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Coexpression cluster:C3298: Difference between revisions

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|full_id=C3298_CD4_CD14_cord_chronic_adult_mycosis_acute
|full_id=C3298_CD4_CD14_cord_chronic_adult_mycosis_acute
|id=C3298
|id=C3298
|ontology_enrichment_celltype=CL:0000791!1.65e-07!18;CL:0000789!1.65e-07!18;CL:0002420!1.65e-07!18;CL:0002419!1.65e-07!18;CL:0000790!1.65e-07!18
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.18e-21!115;UBERON:0001049!3.74e-11!57;UBERON:0005068!3.74e-11!57;UBERON:0006241!3.74e-11!57;UBERON:0007135!3.74e-11!57;UBERON:0003075!2.30e-10!86;UBERON:0007284!2.30e-10!86;UBERON:0002616!2.16e-09!59;UBERON:0002346!4.47e-09!90;UBERON:0005743!5.16e-08!86;UBERON:0000178!6.85e-08!15;UBERON:0000179!6.85e-08!15;UBERON:0000463!6.85e-08!15;UBERON:0001017!1.03e-07!82;UBERON:0000073!1.16e-07!94;UBERON:0001016!1.16e-07!94;UBERON:0003080!4.95e-07!42;UBERON:0002020!7.28e-07!34;UBERON:0003528!7.28e-07!34;UBERON:0001869!8.74e-07!32
|ontology_enrichment_uberon=UBERON:0007023!2.63e-21!114;UBERON:0000073!1.74e-10!53;UBERON:0002616!1.74e-10!53;UBERON:0001049!3.13e-10!56;UBERON:0005068!3.13e-10!56;UBERON:0006241!3.13e-10!56;UBERON:0007135!3.13e-10!56;UBERON:0003075!4.41e-09!82;UBERON:0007284!4.41e-09!82;UBERON:0002346!3.84e-08!86;UBERON:0003528!4.34e-08!34;UBERON:0002020!4.34e-08!34;UBERON:0000178!4.95e-08!15;UBERON:0000179!4.95e-08!15;UBERON:0000463!4.95e-08!15;UBERON:0001869!9.46e-08!32;UBERON:0001016!1.53e-07!89;UBERON:0002780!3.44e-07!41;UBERON:0001890!3.44e-07!41;UBERON:0003080!3.44e-07!41;UBERON:0006240!3.44e-07!41;UBERON:0001017!3.92e-07!81;UBERON:0000955!5.03e-07!68;UBERON:0006238!5.03e-07!68;UBERON:0001893!5.64e-07!34;UBERON:0002791!6.83e-07!32
|tf_chipseq_enrich=STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154550564529469
|tf_chipseq_enrich=STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154550564529469
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.0172144,0.03272,0.0257057,0.139423,0.000144577,0.188771,0.125978,0.148679,0.00195662,0.140982,0.0982016,0.0528514,0.00606063,0.0190294,0.00920475,0.081977,0.0948982,0.0415721,0.0250931,0.0236364,0.00424558,0.143747,0.0933697,0.204953,0.00676561,0.0180314,0.00178278,0.00226357,0.0844722,0.0308399,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.0102981,0.184019,0.00762432,0.0362416,0.0380166,0.00115331,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.0212153,0.0384161,0.00599201,0.0244227,0.00315066,0.105572,0.0294301,0.149417,0.00612307,0.0759481,0.054569,0.0504887,0.00104991,0.0600088,0.0860723,0.167053,1.07995e-05,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.00686288,0.291327,0.0347684,0.064341,0.0235519,0.0154619,0.00201111,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.00212123,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.0259741,0.0409286,0.0669887,0.338096,0.144217,0.269326,2.34829e-06,0.0339971,0.000627743,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.000512275,0.0857827,0.00542817,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0028727,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.00156008,0.0330399,0.00395526,0.022776,0.127606,4.25353e-06,0.155998,4.57719e-05,0.0693171,0.00505227,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,1.12411e-06,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,1.78489e-05,0.0255071,0.0014925,0.00328329,0.090079,0.0103428,0.181817,0.0169639,0.0356339,0.158844,0.00782633,0.0274061,0.00695194,0.0737247,0.118847,5.92269e-05,0.0401756,0.0828697,0.173562,0.00595679,0.187297,0.122935,0.228812,0.000260351,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.037005,0.0413967,0.15185,0.206299,0.0010913,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.000841257,0.100942,0.062995,0.10299,0.0105855,0.37245,0.15606,0.0137227,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0108418,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.000830039,0.0249262,0.182472,6.0212e-06,0.00500828,0.0830921,0.116283,0.00982118,0.0815104,0.111647,9.61262e-06,0.117027,0.0133783,0.0183114,0.185743,0.0980288,0.0980899,0.000770586,0.107242,4.02609e-06,0.0695832,0.00206011,0.0619218,0.1751,0.0141386,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.0429376,0.063292,0.0356268,3.60802e-05,0.0865903,0.0380459,0.130174,0.0124596,0.00909613,0.000191546,0.0821962,2.57506e-05,8.37562e-05,0.00156905,6.76379e-05,1.06235e-06,0.261553,0.0222487,0.0120704,0.000581634,0.0313047,0.330703,0.0146881,6.11235e-05,1.24683e-07,0.000471837,0.271958,0.00045121,0.00202409,0.0921263,0.217139,0.0643874,0.187251,0.0109219,0.181715,0.000269589,0.109988,0.00802393,0.218329,0.427027,0.0821552,4.73835e-05,0.00436109,0.0407001,0.000117606,0.370782,0.101703,0.00475652,0.00335333,0.00445889,0.00591608,0.00462582,0.316882,0.223503,0.00574256,0.603208,0.283727,0.00679651,0.000273712,1.74119e-06,0.448095,0.00192508,2.15615e-05,0.00535876,0.000556036,0.00296083,0.0807167,0.57762,5.64141e-05,0.18237,4.27123e-05,7.87727e-05,0.00296206,0.275351,0.236471,0.185661,0.00934251,0.535598,0.270984,0.0179843,8.95275e-05,9.59087e-07,0.00691094,0.248634,0.0439966,0.000524881,0.163244,0.0670502,0.0730934,0.184794,0.0138549,0.00365572,3.1752e-08,0.0002295,0.000159654,0.000174153,0.191921,0.00324632,8.89494e-09,0.312808,0.000236487,0.0451077,0.0747529,0.229003,0.0897888,0.061213,5.75666e-08,3.2354e-05,0.00907354,0.00441816,0.289204,0.327108,0.00120886,2.33387e-05,1.35506e-06,0.000288232,0.00238478,0.336314,0.19763,0.000720848,0.000235935,0.000260039,6.03732e-06,0.000256922,1.12737e-05,0.000957476,0.335105,0.0110311,0.145539,0.00159233,0.001421,3.64245e-05,0.127215,0.252232,0.152681,0.0465712,0.137098,0.0369524,0.134788,0.0985856,0.00870714,9.0012e-08,0.0450006,0.000938454,0.306556,0.0524121,4.97127e-05,8.95617e-05,1.2662e-05,0.284629,0.262537,0.000101021,0.0277799,0.016014,0.00230458,0.0760312,0.000474832,0.0538047,0.206222,0.171685,0.000779217,0.00288466,0.269226,2.82679e-11,0.000188895,0.281425,0.141758,0.00351186,6.51266e-09,0.159617,0.238587,0.00135387,0.0293409,0.189515,0.00409641,0.0595618,0.171389,0.000539973,0.347298,0.000155843,0.00966846,0.000543876,8.17922e-08,0.00403911,0.00358327,0.0562865,0.0697683,0.0556835,0.0198561,0.0779981,0.0575676,2.17134e-05,0.223391,0.0223093,0.00307017,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.000143044,0.0179103,5.34095e-09,0.00461664,0.00168854,0.0464827,0.169603,0.00683084,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.0238665,0.193675,0.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}}
}}

Revision as of 14:58, 19 October 2012


Full id: C3298_CD4_CD14_cord_chronic_adult_mycosis_acute



Phase1 CAGE Peaks

Hg19::chr12:56415246..56415286,+p2@IKZF4
Hg19::chr12:56415287..56415300,+p5@IKZF4
Hg19::chr6:37140322..37140335,+p7@PIM1


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism2.63e-21114
regional part of nervous system1.74e-1053
regional part of brain1.74e-1053
neural tube3.13e-1056
neural rod3.13e-1056
future spinal cord3.13e-1056
neural keel3.13e-1056
neural plate4.41e-0982
presumptive neural plate4.41e-0982
neurectoderm3.84e-0886
brain grey matter4.34e-0834
gray matter4.34e-0834
blood4.95e-0815
haemolymphatic fluid4.95e-0815
organism substance4.95e-0815
cerebral hemisphere9.46e-0832
nervous system1.53e-0789
regional part of forebrain3.44e-0741
forebrain3.44e-0741
anterior neural tube3.44e-0741
future forebrain3.44e-0741
central nervous system3.92e-0781
brain5.03e-0768
future brain5.03e-0768
telencephalon5.64e-0734
regional part of telencephalon6.83e-0732


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
STAT1#6772320.70658749719920.0001125992441046670.00154550564529469



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.