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Difference between revisions of "Coexpression cluster:C4333"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0002193!4.01e-37!112;UBERON:0002390!3.78e-36!102;UBERON:0003061!3.78e-36!102;UBERON:0002371!4.13e-28!80;UBERON:0001474!5.32e-25!86;UBERON:0002405!4.22e-22!115;UBERON:0004765!4.65e-19!101;UBERON:0001434!4.65e-19!101;UBERON:0002384!4.63e-13!375;UBERON:0003081!5.49e-13!216;UBERON:0002204!1.88e-09!167;UBERON:0007023!2.01e-09!115
 
|ontology_enrichment_uberon=UBERON:0002193!4.01e-37!112;UBERON:0002390!3.78e-36!102;UBERON:0003061!3.78e-36!102;UBERON:0002371!4.13e-28!80;UBERON:0001474!5.32e-25!86;UBERON:0002405!4.22e-22!115;UBERON:0004765!4.65e-19!101;UBERON:0001434!4.65e-19!101;UBERON:0002384!4.63e-13!375;UBERON:0003081!5.49e-13!216;UBERON:0002204!1.88e-09!167;UBERON:0007023!2.01e-09!115
 +
|tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.199763,0.287811,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.113083,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.0105769,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.0249033,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.0082662,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.0281563,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.00384591,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.00081807,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.014161,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0585224,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.00909613,0.198118,0.0821962,0.20128,0.0319444,0.228731,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.0914012,0.329568,0.53472,0.248224,0.271958,0.292154,0.405773,0.39729,0.217139,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.280025,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.0447111,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.137839,0.115044,0.373868,0.57762,0.241757,0.18237,0.126021,0.0310069,0.400457,0.275351,0.236471,0.185661,0.346319,0.00787142,0.270984,0.625945,0.503058,0.513852,0.169228,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.421596,0.581837,0.1002,0.671377,0.546839,0.551561,0.0225539,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.229003,0.28275,0.589326,0.154921,0.294698,0.34331,0.477304,0.289204,0.327108,0.0295492,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.165111,0.858756,0.335105,0.144809,0.145539,0.0134194,0.0818086,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.0450125,0.262537,0.359455,0.226257,0.405955,0.41707,0.0110128,0.464871,0.166672,0.206222,0.171685,0.0905337,0.113671,0.269226,0.339277,0.192529,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.0397695,0.625309,0.347298,0.539392,0.34988,0.475069,0.0958562,0.6408,0.262389,0.316179,0.0697683,0.0556835,0.0198561,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.0190418,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.00395801,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.51771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361435
 
}}
 
}}

Revision as of 10:56, 8 August 2012


Full id: C4333_CD14_Mesenchymal_Eosinophils_CD14CD16_Smooth_xeroderma_Monocytederived



Phase1 CAGE Peaks

  Short description
Hg19::chr3:48507621..48507689,+ p1@TREX1
Hg19::chr6:37401042..37401063,+ p2@FTSJD2
Hg19::chr6:37401066..37401079,+ p4@FTSJD2


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


GO IDGO nameFDR corrected p-value
GO:00082963'-5'-exodeoxyribonuclease activity0.00191754554170662
GO:0008853exodeoxyribonuclease III activity0.00191754554170662
GO:0032405MutLalpha complex binding0.00191754554170662
GO:0032407MutSalpha complex binding0.00191754554170662
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.00191754554170662
GO:0032404mismatch repair complex binding0.00191754554170662
GO:0004529exodeoxyribonuclease activity0.00191754554170662
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.00461409395973154
GO:00084083'-5' exonuclease activity0.00503355704697986
GO:0004536deoxyribonuclease activity0.00838926174496644
GO:0003697single-stranded DNA binding0.00922818791946309
GO:0004527exonuclease activity0.00922818791946309
GO:0006298mismatch repair0.00922818791946309
GO:0045005maintenance of fidelity during DNA-dependent DNA replication0.00922818791946309
GO:0032403protein complex binding0.0112975391498881
GO:0042803protein homodimerization activity0.0153803131991051
GO:0043566structure-specific DNA binding0.0153803131991051
GO:0006261DNA-dependent DNA replication0.0153803131991051
GO:0005635nuclear envelope0.0165268456375839
GO:0006310DNA recombination0.0165268456375839
GO:0004518nuclease activity0.0196548418024928
GO:0006260DNA replication0.0255872483221476
GO:0042802identical protein binding0.0255872483221476
GO:0046983protein dimerization activity0.0255872483221476
GO:0006281DNA repair0.0263087248322147
GO:0000287magnesium ion binding0.0278399204573701
GO:0006974response to DNA damage stimulus0.0278399204573701
GO:0009719response to endogenous stimulus0.0316994247363375
GO:0031967organelle envelope0.0348993288590604
GO:0031975envelope0.0348993288590604



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
leukocyte1.49e-57140
nongranular leukocyte3.03e-52119
hematopoietic lineage restricted progenitor cell1.50e-48124
hematopoietic stem cell1.65e-45172
angioblastic mesenchymal cell1.65e-45172
hematopoietic cell1.33e-44182
hematopoietic oligopotent progenitor cell4.32e-42165
hematopoietic multipotent progenitor cell4.32e-42165
myeloid leukocyte5.73e-3276
macrophage dendritic cell progenitor1.14e-3065
monopoietic cell1.14e-3063
monocyte1.14e-3063
monoblast1.14e-3063
promonocyte1.14e-3063
granulocyte monocyte progenitor cell2.51e-2971
myeloid lineage restricted progenitor cell1.39e-2870
CD14-positive, CD16-negative classical monocyte3.86e-2642
classical monocyte1.39e-2545
myeloid cell3.56e-22112
common myeloid progenitor3.56e-22112
lymphocyte9.09e-1953
common lymphoid progenitor9.09e-1953
lymphoid lineage restricted progenitor cell1.66e-1852
mesenchymal cell1.88e-15358
connective tissue cell1.59e-14365
motile cell3.24e-13390
lymphocyte of B lineage5.73e-1224
pro-B cell5.73e-1224
multi fate stem cell7.03e-11430
somatic stem cell2.27e-10436
stem cell1.47e-09444
B cell5.08e-0814
T cell6.15e-0725
pro-T cell6.15e-0725
intermediate monocyte9.91e-079
CD14-positive, CD16-positive monocyte9.91e-079
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.01e-37112
hematopoietic system3.78e-36102
blood island3.78e-36102
bone marrow4.13e-2880
bone element5.32e-2586
immune system4.22e-22115
skeletal element4.65e-19101
skeletal system4.65e-19101
connective tissue4.63e-13375
lateral plate mesoderm5.49e-13216
musculoskeletal system1.88e-09167
adult organism2.01e-09115


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)

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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.