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Coexpression cluster:C4371: Difference between revisions

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|full_id=C4371_Fibroblast_gastric_normal_Mesenchymal_Nucleus_Preadipocyte_mesenchymal
|full_id=C4371_Fibroblast_gastric_normal_Mesenchymal_Nucleus_Preadipocyte_mesenchymal
|id=C4371
|id=C4371
|ontology_enrichment_celltype=CL:0000055!4.86e-33!180;CL:0000057!6.65e-23!75;CL:0002620!2.15e-12!23;CL:0000680!2.35e-08!57;CL:0000056!2.35e-08!57;CL:0000355!2.35e-08!57;CL:0000393!4.51e-08!60;CL:0000211!4.51e-08!60;CL:0000187!8.64e-08!54;CL:0000136!8.99e-08!15;CL:0000183!1.16e-07!59
|ontology_enrichment_celltype=CL:0000057!7.58e-22!76;CL:0002620!1.05e-12!23;CL:0000136!3.45e-08!15;CL:0000680!6.79e-08!58;CL:0000056!6.79e-08!58;CL:0000355!6.79e-08!58;CL:0000187!3.85e-07!55;CL:0000183!5.63e-07!59;CL:0000055!6.05e-07!106
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!7.81e-17!365;UBERON:0003102!7.60e-14!95;UBERON:0000914!1.29e-13!83;UBERON:0002329!1.29e-13!83;UBERON:0003077!1.29e-13!83;UBERON:0003059!1.29e-13!83;UBERON:0007282!1.29e-13!83;UBERON:0009618!1.29e-13!83;UBERON:0007285!1.29e-13!83;UBERON:0004290!3.31e-11!70;UBERON:0000468!6.19e-11!659;UBERON:0000481!2.18e-10!347;UBERON:0002199!3.26e-10!45;UBERON:0002416!3.26e-10!45;UBERON:0002385!2.34e-09!63;UBERON:0001015!2.34e-09!63;UBERON:0000383!2.34e-09!63;UBERON:0000486!5.52e-09!82;UBERON:0002097!8.96e-09!40;UBERON:0001134!9.97e-09!61;UBERON:0002036!9.97e-09!61;UBERON:0003082!9.97e-09!61;UBERON:0000033!7.20e-08!123;UBERON:0004121!7.71e-08!169;UBERON:0000924!1.00e-07!173;UBERON:0006601!1.00e-07!173;UBERON:0000153!1.11e-07!129;UBERON:0007811!1.11e-07!129;UBERON:0005256!7.66e-07!143
|ontology_enrichment_uberon=UBERON:0003102!8.31e-12!99;UBERON:0007524!3.83e-09!73;UBERON:0002199!4.11e-09!46;UBERON:0002416!4.11e-09!46;UBERON:0003077!1.06e-08!72;UBERON:0007285!1.06e-08!72;UBERON:0002329!1.36e-08!71;UBERON:0003059!1.36e-08!71;UBERON:0007282!1.36e-08!71;UBERON:0004290!1.36e-08!71;UBERON:0009618!1.36e-08!71;UBERON:0000468!2.64e-08!656;UBERON:0002097!3.27e-08!41;UBERON:0002385!6.81e-08!64;UBERON:0001015!6.81e-08!64;UBERON:0000383!6.81e-08!64;UBERON:0001134!4.42e-07!62;UBERON:0002036!4.42e-07!62;UBERON:0003082!4.42e-07!62;UBERON:0000486!4.65e-07!83;UBERON:0000481!5.08e-07!342;UBERON:0000479!9.04e-07!773
|tf_chipseq_enrich=TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329344497318621
|tf_chipseq_enrich=TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329344497318621
|tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.0214323,0.0050633,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.000616359,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.0250931,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.0233668,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.0102981,0.184019,0.120917,0.0362416,0.0380166,0.0175714,0.0064353,0.121201,0.154071,0.0541794,0.0701653,0.00446469,0.198787,0.0384161,0.107455,0.212709,0.00315066,0.105572,0.0294301,0.149417,1.52083e-07,0.0759481,0.054569,0.0504887,0.0709764,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.000126043,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.000276216,0.291327,0.251834,0.064341,0.00180443,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.0259741,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.005305,0.0337525,0.0203386,0.00163609,0.139021,0.00361707,0.16671,0.214708,1.91863e-05,0.0857827,0.102368,0.0166632,0.00424238,0.0147934,0.00366285,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.0223702,0.155998,0.596561,0.0693171,0.00505227,0.0842275,0.0389418,1.03405e-05,8.76789e-05,0.0108547,0.0174119,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.00136001,0.0337251,0.000151223,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.000380678,0.0403542,0.0547453,0.179689,0.00995227,0.0255071,0.0541353,0.0799324,0.00418474,0.140334,0.0176328,0.00109304,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.00735999,0.183031,0.0401756,0.0828697,0.0160177,0.107145,0.0187509,0.122935,0.000154392,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.000471598,0.259411,0.27358,0.15185,0.0229156,0.178359,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.0151713,0.164202,0.000185442,0.062995,0.10299,0.0105855,0.0800546,0.15606,0.00079124,0.0738599,0.126611,0.138852,0.085973,3.85687e-05,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.0381183,0.163502,0.214803,0.182472,0.0695582,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.0183114,0.01843,0.0980288,0.0980899,0.000770586,0.107242,0.201859,0.0695832,0.00206011,0.0619218,0.0163125,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.0223286,0.0865903,0.0380459,0.00886625,0.059488,0.355018,0.000191546,0.000626254,0.00163772,0.00879988,0.228731,0.00083951,0.00355277,0.261553,0.00318602,0.0806291,0.053682,0.147559,0.330703,0.0914012,0.061507,0.53472,0.000471837,0.271958,0.00531795,0.000206884,0.0148713,0.0582602,0.000362379,0.187251,0.0109219,0.0176124,0.10624,0.109988,0.0620388,0.218329,0.427027,0.376924,0.025356,0.280025,0.528324,0.03861,0.0792797,0.101703,0.484505,0.253571,0.000355279,0.301787,0.481778,0.0565541,0.00223433,0.00574256,5.12277e-05,0.0447111,0.314747,0.0116619,0.00529148,0.0225637,0.0115542,0.0175396,0.0478086,0.137839,0.0210941,0.0807167,3.33907e-07,0.241757,0.00117064,0.346458,0.513427,0.00296206,0.275351,0.236471,0.185661,8.13568e-05,0.535598,0.270984,0.0179843,8.95275e-05,0.0367769,0.000993751,0.0338468,0.0439966,0.00419907,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.0582356,0.217247,0.0021959,0.305671,0.188159,0.551561,0.0225539,0.0258593,0.312808,0.117923,0.0451077,0.0747529,0.229003,0.650179,0.223844,0.50215,0.0054714,0.34331,0.138202,0.289204,0.327108,0.109738,0.0428373,5.66339e-05,0.428671,0.0282539,0.000849693,0.19763,3.03667e-05,0.20495,0.104858,0.0293525,0.420626,0.165111,0.311758,0.335105,0.144809,0.145539,0.385517,0.0818086,0.447325,0.0247309,0.252232,0.152681,0.0465712,0.000478592,0.00360191,0.00952201,0.00502762,0.0460163,0.000461929,0.284593,0.00911104,0.00622965,0.0524121,0.2348,0.155572,0.00696513,0.284629,0.0379506,0.359455,0.226257,0.0965765,0.102469,0.0760312,4.87051e-05,0.166672,0.0228979,0.525396,0.284166,0.113671,0.040018,0.339277,0.0479524,0.0439467,0.141758,0.124432,0.168058,0.0134764,0.238587,0.372281,0.232251,0.0192138,0.0891382,0.0595618,0.171389,0.257493,0.00943126,0.0439245,8.63298e-05,0.136757,0.0158269,0.00403911,0.262389,0.316179,0.00249247,0.0556835,0.0198561,0.0779981,0.00168976,0.144322,0.223391,0.0223093,0.116981,0.441735,0.191777,0.111931,0.0051519,0.0435386,0.00601662,0.00835866,0.134852,0.10689,0.0413156,0.0627924,0.0129363,0.0179103,0.303939,0.0434097,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.0059529,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.00141596,0.00934729,0.0499762,0.0828956,0.0666953,0.0177068,0.111277,0.026047,0.332809,0.0205132,0.132201,0.188694,0.0481795,0.199971,0.0966069,1.30417e-05,0.175785,0.18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}}
}}

Revision as of 15:54, 19 October 2012


Full id: C4371_Fibroblast_gastric_normal_Mesenchymal_Nucleus_Preadipocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr4:138450850..138450867,-p@chr4:138450850..138450867
-
Hg19::chr4:138453559..138453572,-p2@PCDH18
Hg19::chr4:138453606..138453673,-p1@PCDH18


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
fibroblast7.58e-2276
skin fibroblast1.05e-1223
fat cell3.45e-0815
muscle precursor cell6.79e-0858
myoblast6.79e-0858
multi-potent skeletal muscle stem cell6.79e-0858
muscle cell3.85e-0755
contractile cell5.63e-0759
non-terminally differentiated cell6.05e-07106
Uber Anatomy
Ontology termp-valuen
surface structure8.31e-1299
dense mesenchyme tissue3.83e-0973
integument4.11e-0946
integumental system4.11e-0946
paraxial mesoderm1.06e-0872
presumptive paraxial mesoderm1.06e-0872
somite1.36e-0871
presomitic mesoderm1.36e-0871
presumptive segmental plate1.36e-0871
dermomyotome1.36e-0871
trunk paraxial mesoderm1.36e-0871
multi-cellular organism2.64e-08656
skin of body3.27e-0841
muscle tissue6.81e-0864
musculature6.81e-0864
musculature of body6.81e-0864
skeletal muscle tissue4.42e-0762
striated muscle tissue4.42e-0762
myotome4.42e-0762
multilaminar epithelium4.65e-0783
multi-tissue structure5.08e-07342
tissue9.04e-07773


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
TRIM28#10155212.39368336350830.008368344129438470.0329344497318621



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.