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Coexpression cluster:C4626: Difference between revisions

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|ontology_enrichment_disease=DOID:305!6.76e-22!106;DOID:0050687!3.13e-14!143;DOID:299!3.43e-07!25
|ontology_enrichment_disease=DOID:305!6.76e-22!106;DOID:0050687!3.13e-14!143;DOID:299!3.43e-07!25
|ontology_enrichment_uberon=UBERON:0004119!1.07e-21!169;UBERON:0000925!1.07e-21!169;UBERON:0006595!1.07e-21!169;UBERON:0001007!4.01e-17!155;UBERON:0001555!4.01e-17!155;UBERON:0007026!4.01e-17!155;UBERON:0004921!9.13e-16!129;UBERON:0004185!9.13e-16!129;UBERON:0000062!1.55e-15!511;UBERON:0000077!3.76e-15!130;UBERON:0000468!1.57e-14!659;UBERON:0000466!9.00e-14!126;UBERON:0000064!8.97e-13!219;UBERON:0001041!1.05e-12!98;UBERON:0000475!3.43e-12!365;UBERON:0000481!5.15e-12!347;UBERON:0001004!6.18e-12!72;UBERON:0000464!9.04e-12!104;UBERON:0000467!6.00e-11!625;UBERON:0009569!9.79e-11!113;UBERON:0000480!1.02e-10!626;UBERON:0001048!1.40e-10!168;UBERON:0003104!5.35e-10!238;UBERON:0009142!5.35e-10!238;UBERON:0005911!1.50e-09!82;UBERON:0000065!6.73e-09!53;UBERON:0005177!2.38e-08!107;UBERON:0002553!6.27e-08!70;UBERON:0000922!1.52e-07!612;UBERON:0004923!2.70e-07!57;UBERON:0005631!4.89e-07!14;UBERON:0000158!4.89e-07!14;UBERON:0008947!6.63e-07!38;UBERON:0003258!6.63e-07!38
|ontology_enrichment_uberon=UBERON:0004119!1.07e-21!169;UBERON:0000925!1.07e-21!169;UBERON:0006595!1.07e-21!169;UBERON:0001007!4.01e-17!155;UBERON:0001555!4.01e-17!155;UBERON:0007026!4.01e-17!155;UBERON:0004921!9.13e-16!129;UBERON:0004185!9.13e-16!129;UBERON:0000062!1.55e-15!511;UBERON:0000077!3.76e-15!130;UBERON:0000468!1.57e-14!659;UBERON:0000466!9.00e-14!126;UBERON:0000064!8.97e-13!219;UBERON:0001041!1.05e-12!98;UBERON:0000475!3.43e-12!365;UBERON:0000481!5.15e-12!347;UBERON:0001004!6.18e-12!72;UBERON:0000464!9.04e-12!104;UBERON:0000467!6.00e-11!625;UBERON:0009569!9.79e-11!113;UBERON:0000480!1.02e-10!626;UBERON:0001048!1.40e-10!168;UBERON:0003104!5.35e-10!238;UBERON:0009142!5.35e-10!238;UBERON:0005911!1.50e-09!82;UBERON:0000065!6.73e-09!53;UBERON:0005177!2.38e-08!107;UBERON:0002553!6.27e-08!70;UBERON:0000922!1.52e-07!612;UBERON:0004923!2.70e-07!57;UBERON:0005631!4.89e-07!14;UBERON:0000158!4.89e-07!14;UBERON:0008947!6.63e-07!38;UBERON:0003258!6.63e-07!38
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285712190507406!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662596186157583!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327522923899309!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464756196429577!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168354270670645!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.0024403001550549!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583996242303602!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.0010768804714855!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393357267454691!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123363075420166!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000760144281397273!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295927799259725!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165948877279045!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278176559610292!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247808764260864!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617178063666417!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249407020320151!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618736133821059!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.011008340083324
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5237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.000389382,1.15329e-05,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.0178982,0.122476,0.108872,0.11002,0.26144,0.0286025,1.99608e-06,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.0353101,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,6.72149e-05,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.000356768,1.59254e-06,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.0088427,0.057571,0.047591,1.40366e-05,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.000444106,0.0355833,0.125606,0.175094,4.67397e-05,3.95406e-08,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.00217546,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.0126914,0.000943322,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.249049,0.0103728,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0001026,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,8.08672e-06,0.0360851,0.412187,0.000416337,0.0434602,0.133616,0.103051,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.0789454,0.42622,0.448797,0.197484,0.396996,0.0107863,0.406019,0.381071,0.216033,0.276075,0.11074,0.0411943,0.390366,0.48809,0.50058,0.443185,0.522904,8.73306e-10,0.0572701,0.227104,0.000951286,0.00310917,0.00161115,0.284625,0.504757,0.192225,0.0437169,0.28907,0.164197,0.462688,2.83608e-05,0.21103,0.000566617,0.0642229,0.468444,0.00355636,0.446557,0.243383,0.0659137,0.0889613,0.382874,0.109758,0.161598,0.000101989,0.277094,0.00534461,7.35021e-06,0.0805771,0.0704414,0.0282154,1.07991e-09,0.0132585,0.00415823,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.0101316,0.163828,0.230581,0.120226,0.0448825,0.00162521,0.314429,0.181415,0.282286,0.000976922,0.0727621,0.01635,0.000926901,0.0073454,0.656109,0.33942,0.61031,0.387276,0.522605,0.000283063,0.0433137,0.222037,0.0175112,0.416292,0.462712,0.382478,0.579431,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.00818864,0.0120568,0.523625,0.408861,0.365487,1.5656e-05,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.00388821,0.00618487,0.241132,0.0795725,0.30666,0.303709,0.495883,0.0135408,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.159791,0.196976,0.191517,0.000467747,0.235208,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.0283414,0.359231,0.339729,0.197805,0.00278185,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.00321654,0.179412,0.193601,0.220904,0.222977,0.0664606,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.00803363,0.179889,0.226869,0.0430576,0.000111542,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.0398662,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.00632223,0.00113527,0.159884,0.257294,0.0119784,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.187731,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.286691,0.0687209,0.141729,0.0381402,0.255956,0.200105,0.227491,0.0497481,0.253509,0.0168099,0.28365,0.00384051,0.131761,0.160658,0.206239,0.19924,2.78165e-05,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.0203812,0.190993,0.281727,0.2832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}}
}}

Revision as of 14:15, 5 September 2012


Full id: C4626_salivary_amniotic_choriocarcinoma_Keratinocyte_maxillary_cervical_esophagus



Phase1 CAGE Peaks

Hg19::chr6:7541814..7541825,+p7@DSP
Hg19::chr6:7541832..7541844,+p3@DSP
Hg19::chr6:7541845..7541878,+p2@DSP


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 cell2.60e-35254
endodermal cell2.40e-1859
endo-epithelial cell3.60e-1643
epithelial cell of alimentary canal5.88e-0921
respiratory epithelial cell8.51e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.07e-21169
endoderm1.07e-21169
presumptive endoderm1.07e-21169
digestive system4.01e-17155
digestive tract4.01e-17155
primitive gut4.01e-17155
subdivision of digestive tract9.13e-16129
endodermal part of digestive tract9.13e-16129
organ1.55e-15511
mixed endoderm/mesoderm-derived structure3.76e-15130
multi-cellular organism1.57e-14659
immaterial anatomical entity9.00e-14126
organ part8.97e-13219
foregut1.05e-1298
organism subdivision3.43e-12365
multi-tissue structure5.15e-12347
respiratory system6.18e-1272
anatomical space9.04e-12104
anatomical system6.00e-11625
subdivision of trunk9.79e-11113
anatomical group1.02e-10626
primordium1.40e-10168
mesenchyme5.35e-10238
entire embryonic mesenchyme5.35e-10238
endo-epithelium1.50e-0982
respiratory tract6.73e-0953
trunk region element2.38e-08107
anatomical cavity6.27e-0870
embryo1.52e-07612
organ component layer2.70e-0757
extraembryonic membrane4.89e-0714
membranous layer4.89e-0714
respiratory primordium6.63e-0738
endoderm of foregut6.63e-0738
Disease
Ontology termp-valuen
carcinoma6.76e-22106
cell type cancer3.13e-14143
adenocarcinoma3.43e-0725


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285712190507406
CHD2#1106310.34402283411690.0009033701102746880.00662596186157583
E2F1#186934.907389214879320.008460985347239390.0327522923899309
ELF1#199734.258097958807540.01295179875054610.0464756196429577
EP300#203336.77394172622320.003216880500103790.0168354270670645
FOSL2#2355316.93020060456170.0002060162053171620.0024403001550549
FOXA1#3169311.08141974938550.000734755275698670.00583996242303602
FOXA2#3170324.63046375266526.68983856509345e-050.0010768804714855
HDAC2#3066313.41562023662630.0004140761399857210.00393357267454691
HNF4A#3172323.13229036295378.07584663437677e-050.00123363075420166
HNF4G#3174328.75342252644684.20470658818262e-050.000760144281397273
MYC#460935.22228187160940.007020843755740150.0295927799259725
RXRA#6256320.07461713913330.0001235730348432220.00165948877279045
SIN3A#2594235.408884726815140.006318961977991520.0278176559610292
SP1#666735.69838137814090.005403962701712170.0247808764260864
TCF7L2#6934310.77017656313730.0008003181298398380.00617178063666417
TFAP2A#7020316.5186343730450.0002218033880766340.00249407020320151
TFAP2C#7022310.80922860986020.0007916746575753130.00618736133821059
ZNF263#1012738.221841637010680.001799043925565870.011008340083324



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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