyngeal gland9.92e-114
thymus primordium9.92e-114
pharyngeal epithelium3.90e-076


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)

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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
CTCF#1066453.828754552196450.003387371192681340.0172909902244598
FOXA1#316946.332239856791690.001854681016920170.0109429428126165
GATA3#2625311.67279272451690.001549108698473610.0098440744362571
RAD21#588557.39645278246880.0001491014505228370.00192318221454299



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.