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Difference between revisions of "Coexpression cluster:C2180"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0002193!2.61e-39!112;UBERON:0002390!1.96e-38!102;UBERON:0003061!1.96e-38!102;UBERON:0002371!1.46e-28!80;UBERON:0001474!4.03e-26!86;UBERON:0002405!1.28e-25!115;UBERON:0003081!2.70e-19!216;UBERON:0004765!5.12e-19!101;UBERON:0001434!5.12e-19!101;UBERON:0002384!8.23e-17!375;UBERON:0000178!7.33e-08!15;UBERON:0000179!7.33e-08!15;UBERON:0000463!7.33e-08!15;UBERON:0002204!5.88e-07!167
 
|ontology_enrichment_uberon=UBERON:0002193!2.61e-39!112;UBERON:0002390!1.96e-38!102;UBERON:0003061!1.96e-38!102;UBERON:0002371!1.46e-28!80;UBERON:0001474!4.03e-26!86;UBERON:0002405!1.28e-25!115;UBERON:0003081!2.70e-19!216;UBERON:0004765!5.12e-19!101;UBERON:0001434!5.12e-19!101;UBERON:0002384!8.23e-17!375;UBERON:0000178!7.33e-08!15;UBERON:0000179!7.33e-08!15;UBERON:0000463!7.33e-08!15;UBERON:0002204!5.88e-07!167
 +
|tf_chipseq_enrich=BCL3#602;2:17.2735514018692:0.00483449420807607:0.0226721931116864!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172905381680355!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418728780215783!FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234541628589348!GTF2B#2959;2:15.9719149671621:0.00563658572353722:0.0254685202206673!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319935900267714!IRF3#3661;2:23.4909761057448:0.00264110142537554:0.0145920748963019!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0465953243153984!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284811739551732!NFYA#4800;3:13.8191855248729:0.000613241180673451:0.00508424987444269!NFYB#4801;3:12.5698449401523:0.00081145639769735:0.00618415752474559!NR2C2#7182;2:16.3073054526204:0.00541182534464822:0.0245517408961259!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195713331698581!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123818799414392!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794599164419831!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00404892248440468!STAT2#6773;2:32.6318855932203:0.00137958877512552:0.00898216271338034!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321355844552042!TFAP2A#7020;3:12.3889757797837:0.00084694130358843:0.00637963958207516!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482797297416276!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107147832292137
 
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0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.0262915,0.0367692,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.051371,0.0109447,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.626334,0.881117,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.00442486,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.0689994,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.1267,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.322168,0.399934,0.529642,0.818701,0.14198,0.590496,0.603763,0.541914,0.627201,0.526336,0.934991,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.0610883,0.545608,0.310552,0.865054,0.483764,0.829658,0.784052,0.209437,0.843495,0.748403,0.598945,0.630688,0.464001,0.871271,0.579004,0.605327,0.839946,0.860705,0.261575,0.257956,0.264245,0.0831707,0.326516,0.522925,0.436016,0.136753,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.599068,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.357704,0.479581,0.62689,0.884725,0.642173,0.284496,0.512545,0.512178,0.201413,0.829402,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.129731,0.627953,0.503881,0.454761,0.639483,0.483658,0.122467,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.0696091,0.155207,0.0862349,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.136743,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.0870695,0.559969,0.358813,0.303004,0.210703,0.493455,0.346636,0.125876,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.0874139,0.029604,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.081972,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
 
}}
 
}}

Revision as of 03:32, 5 September 2012


Full id: C2180_Eosinophils_CD14_Neutrophils_CD19_Natural_Basophils_CD4



Phase1 CAGE Peaks

  Short description
Hg19::chr12:105501983..105502018,- p@chr12:105501983..105502018
-
Hg19::chr14:24711806..24711861,- p1@TINF2
Hg19::chr15:45003504..45003582,- p1@PATL2
Hg19::chr16:72127670..72127755,+ p2@DHX38


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:0042162telomeric DNA binding0.0150498688801005
GO:0007004telomere maintenance via telomerase0.0150498688801005
GO:0004004ATP-dependent RNA helicase activity0.0150498688801005
GO:0008186RNA-dependent ATPase activity0.0150498688801005
GO:0032200telomere organization and biogenesis0.0150498688801005
GO:0000723telomere maintenance0.0150498688801005
GO:0003724RNA helicase activity0.0150498688801005
GO:0000781chromosome, telomeric region0.0150498688801005
GO:0006278RNA-dependent DNA replication0.0226427060366972
GO:0000375RNA splicing, via transesterification reactions0.0226427060366972
GO:0000398nuclear mRNA splicing, via spliceosome0.0226427060366972
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0226427060366972
GO:0005681spliceosome0.0414611412249278



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
leukocyte4.04e-66140
hematopoietic stem cell1.70e-58172
angioblastic mesenchymal cell1.70e-58172
hematopoietic cell7.56e-56182
hematopoietic lineage restricted progenitor cell5.03e-55124
hematopoietic oligopotent progenitor cell1.93e-54165
hematopoietic multipotent progenitor cell1.93e-54165
nongranular leukocyte2.43e-54119
myeloid leukocyte1.63e-3476
granulocyte monocyte progenitor cell2.15e-3071
myeloid lineage restricted progenitor cell3.29e-2970
myeloid cell7.94e-29112
common myeloid progenitor7.94e-29112
macrophage dendritic cell progenitor2.72e-2865
monopoietic cell1.74e-2763
monocyte1.74e-2763
monoblast1.74e-2763
promonocyte1.74e-2763
classical monocyte4.52e-2645
CD14-positive, CD16-negative classical monocyte5.97e-2642
lymphocyte1.83e-2353
common lymphoid progenitor1.83e-2353
lymphoid lineage restricted progenitor cell4.18e-2352
mesenchymal cell1.83e-20358
connective tissue cell2.68e-18365
motile cell5.95e-15390
multi fate stem cell2.23e-14430
somatic stem cell9.43e-13436
stem cell4.44e-12444
lymphocyte of B lineage2.71e-1124
pro-B cell2.71e-1124
T cell3.10e-1125
pro-T cell3.10e-1125
mature alpha-beta T cell4.93e-1018
alpha-beta T cell4.93e-1018
immature T cell4.93e-1018
mature T cell4.93e-1018
immature alpha-beta T cell4.93e-1018
B cell1.41e-0814
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.61e-39112
hematopoietic system1.96e-38102
blood island1.96e-38102
bone marrow1.46e-2880
bone element4.03e-2686
immune system1.28e-25115
lateral plate mesoderm2.70e-19216
skeletal element5.12e-19101
skeletal system5.12e-19101
connective tissue8.23e-17375
blood7.33e-0815
haemolymphatic fluid7.33e-0815
organism substance7.33e-0815
musculoskeletal system5.88e-07167


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCL3#602217.27355140186920.004834494208076070.0226721931116864
CHD2#110637.758017125587640.003351522464536340.0172905381680355
EP300#203335.08045629466740.01144298405398240.0418728780215783
FOS#235336.74846648167080.005032452776317940.0234541628589348
GTF2B#2959215.97191496716210.005636585723537220.0254685202206673
IRF1#365935.727872815172930.008097114790333330.0319935900267714
IRF3#3661223.49097610574480.002641101425375540.0145920748963019
MAX#414934.839416631755340.01315737137836840.0465953243153984
NANOG#79923214.62238924050630.006698757715363760.0284811739551732
NFYA#4800313.81918552487290.0006132411806734510.00508424987444269
NFYB#4801312.56984494015230.000811456397697350.00618415752474559
NR2C2#7182216.30730545262040.005411825344648220.0245517408961259
REST#597837.237521537096020.004104697304192610.0195713331698581
RFX5#599339.035933120396320.002144561191324070.0123818799414392
SIN3A#2594245.408884726815140.001168172384885160.00794599164419831
STAT1#6772315.52994062289940.000434088655175550.00404892248440468
STAT2#6773232.63188559322030.001379588775125520.00898216271338034
TAF1#687243.343046285745290.008005664898701650.0321355844552042
TFAP2A#7020312.38897577978370.000846941303588430.00637963958207516
USF1#739134.771124457905970.01370465887188020.0482797297416276
USF2#739239.74414803880220.001718341848410070.0107147832292137



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.