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Coexpression cluster:C3872: Difference between revisions

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|ontology_enrichment_disease=DOID:1749!2.55e-11!14;DOID:305!6.36e-07!106
|ontology_enrichment_disease=DOID:1749!2.55e-11!14;DOID:305!6.36e-07!106
|ontology_enrichment_uberon=UBERON:0004119!1.40e-20!169;UBERON:0000925!1.40e-20!169;UBERON:0006595!1.40e-20!169;UBERON:0001007!1.26e-13!155;UBERON:0001555!1.26e-13!155;UBERON:0007026!1.26e-13!155;UBERON:0001004!8.21e-13!72;UBERON:0000065!4.43e-10!53;UBERON:0000161!4.91e-10!35;UBERON:0004921!1.27e-09!129;UBERON:0004185!1.27e-09!129;UBERON:0000166!5.55e-09!21;UBERON:0005911!6.58e-09!82;UBERON:0000077!4.00e-08!130;UBERON:0000974!4.88e-08!10;UBERON:0007196!7.57e-08!14;UBERON:0001558!7.57e-08!14;UBERON:0005153!8.01e-08!37;UBERON:0001911!8.50e-08!4;UBERON:0005333!8.50e-08!4;UBERON:0008425!8.50e-08!4;UBERON:0005311!8.50e-08!4;UBERON:0004815!2.04e-07!3;UBERON:0002031!2.04e-07!3;UBERON:0000165!2.10e-07!28;UBERON:0000930!2.10e-07!28;UBERON:0006562!3.81e-07!11;UBERON:0001723!5.00e-07!3;UBERON:0001033!5.00e-07!3;UBERON:0010056!5.00e-07!3;UBERON:0000344!7.92e-07!12;UBERON:0001949!8.61e-07!3
|ontology_enrichment_uberon=UBERON:0004119!1.40e-20!169;UBERON:0000925!1.40e-20!169;UBERON:0006595!1.40e-20!169;UBERON:0001007!1.26e-13!155;UBERON:0001555!1.26e-13!155;UBERON:0007026!1.26e-13!155;UBERON:0001004!8.21e-13!72;UBERON:0000065!4.43e-10!53;UBERON:0000161!4.91e-10!35;UBERON:0004921!1.27e-09!129;UBERON:0004185!1.27e-09!129;UBERON:0000166!5.55e-09!21;UBERON:0005911!6.58e-09!82;UBERON:0000077!4.00e-08!130;UBERON:0000974!4.88e-08!10;UBERON:0007196!7.57e-08!14;UBERON:0001558!7.57e-08!14;UBERON:0005153!8.01e-08!37;UBERON:0001911!8.50e-08!4;UBERON:0005333!8.50e-08!4;UBERON:0008425!8.50e-08!4;UBERON:0005311!8.50e-08!4;UBERON:0004815!2.04e-07!3;UBERON:0002031!2.04e-07!3;UBERON:0000165!2.10e-07!28;UBERON:0000930!2.10e-07!28;UBERON:0006562!3.81e-07!11;UBERON:0001723!5.00e-07!3;UBERON:0001033!5.00e-07!3;UBERON:0010056!5.00e-07!3;UBERON:0000344!7.92e-07!12;UBERON:0001949!8.61e-07!3
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279513242033774
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3526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.00140535,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.655293,0.21727,0.289306,0.119215,0.192475,0.0168693,0.547859,0.057571,0.047591,0.0143259,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.936279,0.206454,0.0257531,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.00171529,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.000795326,0.113145,0.00659775,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.00233292,0.0115948,0.120614,0.00206189,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.0919774,0.36145,0.0966095,0.381071,0.580441,0.276075,0.11074,0.722159,0.390366,0.145312,0.153829,0.0217093,0.522904,0.616975,0.871256,0.227104,0.518585,0.617852,0.38649,0.284625,0.504757,0.55194,0.729153,0.28907,0.164197,0.462688,0.287881,0.21103,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.777351,0.390974,0.73485,0.683217,0.161598,0.751174,0.644754,0.00534461,0.799185,0.0013757,0.78509,0.000560517,0.78384,0.746954,0.185744,0.0222555,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.383291,0.156104,0.000526011,0.411941,0.0961477,0.314438,0.0720718,0.000835245,0.230581,0.120226,0.28424,0.20075,0.0556238,0.181415,0.282286,0.194707,0.0727621,0.408413,0.0374737,0.322213,0.00480191,0.33942,0.61031,0.387276,0.522605,0.802166,0.537348,0.222037,0.0175112,0.10205,0.0252635,0.734551,0.579431,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.0425451,0.39088,0.0109626,0.236011,0.203486,0.273398,0.375787,0.0223007,0.351067,0.275347,0.269604,0.305885,0.241132,0.0795725,0.30666,0.303709,0.495883,0.386538,0.035296,0.250964,0.383276,0.0243456,0.504711,0.220231,0.159791,0.00149391,0.191517,0.129584,0.235208,0.0529819,0.459728,0.283463,0.563586,0.135386,1.58356e-05,0.273281,0.368095,0.275089,0.384593,0.00444763,0.0740334,0.339729,0.197805,0.0153645,0.0870376,0.0627969,0.173874,0.299887,0.634365,0.205413,0.17639,0.0779009,0.0424553,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.0139948,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.0232009,0.0224033,0.0171537,0.193601,0.220904,0.222977,0.0664606,0.310674,0.0257082,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.00899848,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.0398662,0.00160819,0.00972162,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.00213411,0.195218,0.124213,0.259632,0.30793,0.0173907,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.0183464,0.0723291,0.0367308,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.0331281,0.0159159,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.036274,0.222798,0.172134,0.176789,0.0969345,0.0219648,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.0105548,0.263159,0.255956,0.200105,0.00236454,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.0597546,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.0607319,0.0276507,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.00417402,0.071111,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}}
}}

Revision as of 11:53, 5 September 2012


Full id: C3872_tongue_Prostate_Bronchial_Sebocyte_Keratinocyte_Corneal_Urothelial



Phase1 CAGE Peaks

Hg19::chr1:153587142..153587155,-p@chr1:153587142..153587155
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Hg19::chr1:153587170..153587185,-p@chr1:153587170..153587185
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Hg19::chr1:153587360..153587377,-p@chr1:153587360..153587377
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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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.40e-20169
endoderm1.40e-20169
presumptive endoderm1.40e-20169
digestive system1.26e-13155
digestive tract1.26e-13155
primitive gut1.26e-13155
respiratory system8.21e-1372
respiratory tract4.43e-1053
orifice4.91e-1035
subdivision of digestive tract1.27e-09129
endodermal part of digestive tract1.27e-09129
oral opening5.55e-0921
endo-epithelium6.58e-0982
mixed endoderm/mesoderm-derived structure4.00e-08130
neck4.88e-0810
tracheobronchial tree7.57e-0814
lower respiratory tract7.57e-0814
epithelial bud8.01e-0837
mammary gland8.50e-084
mammary bud8.50e-084
mammary ridge8.50e-084
mammary placode8.50e-084
lower respiratory tract epithelium2.04e-073
epithelium of bronchus2.04e-073
mouth2.10e-0728
stomodeum2.10e-0728
pharynx3.81e-0711
tongue5.00e-073
gustatory system5.00e-073
future tongue5.00e-073
mucosa7.92e-0712
gingival epithelium8.61e-073
Disease
Ontology termp-valuen
squamous cell carcinoma2.55e-1114
carcinoma6.36e-07106


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
CTCF#1066435.360256373075030.0064925092527670.0279513242033774



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.