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Difference between revisions of "Coexpression cluster:C1939"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0002390!8.72e-60!102;UBERON:0003061!8.72e-60!102;UBERON:0002193!9.05e-53!112;UBERON:0002371!3.70e-41!80;UBERON:0001474!2.79e-37!86;UBERON:0004765!1.28e-29!101;UBERON:0001434!1.28e-29!101;UBERON:0002405!4.69e-28!115;UBERON:0003081!2.50e-20!216;UBERON:0000178!5.59e-20!15;UBERON:0000179!5.59e-20!15;UBERON:0000463!5.59e-20!15;UBERON:0002204!1.37e-12!167;UBERON:0002384!1.02e-07!375
 
|ontology_enrichment_uberon=UBERON:0002390!8.72e-60!102;UBERON:0003061!8.72e-60!102;UBERON:0002193!9.05e-53!112;UBERON:0002371!3.70e-41!80;UBERON:0001474!2.79e-37!86;UBERON:0004765!1.28e-29!101;UBERON:0001434!1.28e-29!101;UBERON:0002405!4.69e-28!115;UBERON:0003081!2.50e-20!216;UBERON:0000178!5.59e-20!15;UBERON:0000179!5.59e-20!15;UBERON:0000463!5.59e-20!15;UBERON:0002204!1.37e-12!167;UBERON:0002384!1.02e-07!375
 +
|tfbs_overrepresentation=0.23317,0.0958562,0.351299,0.078254,0.310241,0.43203,0.0706464,0.224712,0.0539364,0.0424746,0.221396,0.346629,0.294377,0.201017,0.235304,0.101024,0.223746,0.158251,0.0865245,0.173528,0.29418,0.211047,0.13286,0.153106,0.0683222,0.332688,0.324018,0.146582,0.227906,0.150721,0.31768,0.182756,0.0298713,0.322378,0.108398,0.136785,0.856615,0.070583,0.192426,0.108683,0.155571,0.0406818,0.222325,0.005044,0.193292,0.0596699,0.0625547,0.28382,0.178503,0.193726,0.243359,0.0886583,0.114185,0.150136,0.308837,0.0632035,0.172598,0.328738,0.127101,0.169687,0.0485674,0.236408,0.174369,0.123348,0.0892839,0.0827236,0.515105,0.0980005,0.139298,0.262613,0.547889,0.110232,0.143944,0.190944,0.012429,0.0283664,0.155593,0.0717582,0.0613084,0.0120583,0.154245,0.348799,0.0698251,0.183986,0.436695,0.38341,0.104918,0.323505,0.790836,0.102375,0.138802,0.0812726,0.153861,0.0777027,0.138224,0.184264,0.769004,0.242703,0.149747,0.413729,0.0939617,0.416542,0.225088,0.0610111,0.337778,0.0672793,0.109136,0.497282,0.228612,0.407248,0.285407,0.0560173,0.23661,0.0293017,0.162943,0.0556189,0.0336673,0.0926302,0.220791,0.13579,0.262107,0.331577,0.222452,0.138843,0.164723,0.277102,0.146529,0.0245339,0.136609,0.214614,0.0973103,0.121587,0.0935301,0.0376876,0.200735,0.173595,0.105753,0.0905147,0.0544577,0.0065834,0.037671,0.203496,0.316207,0.0331631,0.779726,0.112838,0.159217,0.1364,0.0640569,0.193163,0.311509,0.227801,0.282656,0.0439093,0.070163,0.188135,0.121467,0.350865,0.0846706,0.0555742,0.349932,0.153706,0.186743,0.23397,0.412853,0.183121,0.065826,0.203135,0.0663482,0.463935,0.281162,0.218835,0.646289,0.0885874,0.129639,0.145577,0.22277,0.284267,0.27935,0.0586816,0.250461,0.195671,0.0452583,0.185103,0.11983,0.190123,0.286036,0.0660586,0.134265,0.272191,0.172119,0.292239,0.196376,0.351465,0.18064,0.0772176,0.126988,0.0984435,0.110187,0.176022,0.144361,0.0986228,0.0508565,0.0989516,0.21691,0.393782,0.412989,0.240045,0.319604,0.279218,0.0752697,0.167805,0.193654,0.180992,0.464566,0.265567,0.258402,0.162511,0.102771,0.165687,0.225173,0.540012,0.246322,0.253699,0.120044,0.201982,0.220536,0.139142,0.0987108,0.09782,0.754769,0.554981,0.0687568,0.124225,0.1547,0.150448,0.0774663,0.398789,0.257365,0.331711,0.285222,0.511,0.158559,0.134615,0.186192,0.217494,0.132125,0.179065,0.540443,0.187334,0.250769,0.289141,0.289982,0.157983,0.158078,0.251693,0.172268,0.313249,0.113261,0.766691,0.101058,0.274448,0.25718,0.204241,0.0568578,0.131428,0.131579,0.148683,0.188945,0.122666,0.419402,0.103245,0.387442,0.627158,0.14011,0.0626022,0.2074,0.430549,0.875285,0.921608,0.814323,0.748392,0.944588,0.935701,0.493893,0.808889,0.396701,0.626645,0.541514,0.460217,0.310815,0.487888,0.568246,0.486439,0.720623,0.796904,0.410803,0.43779,0.579996,0.569955,0.766049,0.780281,0.292173,0.528152,0.284119,0.601223,0.176507,0.488132,0.336705,0.604733,0.545464,0.645432,0.824163,0.132079,0.706516,0.537972,0.591562,0.668584,0.385794,0.417358,0.450485,0.665656,0.470142,0.344006,0.688397,0.785741,0.426591,0.467379,0.762263,0.437202,0.628658,0.761311,0.592924,0.438692,0.660225,0.619033,0.541742,0.762222,0.790857,0.285074,0.870229,0.943261,0.899362,0.415372,0.362164,0.289863,0.507647,0.721501,0.409489,0.80581,0.688223,0.699429,0.707862,0.379008,0.423719,0.655494,0.256985,0.109234,0.11883,0.288602,0.779806,0.429909,0.766165,0.588284,0.843506,0.732646,0.737273,0.628596,0.337121,0.464864,0.861932,0.0740433,0.121457,0.351733,0.826323,0.773103,0.687274,0.441154,0.503865,0.660832,0.43388,0.483295,0.852766,0.418989,0.935814,0.606622,0.350461,0.495024,0.307173,0.246694,0.752605,0.598317,0.666615,0.597346,0.702113,0.961692,0.493489,0.229501,0.230597,0.555864,0.544572,0.627794,0.641833,0.383956,0.031782,0.0764074,0.217887,0.393543,0.214395,0.158849,0.732038,0.439833,0.427746,0.504398,0.456725,0.455709,0.784142,0.688249,0.708682,0.427794,0.398041,0.524026,0.347879,0.0119366,0.593219,0.529253,0.64728,0.903142,0.319495,0.711229,0.827435,0.616333,0.407113,0.498776,0.738012,0.423517,0.224914,0.636791,0.706243,0.251608,0.365107,0.00819351,0.0102753,0.295455,0.144104,0.0972855,0.710825,0.80526,0.508875,0.725283,0.512109,0.658411,0.578577,0.818493,0.809533,0.469232,0.113555,0.0910724,0.299839,0.126587,0.0940929,0.22877,0.343849,0.315824,0.622796,0.621499,0.29873,0.179502,0.43406,0.0715061,0.452515,0.201779,0.214491,0.171725,0.412647,0.102448,0.550877,0.029672,0.453305,0.421335,0.561724,0.0762646,0.266371,0.183582,0.168118,0.145381,0.140277,0.251925,0.172066,0.0720324,0.00647589,0.19738,0.205854,0.32541,0.301472,0.507714,0.0818982,0.134306,0.108669,0.284804,0.178494,0.338195,0.490571,0.304235,0.210475,0.294266,0.0790025,0.310539,0.580279,0.203728,0.275452,0.288155,0.265827,0.141761,0.153627,0.0186891,0.0668022,0.171961,0.415228,0.00800917,0.272406,0.223952,0.327153,0.0496113,0.20949,0.0730994,0.0857377,0.323267,0.24204,0.129414,0.157037,1.36307e-05,0.197279,0.146467,0.0912686,0.425114,0.7034,0.218241,0.0242146,0.10708,0.327369,0.339826,0.12998,0.123097,0.254847,0.300809,0.0898207,0.126545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}}
 
}}

Revision as of 08:48, 8 August 2012


Full id: C1939_cord_myeloma_CD14_Neutrophils_b_Whole_anaplastic



Phase1 CAGE Peaks

  Short description
Hg19::chr4:185771717..185771736,- p@chr4:185771717..185771736
-
Hg19::chr4:185771741..185771768,- p@chr4:185771741..185771768
-
Hg19::chr4:185771791..185771803,- p@chr4:185771791..185771803
-
Hg19::chr4:185771819..185771833,- p@chr4:185771819..185771833
-
Hg19::chr4:185771870..185771884,- p@chr4:185771870..185771884
-


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
CD14-positive, CD16-negative classical monocyte1.64e-6642
classical monocyte3.62e-6145
myeloid leukocyte1.25e-5576
monopoietic cell3.27e-5363
monocyte3.27e-5363
monoblast3.27e-5363
promonocyte3.27e-5363
macrophage dendritic cell progenitor3.84e-5165
myeloid lineage restricted progenitor cell1.76e-4670
leukocyte2.61e-46140
nongranular leukocyte4.15e-46119
granulocyte monocyte progenitor cell1.25e-4571
hematopoietic lineage restricted progenitor cell1.61e-38124
hematopoietic cell6.22e-38182
hematopoietic stem cell1.60e-36172
angioblastic mesenchymal cell1.60e-36172
myeloid cell1.36e-35112
common myeloid progenitor1.36e-35112
hematopoietic oligopotent progenitor cell1.01e-34165
hematopoietic multipotent progenitor cell1.01e-34165
circulating cell5.11e-126
intermediate monocyte3.49e-099
CD14-positive, CD16-positive monocyte3.49e-099
mesenchymal cell2.17e-08358
granulocyte2.68e-088
blood cell5.44e-0811
connective tissue cell6.55e-08365
neutrophil7.28e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.72e-60102
blood island8.72e-60102
hemolymphoid system9.05e-53112
bone marrow3.70e-4180
bone element2.79e-3786
skeletal element1.28e-29101
skeletal system1.28e-29101
immune system4.69e-28115
lateral plate mesoderm2.50e-20216
blood5.59e-2015
haemolymphatic fluid5.59e-2015
organism substance5.59e-2015
musculoskeletal system1.37e-12167
connective tissue1.02e-07375


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.