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Coexpression cluster:C3760: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.53e-22!106;DOID:0050687!3.07e-15!143;DOID:299!4.89e-12!25;DOID:1749!8.76e-10!14;DOID:7!3.01e-07!39;DOID:162!9.16e-07!235
|ontology_enrichment_disease=DOID:305!3.53e-22!106;DOID:0050687!3.07e-15!143;DOID:299!4.89e-12!25;DOID:1749!8.76e-10!14;DOID:7!3.01e-07!39;DOID:162!9.16e-07!235
|ontology_enrichment_uberon=UBERON:0007023!5.19e-31!115;UBERON:0000062!4.26e-19!511;UBERON:0001049!1.68e-16!57;UBERON:0005068!1.68e-16!57;UBERON:0006241!1.68e-16!57;UBERON:0007135!1.68e-16!57;UBERON:0004119!3.32e-14!169;UBERON:0000925!3.32e-14!169;UBERON:0006595!3.32e-14!169;UBERON:0000955!4.72e-13!69;UBERON:0006238!4.72e-13!69;UBERON:0001017!5.35e-13!82;UBERON:0003080!6.02e-13!42;UBERON:0001007!9.39e-13!155;UBERON:0001555!9.39e-13!155;UBERON:0007026!9.39e-13!155;UBERON:0002780!1.15e-12!41;UBERON:0001890!1.15e-12!41;UBERON:0006240!1.15e-12!41;UBERON:0002616!2.07e-12!59;UBERON:0000033!2.22e-12!123;UBERON:0005743!2.83e-12!86;UBERON:0005177!7.57e-12!107;UBERON:0003075!7.88e-12!86;UBERON:0007284!7.88e-12!86;UBERON:0000475!9.74e-12!365;UBERON:0004921!1.10e-11!129;UBERON:0004185!1.10e-11!129;UBERON:0005911!1.24e-11!82;UBERON:0000153!1.92e-11!129;UBERON:0007811!1.92e-11!129;UBERON:0002020!3.24e-11!34;UBERON:0003528!3.24e-11!34;UBERON:0001893!3.40e-11!34;UBERON:0004111!3.63e-11!241;UBERON:0002050!5.25e-11!605;UBERON:0005423!5.25e-11!605;UBERON:0002791!8.40e-11!33;UBERON:0000923!9.15e-11!604;UBERON:0005291!9.15e-11!604;UBERON:0006598!9.15e-11!604;UBERON:0002532!9.15e-11!604;UBERON:0001041!9.40e-11!98;UBERON:0000467!1.43e-10!625;UBERON:0002346!1.60e-10!90;UBERON:0004121!1.63e-10!169;UBERON:0000480!1.92e-10!626;UBERON:0001869!3.20e-10!32;UBERON:0000077!4.10e-10!130;UBERON:0000922!4.16e-10!612;UBERON:0000073!5.51e-10!94;UBERON:0001016!5.51e-10!94;UBERON:0000924!1.05e-09!173;UBERON:0006601!1.05e-09!173;UBERON:0000481!1.46e-09!347;UBERON:0001004!1.60e-09!72;UBERON:0000468!2.63e-09!659;UBERON:0000466!2.92e-09!126;UBERON:0009569!9.56e-09!113;UBERON:0003056!2.21e-08!61;UBERON:0002619!2.91e-08!22;UBERON:0000025!3.90e-08!194;UBERON:0000477!4.28e-08!286;UBERON:0000064!1.08e-07!219;UBERON:0002365!1.23e-07!31;UBERON:0002330!1.23e-07!31;UBERON:0000483!1.40e-07!309;UBERON:0005157!1.44e-07!51;UBERON:0005153!1.56e-07!37;UBERON:0002530!2.45e-07!59;UBERON:0000065!3.05e-07!53;UBERON:0000119!3.29e-07!312;UBERON:0001950!3.62e-07!20;UBERON:0000956!3.76e-07!25;UBERON:0000203!3.76e-07!25;UBERON:0005178!5.12e-07!34;UBERON:0002224!5.12e-07!34;UBERON:0002048!8.74e-07!22;UBERON:0000117!8.74e-07!22;UBERON:0000171!8.74e-07!22;UBERON:0000170!8.74e-07!22;UBERON:0005597!8.74e-07!22;UBERON:0000118!8.74e-07!22;UBERON:0009497!8.75e-07!25;UBERON:0000015!8.75e-07!25;UBERON:0002423!8.75e-07!25;UBERON:0006235!8.75e-07!25;UBERON:0004161!8.75e-07!25
|ontology_enrichment_uberon=UBERON:0007023!5.19e-31!115;UBERON:0000062!4.26e-19!511;UBERON:0001049!1.68e-16!57;UBERON:0005068!1.68e-16!57;UBERON:0006241!1.68e-16!57;UBERON:0007135!1.68e-16!57;UBERON:0004119!3.32e-14!169;UBERON:0000925!3.32e-14!169;UBERON:0006595!3.32e-14!169;UBERON:0000955!4.72e-13!69;UBERON:0006238!4.72e-13!69;UBERON:0001017!5.35e-13!82;UBERON:0003080!6.02e-13!42;UBERON:0001007!9.39e-13!155;UBERON:0001555!9.39e-13!155;UBERON:0007026!9.39e-13!155;UBERON:0002780!1.15e-12!41;UBERON:0001890!1.15e-12!41;UBERON:0006240!1.15e-12!41;UBERON:0002616!2.07e-12!59;UBERON:0000033!2.22e-12!123;UBERON:0005743!2.83e-12!86;UBERON:0005177!7.57e-12!107;UBERON:0003075!7.88e-12!86;UBERON:0007284!7.88e-12!86;UBERON:0000475!9.74e-12!365;UBERON:0004921!1.10e-11!129;UBERON:0004185!1.10e-11!129;UBERON:0005911!1.24e-11!82;UBERON:0000153!1.92e-11!129;UBERON:0007811!1.92e-11!129;UBERON:0002020!3.24e-11!34;UBERON:0003528!3.24e-11!34;UBERON:0001893!3.40e-11!34;UBERON:0004111!3.63e-11!241;UBERON:0002050!5.25e-11!605;UBERON:0005423!5.25e-11!605;UBERON:0002791!8.40e-11!33;UBERON:0000923!9.15e-11!604;UBERON:0005291!9.15e-11!604;UBERON:0006598!9.15e-11!604;UBERON:0002532!9.15e-11!604;UBERON:0001041!9.40e-11!98;UBERON:0000467!1.43e-10!625;UBERON:0002346!1.60e-10!90;UBERON:0004121!1.63e-10!169;UBERON:0000480!1.92e-10!626;UBERON:0001869!3.20e-10!32;UBERON:0000077!4.10e-10!130;UBERON:0000922!4.16e-10!612;UBERON:0000073!5.51e-10!94;UBERON:0001016!5.51e-10!94;UBERON:0000924!1.05e-09!173;UBERON:0006601!1.05e-09!173;UBERON:0000481!1.46e-09!347;UBERON:0001004!1.60e-09!72;UBERON:0000468!2.63e-09!659;UBERON:0000466!2.92e-09!126;UBERON:0009569!9.56e-09!113;UBERON:0003056!2.21e-08!61;UBERON:0002619!2.91e-08!22;UBERON:0000025!3.90e-08!194;UBERON:0000477!4.28e-08!286;UBERON:0000064!1.08e-07!219;UBERON:0002365!1.23e-07!31;UBERON:0002330!1.23e-07!31;UBERON:0000483!1.40e-07!309;UBERON:0005157!1.44e-07!51;UBERON:0005153!1.56e-07!37;UBERON:0002530!2.45e-07!59;UBERON:0000065!3.05e-07!53;UBERON:0000119!3.29e-07!312;UBERON:0001950!3.62e-07!20;UBERON:0000956!3.76e-07!25;UBERON:0000203!3.76e-07!25;UBERON:0005178!5.12e-07!34;UBERON:0002224!5.12e-07!34;UBERON:0002048!8.74e-07!22;UBERON:0000117!8.74e-07!22;UBERON:0000171!8.74e-07!22;UBERON:0000170!8.74e-07!22;UBERON:0005597!8.74e-07!22;UBERON:0000118!8.74e-07!22;UBERON:0009497!8.75e-07!25;UBERON:0000015!8.75e-07!25;UBERON:0002423!8.75e-07!25;UBERON:0006235!8.75e-07!25;UBERON:0004161!8.75e-07!25
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145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.0694567,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.0926491,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.0050797,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.0119618,0.643768,0.432035,0.722159,0.390366,0.0305485,0.0334527,0.443185,0.522904,0.3468,0.871256,0.227104,0.00667974,0.617852,0.38649,0.284625,0.00583062,0.55194,0.729153,0.0465139,0.164197,0.00379441,0.0461094,0.574635,0.478174,0.336276,0.132529,0.258219,0.446557,0.243383,0.777351,0.390974,0.73485,0.683217,0.161598,0.405056,0.277094,0.496032,0.476802,0.0805771,0.78509,0.477353,0.452741,0.746954,0.771991,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,8.53554e-05,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.0720718,0.163828,0.230581,0.120226,0.28424,0.0101317,0.314429,0.181415,0.282286,0.194707,0.24884,0.408413,0.516511,0.322213,0.656109,0.33942,0.0700181,0.387276,0.522605,0.802166,0.537348,0.222037,0.416621,0.416292,0.462712,0.734551,0.057399,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.0393909,0.408861,0.365487,0.178743,0.39088,0.363192,0.236011,0.0222706,0.273398,0.375787,0.119167,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.24107,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.0828367,0.0358457,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.0219648,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.0203812,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 12:09, 5 September 2012


Full id: C3760_lung_bile_large_papillotubular_keratoacanthoma_oral_endometrial



Phase1 CAGE Peaks

Hg19::chr19:16045510..16045553,-p8@CYP4F11
Hg19::chr19:16045619..16045649,-p2@CYP4F11
Hg19::chr19:16045665..16045708,-p1@CYP4F11


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>

Cell Type
Ontology termp-valuen
epithelial cell3.74e-18254
endodermal cell1.84e-1559
endo-epithelial cell3.70e-1343
Uber Anatomy
Ontology termp-valuen
adult organism5.19e-31115
organ4.26e-19511
neural tube1.68e-1657
neural rod1.68e-1657
future spinal cord1.68e-1657
neural keel1.68e-1657
endoderm-derived structure3.32e-14169
endoderm3.32e-14169
presumptive endoderm3.32e-14169
brain4.72e-1369
future brain4.72e-1369
central nervous system5.35e-1382
anterior neural tube6.02e-1342
digestive system9.39e-13155
digestive tract9.39e-13155
primitive gut9.39e-13155
regional part of forebrain1.15e-1241
forebrain1.15e-1241
future forebrain1.15e-1241
regional part of brain2.07e-1259
head2.22e-12123
trunk region element7.57e-12107
neural plate7.88e-1286
presumptive neural plate7.88e-1286
organism subdivision9.74e-12365
subdivision of digestive tract1.10e-11129
endodermal part of digestive tract1.10e-11129
endo-epithelium1.24e-1182
anterior region of body1.92e-11129
craniocervical region1.92e-11129
gray matter3.24e-1134
brain grey matter3.24e-1134
telencephalon3.40e-1134
anatomical conduit3.63e-11241
embryonic structure5.25e-11605
developing anatomical structure5.25e-11605
regional part of telencephalon8.40e-1133
germ layer9.15e-11604
embryonic tissue9.15e-11604
presumptive structure9.15e-11604
epiblast (generic)9.15e-11604
foregut9.40e-1198
anatomical system1.43e-10625
neurectoderm1.60e-1090
ectoderm-derived structure1.63e-10169
anatomical group1.92e-10626
cerebral hemisphere3.20e-1032
mixed endoderm/mesoderm-derived structure4.10e-10130
embryo4.16e-10612
regional part of nervous system5.51e-1094
nervous system5.51e-1094
ectoderm1.05e-09173
presumptive ectoderm1.05e-09173
multi-tissue structure1.46e-09347
respiratory system1.60e-0972
multi-cellular organism2.63e-09659
immaterial anatomical entity2.92e-09126
subdivision of trunk9.56e-09113
pre-chordal neural plate2.21e-0861
regional part of cerebral cortex2.91e-0822
tube3.90e-08194
anatomical cluster4.28e-08286
organ part1.08e-07219
exocrine gland1.23e-0731
exocrine system1.23e-0731
epithelium1.40e-07309
epithelial fold1.44e-0751
epithelial bud1.56e-0737
gland2.45e-0759
respiratory tract3.05e-0753
cell layer3.29e-07312
neocortex3.62e-0720
cerebral cortex3.76e-0725
pallium3.76e-0725
thoracic cavity element5.12e-0734
thoracic cavity5.12e-0734
lung8.74e-0722
respiratory tube8.74e-0722
respiration organ8.74e-0722
pair of lungs8.74e-0722
lung primordium8.74e-0722
lung bud8.74e-0722
epithelium of foregut-midgut junction8.75e-0725
anatomical boundary8.75e-0725
hepatobiliary system8.75e-0725
foregut-midgut junction8.75e-0725
septum transversum8.75e-0725
Disease
Ontology termp-valuen
carcinoma3.53e-22106
cell type cancer3.07e-15143
adenocarcinoma4.89e-1225
squamous cell carcinoma8.76e-1014
disease of anatomical entity3.01e-0739
cancer9.16e-07235


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
ELF1#199734.258097958807540.01295179875054610.0462136286200302



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.

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