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Coexpression cluster:C1111: Difference between revisions

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|tf_chipseq_enrich=SUZ12#23512;2:14.318794546018:0.00781968192361486:0.0321173415298259
|tf_chipseq_enrich=SUZ12#23512;2:14.318794546018:0.00781968192361486:0.0321173415298259
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5,0.11039,0.361507,0.660283,0.0754745,0.632378,0.439214,0.0896836,0.133679,0.718626,0.262768,0.235824,0.23812,0.506939,0.0654706,0.844302,0.305348,0.0883079,0.192275,0.123717,0.3044,0.494788,0.435034,0.388488,0.27954,0.689314,0.468189,0.545823,0.168686,0.35711,0.180717,0.375467,0.614081,0.311267,0.299453,0.347601,0.297851,0.195385,0.578705,0.546003,0.106912,0.207535,0.747423,0.283013,0.17144,0.236468,0.274647,0.280244,0.933654,0.750867,0.1168,0.216736,0.112879,0.138362,0.1674,0.205022,0.304414,0.0775871,0.1646,0.530976,0.820894,0.916686,0.435374,0.54926,0.25636,0.392755,0.366993,0.843094,0.12921,0.107541,0.688004,0.136306,0.362226,0.565792,0.158567,0.446426,0.551931,0.0810658,0.268889,0.361819,0.92061,0.882829,0.417001,0.436925,0.234633,0.150144,0.235575,0.111506,0.209512,0.415762,0.167545,0.1033,0.238509,0.156356,0.450242,0.322099,0.0857464,0.282499,0.101873,0.121306,0.246526,0.203595,0.0103447,0.227948,0.44271,0.128341,0.463619,0.168391,0.545636,0.320047,0.397073,0.437057,0.221207,0.603174,0.358,0.621995,0.318595,0.140173,0.390753,0.312917,0.805801,0.326484,0.15977,0.201434,0.134947,0.304849,0.316782,0.212636,0.325012,0.353123,0.394821,0.291345,0.453507,0.491263,0.547467,0.255995,0.184894,0.609179,0.244347,0.243363,0.382464,0.361244,0.207462,0.51104,0.487422,0.29768,0.217499,0.500934,0.225368,0.244195,0.0586175,0.348776,0.198885,0.871901,0.347052,0.386025,0.1797,0.379465,0.327304,0.217315,0.812383,0.132491,0.48467,0.367752,0.436987,0.458334,0.704893,0.895348,0.0821811,0.71056,0.279549,0.0984834,0.284421,0.71736,0.658832,0.751141,0.704995,0.458949,0.547863,0.391162,0.29302,0.726427,0.750889,0.401507,0.692805,0.648881,0.703424,0.308086,0.601152,0.910041,0.732853,0.799099,0.684866,0.790371,0.802111,0.744931,0.515017,0.716126,0.991631,0.451787,0.50853,0.656157,0.680172,0.184591,0.805952,0.846379,0.807879,0.54891,0.341975,0.425103,0.547149,0.863925,0.780774,0.615729,0.771117,0.501908,0.74852,0.478352,0.969954,0.685599,0.954834,0.931591,0.337191,0.834663,0.910621,0.797881,0.887926,0.664234,0.972335,0.779967,0.871735,0.829635,0.858681,0.411785,0.40673,0.415502,0.203449,0.499305,0.726141,0.0807208,0.676266,0.327011,0.299176,0.710278,0.210121,0.585578,0.272487,0.341296,0.457524,0.258349,0.541728,0.854621,0.585566,0.373172,0.538803,0.867555,0.386822,0.706206,0.505417,0.230258,0.917146,0.619962,0.88908,0.681127,0.821879,0.727983,0.834451,0.443364,0.358039,0.357569,0.765316,0.954715,0.867478,0.41419,0.7547,0.294507,0.734868,0.346938,0.40211,0.183851,0.588416,0.783193,0.362009,0.611179,0.664218,0.822766,0.706724,0.654039,0.832266,0.685486,0.651111,0.466416,0.411899,0.525367,0.667,0.748565,0.635414,0.528332,0.906271,0.209988,0.474724,0.661532,0.574524,0.570287,0.797742,0.68023,0.808962,0.490466,0.676249,0.760368,0.805909,0.440345,0.809866,0.400622,0.391073,0.766374,0.883398,0.575489,0.762263,0.183236,0.855535,0.775603,0.118405,0.525188,0.657348,0.52794,0.67786,0.780554,0.646027,0.620377,0.402066,0.887664,0.680876,0.610982,0.826815,0.564763,0.904403,0.101471,0.364157,0.172412,0.53064,0.415017,0.0769041,0.387804,0.502902,0.385339,0.159832,0.512288,0.338978,0.390233,0.339879,0.438999,0.41967,0.197678,0.208523,0.34551,0.4924,0.304359,0.497662,0.418843,0.749185,0.369586,0.394729,0.441472,0.444932,0.622992,0.580249,0.436618,0.403472,0.382758,0.264429,0.404954,0.0744027,0.204325,0.265849,0.370442,0.451398,0.533438,0.188364,0.279598,0.420279,0.143312,0.443868,0.150111,0.420451,0.514853,0.244241,0.307495,0.455626,0.3382,0.454846,0.350305,0.0875262,0.147486,0.117583,0.103076,0.518238,0.40865,0.634608,0.324846,0.25829,0.215261,0.235004,0.133496,0.433115,0.331422,0.440492,0.397558,0.266168,0.504119,0.57634,0.371725,0.334024,0.500457,0.316975,0.435107,0.26559,0.378345,0.380153,0.160696,0.502341,0.507413,0.412407,0.42955,0.418893,0.300222,0.393729,0.487504,0.249956,0.447581,0.482721,0.35808,0.406625,0.296254,0.400859,0.473667,0.327684,0.279523,0.499937,0.444635,0.356463,0.364875,0.211724,0.409573,0.579867,0.536787,0.436872,0.181464,0.40945,0.231548,0.120636,0.121001,0.317719,0.172653,0.0924531,0.120918,0.593272,0.507382,0.425328,0.384398,0.462521,0.387627,0.179489,0.214126,0.143317,0.261663,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.050072,0.545381,0.630108,0.299959,0.509613,0.498355,0.406059,0.452427,0.56256,0.494497,0.366448,0.540845,0.511559,0.280842,0.335456,0.416632,0.404559,0.545676,0.467154,0.600528,0.249647,0.43669,0.446356,0.248584,0.397145,0.390152,0.537963,0.540199,0.488863,0.342785,0.447064,0.20487,0.603936,0.449548,0.41929,0.209566,0.189123,0.588995,0.355645,0.332105,0.169259,0.158122,0.521096,0.220023,0.444217,0.363335,0.329186,0.432735,0.493369,0.416144,0.648861
|tfbs_overrepresentation_for_novel_motifs=0.392069,0.247072,0.384703,0.529489,0.343148,0.52784,0.604235,1.20202,0.224331,0.200685,0.497563,1.5614,0.184039,0.592674,1.62257,0.365029,0.827563,0.786991,0.19568,0.32524,1.00032,0.498384,0.520063,0.338096,0.430372,0.670692,0.49486,0.517892,0.346214,0.459534,0.475674,0.864517,0.257226,0.186138,0.309012,0.0934825,0.305874,0.529001,1.4117,0.597792,0.829015,0.459366,0.541549,0.340293,0.0257952,0.415364,0.60533,0.486696,0.876276,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.638689,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,1.90083,0.115253,1.0929,0.179863,0.168304,0.156354,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,1.21234,1.04131,0.0324537,0.097572,0.448771,0.711163,1.65172,1.27705,1.01423,2.04389,0.26423,0.343884,0.759662,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,1.81048,0.915771,0.379203,0.507004,1.22894,0.304323,0.358137,0.474472,1.80003,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.345641,0.0685123,1.0153,0.619774,0.607223,3.1365,0.694887,0.877715,0.430431,1.03728,1.2088,0.996724,1.97961,0.404861,0.7715,0.624608,0.24928,0.602897,0.0992692
}}
}}

Revision as of 14:41, 26 November 2012


Full id: C1111_CD8_Natural_CD14_Basophils_CD4_Peripheral_immature



Phase1 CAGE Peaks

Hg19::chr10:17069064..17069080,+p@chr10:17069064..17069080
+
Hg19::chr11:58341472..58341486,+p@chr11:58341472..58341486
+
Hg19::chr12:92271876..92271896,+p@chr12:92271876..92271896
+
Hg19::chr12:92271935..92271946,+p@chr12:92271935..92271946
+
Hg19::chr1:234747186..234747197,+p@chr1:234747186..234747197
+
Hg19::chr5:42994725..42994739,-p@chr5:42994725..42994739
-
Hg19::chr5:43042044..43042056,-p@chr5:43042044..43042056
-


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
leukocyte2.92e-67136
classical monocyte1.27e-6142
CD14-positive, CD16-negative classical monocyte1.27e-6142
nongranular leukocyte3.80e-54115
hematopoietic lineage restricted progenitor cell2.61e-53120
hematopoietic cell2.68e-53177
defensive cell1.17e-5248
phagocyte1.17e-5248
hematopoietic stem cell2.10e-51168
angioblastic mesenchymal cell2.10e-51168
myeloid leukocyte5.79e-5172
granulocyte monocyte progenitor cell1.35e-4667
hematopoietic oligopotent progenitor cell8.06e-45161
hematopoietic multipotent progenitor cell8.06e-45161
myeloid lineage restricted progenitor cell8.20e-4566
macrophage dendritic cell progenitor8.34e-4461
monopoietic cell6.86e-4359
monocyte6.86e-4359
monoblast6.86e-4359
promonocyte6.86e-4359
myeloid cell1.25e-33108
common myeloid progenitor1.25e-33108
stuff accumulating cell1.20e-2487
mesenchymal cell6.45e-16354
CD4-positive, alpha-beta T cell9.34e-166
connective tissue cell2.68e-15361
circulating cell4.75e-146
motile cell3.96e-13386
mature alpha-beta T cell6.46e-1318
alpha-beta T cell6.46e-1318
immature T cell6.46e-1318
mature T cell6.46e-1318
immature alpha-beta T cell6.46e-1318
stem cell1.33e-11441
multi fate stem cell4.31e-11427
somatic stem cell1.02e-10433
lymphoid lineage restricted progenitor cell1.94e-1052
lymphocyte3.69e-1053
common lymphoid progenitor3.69e-1053
nucleate cell1.23e-0955
natural killer cell1.44e-093
pro-NK cell1.44e-093
basophil3.71e-093
T cell1.12e-0825
pro-T cell1.12e-0825
naive T cell1.48e-083
single nucleate cell3.02e-083
mononuclear cell3.02e-083
plasmacytoid dendritic cell4.07e-083
intermediate monocyte3.66e-079
CD14-positive, CD16-positive monocyte3.66e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.05e-4298
blood island4.05e-4298
bone marrow7.72e-4076
hemolymphoid system4.38e-37108
bone element3.74e-3682
immune system1.18e-3293
skeletal element5.28e-3290
skeletal system9.44e-28100
connective tissue1.86e-14371
lateral plate mesoderm3.96e-14203
musculoskeletal system2.20e-13167


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
SUZ12#23512214.3187945460180.007819681923614860.0321173415298259



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.