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Coexpression cluster:C4473: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!6.10e-30!112;UBERON:0002390!2.35e-29!102;UBERON:0003061!2.35e-29!102;UBERON:0003081!3.68e-25!216;UBERON:0002371!2.92e-24!80;UBERON:0002405!1.44e-23!115;UBERON:0001474!1.07e-22!86;UBERON:0004765!6.10e-19!101;UBERON:0001434!6.10e-19!101;UBERON:0002384!1.56e-14!375;UBERON:0002204!3.77e-13!167;UBERON:0000926!3.09e-08!448;UBERON:0004120!3.09e-08!448;UBERON:0006603!3.09e-08!448
|ontology_enrichment_uberon=UBERON:0002193!6.10e-30!112;UBERON:0002390!2.35e-29!102;UBERON:0003061!2.35e-29!102;UBERON:0003081!3.68e-25!216;UBERON:0002371!2.92e-24!80;UBERON:0002405!1.44e-23!115;UBERON:0001474!1.07e-22!86;UBERON:0004765!6.10e-19!101;UBERON:0001434!6.10e-19!101;UBERON:0002384!1.56e-14!375;UBERON:0002204!3.77e-13!167;UBERON:0000926!3.09e-08!448;UBERON:0004120!3.09e-08!448;UBERON:0006603!3.09e-08!448
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190834698301064!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280832956657583!CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306936077166341!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327086485297725!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323849169191671!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464373273956635!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.0038911009258641!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155877568258534!THAP1#55145;2:20.9127630685675:0.00298344741373694:0.0158763000327765!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330813191160643
|tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.000163551,0.208242,0.0665252,0.0844722,0.00129531,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.00762432,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.0600088,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.0425,0.114846,0.0472875,0.0347684,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.0109386,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.0128549,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.0151713,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.014161,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.00647842,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0585224,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.0356268,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.355018,0.782949,0.0821962,0.20128,0.0986134,0.228731,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.178727,0.0724671,0.271958,0.292154,0.405773,0.39729,0.0582602,0.230901,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.000737505,0.528324,0.520763,0.370782,0.101703,0.142924,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.0669244,0.283727,0.314747,0.21363,0.291709,0.120054,0.0563639,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.0694028,0.18237,0.00166394,0.0020109,0.0512465,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.258117,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.0138549,0.0158541,0.0583074,0.412837,0.671377,0.546839,0.551561,0.120021,0.218623,0.312808,0.032738,0.0451077,0.0747529,0.229003,0.000764752,0.589326,0.154921,0.294698,0.34331,0.477304,0.289204,0.327108,0.0295492,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,2.77948e-05,0.421464,0.141711,0.420626,0.516462,0.000203002,0.00836919,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.0144637,0.155572,0.522888,0.284629,0.0379506,0.359455,0.226257,0.0965765,0.41707,0.363685,0.464871,0.0538047,0.206222,0.00713629,0.284166,0.437176,0.040018,0.339277,0.0479524,0.281425,0.141758,0.455379,0.168058,0.159617,0.238587,0.0799758,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.257493,0.347298,0.539392,0.34988,0.136757,0.0958562,0.0847452,0.262389,0.316179,0.0697683,0.0556835,0.0198561,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.0216577,0.11631,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0842821,0.0179103,0.303939,0.0434097,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.0135136,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.0190418,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.00395801,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.0235128,0.153187,0.0797897,0.0974211,0.160149,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}}
}}

Revision as of 13:25, 5 September 2012


Full id: C4473_Neutrophils_CD14_Eosinophils_lymphangiectasia_Dendritic_myeloma_Burkitt



Phase1 CAGE Peaks

Hg19::chr5:142782862..142782881,-p11@NR3C1
Hg19::chr6:90062427..90062459,-p1@UBE2J1
Hg19::chr6:90062488..90062504,-p3@UBE2J1


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:0004883glucocorticoid receptor activity0.0057694572000471



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
leukocyte5.61e-36140
myeloid leukocyte3.13e-3176
nongranular leukocyte2.05e-30119
hematopoietic lineage restricted progenitor cell4.03e-28124
granulocyte monocyte progenitor cell1.84e-2771
hematopoietic stem cell2.61e-27172
angioblastic mesenchymal cell2.61e-27172
macrophage dendritic cell progenitor1.69e-2665
hematopoietic cell6.54e-26182
CD14-positive, CD16-negative classical monocyte1.47e-2542
monopoietic cell1.48e-2563
monocyte1.48e-2563
monoblast1.48e-2563
promonocyte1.48e-2563
hematopoietic oligopotent progenitor cell4.68e-24165
hematopoietic multipotent progenitor cell4.68e-24165
myeloid lineage restricted progenitor cell1.42e-2370
classical monocyte3.50e-2145
myeloid cell4.53e-18112
common myeloid progenitor4.53e-18112
mesenchymal cell1.21e-15358
connective tissue cell8.41e-15365
multi fate stem cell1.09e-13430
somatic stem cell6.61e-12436
lymphocyte of B lineage6.89e-1224
pro-B cell6.89e-1224
stem cell4.24e-11444
motile cell1.78e-09390
B cell2.69e-0814
granulocyte8.38e-078
intermediate monocyte9.35e-079
CD14-positive, CD16-positive monocyte9.35e-079
Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.10e-30112
hematopoietic system2.35e-29102
blood island2.35e-29102
lateral plate mesoderm3.68e-25216
bone marrow2.92e-2480
immune system1.44e-23115
bone element1.07e-2286
skeletal element6.10e-19101
skeletal system6.10e-19101
connective tissue1.56e-14375
musculoskeletal system3.77e-13167
mesoderm3.09e-08448
mesoderm-derived structure3.09e-08448
presumptive mesoderm3.09e-08448


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
CCNT2#90536.336201576962630.003930750035764890.0190834698301064
CTCF#1066435.360256373075030.0064925092527670.0280832956657583
CTCFL#140690213.16431623931620.007433367036996010.0306936077166341
E2F1#186934.907389214879320.008460985347239390.0327086485297725
E2F6#187635.017155731697390.00791769806886330.0323849169191671
ELF1#199734.258097958807540.01295179875054610.0464373273956635
GATA1#2623313.56030814380040.0004009615963782630.0038911009258641
GTF2B#2959221.29588662288280.002878180589911410.0155877568258534
THAP1#55145220.91276306856750.002983447413736940.0158763000327765
YY1#752834.911170749853860.008441455341808260.0330813191160643



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.