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Coexpression cluster:C3807: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!4.38e-18!143;DOID:305!2.19e-14!106;DOID:14566!2.60e-13!239;DOID:162!4.09e-13!235;DOID:0050615!6.21e-08!16;DOID:1324!3.08e-07!15
|ontology_enrichment_disease=DOID:0050687!4.38e-18!143;DOID:305!2.19e-14!106;DOID:14566!2.60e-13!239;DOID:162!4.09e-13!235;DOID:0050615!6.21e-08!16;DOID:1324!3.08e-07!15
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129638475185414!BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.001392057564326!BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000284515858675232!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190022034338664!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115217726665147!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279409582103895!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171689888437273!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325364280231354!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00437168818581036!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322196169341131!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320598805326801!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462262630615912!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255684442144367!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167448057491198!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00762226464776635!FOS#2353;3:8.9979553088944:0.00137249927241713:0.008974046923682!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.0024303768741804!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154091204039263!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387920594387674!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436891332964656!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108701185395301!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000756608117441773!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444191191004531!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000680400193900994!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156778963428997!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186495686291251!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294477871889858!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269604586261517!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172900000842565!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664028815964907!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767469896389939!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484465282148962!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309025066597679!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246488387388792!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109083670094517!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00375091109236292!STAT2#6773;3:65.2637711864407:3.59360517547754e-06:0.000118320470025756!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000720004352453319!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613688877843927!YY1#7528;3:4.91117074985386:0.00844145534180826:0.03293794942999!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140179893205323!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388994579694225!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109403952802011
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97897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.000389382,0.000112257,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.00896808,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.0144628,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,4.27652e-05,0.00502301,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.0271723,0.291114,0.0355833,0.125606,0.175094,0.696435,0.0225581,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.00921075,0.0450031,0.0539144,0.114242,0.0929549,0.000980951,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.286863,0.152372,0.194941,0.0257725,0.101607,0.327067,0.172982,0.0661495,0.151597,0.0626744,0.191335,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.00238639,0.251466,0.0461822,0.11903,0.0838874,0.00806892,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.0339656,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.000874248,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0020598,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.0115948,0.449036,0.407369,0.231447,0.00131394,0.43956,0.37006,0.42622,0.448797,0.197484,0.0919774,0.36145,0.00202987,0.381071,0.580441,0.643768,0.432035,0.722159,0.390366,0.48809,0.000757632,0.0217093,0.522904,0.875915,0.336835,0.227104,0.00667974,0.617852,0.0867545,0.284625,0.504757,0.04783,0.729153,0.28907,0.164197,0.128922,0.287881,0.574635,6.0419e-05,0.336276,0.132529,0.258219,0.446557,0.243383,0.0186777,0.390974,0.382874,0.319063,0.161598,0.405056,0.644754,0.496032,0.0795555,0.37357,0.00500957,0.477353,0.452741,0.746954,0.185744,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.0131573,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,8.29376e-06,0.120226,0.28424,0.20075,0.314429,0.181415,0.282286,0.78,0.616388,0.408413,0.516511,0.322213,0.28903,0.33942,0.0700181,0.387276,0.0391112,0.0816402,0.180745,0.222037,0.416621,0.416292,0.128937,0.0115406,0.579431,0.204817,0.122646,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.00457272,0.175199,0.332919,0.373557,0.523625,0.0980968,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.119167,0.351067,0.275347,0.000640194,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.00161207,0.508064,0.250964,0.383276,0.457886,0.00582796,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.00367772,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.000131919,0.299887,0.0193657,0.00170684,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.0192444,0.258854,0.188263,0.00265057,0.264884,0.0139948,0.19104,0.0140817,0.219428,0.208013,0.00418416,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.0269454,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.00899848,0.20837,0.247588,0.222339,0.0673329,0.0234202,0.0391817,0.113092,0.145701,0.229428,0.0139199,0.0284767,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.00753169,0.0986735,0.108462,0.0595618,0.0251995,0.158479,0.00213411,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.00351525,0.150733,5.97373e-06,0.123917,0.0181384,0.0183464,0.0723291,0.258496,0.0377094,0.203781,0.0246892,0.0232077,0.141867,7.4303e-05,0.0339803,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.0129343,0.13108,0.256963,0.0269005,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.00161996,0.106739,0.0536053,0.0537737,0.0120432,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.0457063,0.347036,0.141729,0.263159,0.00345643,0.200105,0.227491,0.29837,0.253509,0.177664,0.00482769,0.00384051,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.0268373,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 11:33, 5 September 2012


Full id: C3807_breast_cervical_cord_Fibroblast_maxillary_giant_embryonic



Phase1 CAGE Peaks

Hg19::chr19:47747474..47747505,-p@chr19:47747474..47747505
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Hg19::chr19:47747509..47747525,-p@chr19:47747509..47747525
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Hg19::chr19:47747535..47747555,-p@chr19:47747535..47747555
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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><br><br>disease_data<br>

Disease
Ontology termp-valuen
cell type cancer4.38e-18143
carcinoma2.19e-14106
disease of cellular proliferation2.60e-13239
cancer4.09e-13235
respiratory system cancer6.21e-0816
lung cancer3.08e-0715


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
ATF3#467322.46317452600878.81932387510763e-050.00129638475185414
BCLAF1#9774321.65264761012189.8473954032885e-050.001392057564326
BHLHE40#8553344.87181354697741.10603738662898e-050.000284515858675232
CCNT2#90536.336201576962630.003930750035764890.0190022034338664
CEBPB#105137.971147625824820.001974187055288560.0115217726665147
CTCF#1066435.360256373075030.0064925092527670.0279409582103895
CTCFL#140690319.74647435897440.0001298372005551160.00171689888437273
E2F1#186934.907389214879320.008460985347239390.0325364280231354
E2F4#1874312.66806031528440.0004917987006298980.00437168818581036
E2F6#187635.017155731697390.00791769806886330.0322196169341131
EGR1#195834.988179094810140.008056488137383440.0320598805326801
ELF1#199734.258097958807540.01295179875054610.0462262630615912
ELK4#2005316.2356816584680.0002336043955745990.00255684442144367
EP300#203336.77394172622320.003216880500103790.0167448057491198
ETS1#211339.728760922202340.001085840092584840.00762226464776635
FOS#235338.99795530889440.001372499272417130.008974046923682
FOSL2#2355316.93020060456170.0002060162053171620.0024303768741804
GABPB1#255337.067683836182170.002832212825417420.0154091204039263
GATA1#2623313.56030814380040.0004009615963782630.00387920594387674
GATA2#2624312.7449317335540.0004829527704283790.00436891332964656
HMGN3#932438.178547723350590.001827766942164210.0108701185395301
HNF4G#3174328.75342252644684.20470658818262e-050.000756608117441773
JUN#3725312.51282919233630.0005103313992726250.00444191191004531
JUNB#3726330.61063265982113.4847716247536e-050.000680400193900994
JUND#372736.994663941871030.002921845042734990.0156778963428997
MAX#414936.452555509007120.003721913834265510.0186495686291251
MYC#460935.22228187160940.007020843755740150.0294477871889858
NFKB1#479035.488063424193840.006049381815655430.0269604586261517
PAX5#507936.669565531177830.003370290999677260.0172900000842565
RAD21#5885310.35503389545630.0009004912073565420.00664028815964907
REST#597839.650028716128020.001112636247114590.00767469896389939
RFX5#5993312.04791082719510.0005717246050312580.00484465282148962
SMC3#9126315.04493284493280.0002935825420371870.00309025066597679
SP1#666735.69838137814090.005403962701712170.0246488387388792
SPI1#668838.204323508522730.001810593189410520.0109083670094517
SRF#6722313.79717826216780.0003806615025800190.00375091109236292
STAT2#6773365.26377118644073.59360517547754e-060.000118320470025756
TAL1#6886329.86861667744023.75103522793067e-050.000720004352453319
TCF7L2#6934310.77017656313730.0008003181298398380.00613688877843927
YY1#752834.911170749853860.008441455341808260.03293794942999
ZBTB7A#5134137.35190930787590.002516255860282270.0140179893205323
ZNF143#7702313.50087655222790.0004062804962997170.00388994579694225
ZNF263#1012738.221841637010680.001799043925565870.0109403952802011



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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