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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0.242610589789054,0.496780210613549,0.182546835497931,0.440805226204927,0.199883803944283,0,0,0,0.00119681973657774,0,0,0.0477476630834935,0,0.0506760246065907,0,0.223320720221072,0.343485215114616,0.238123940398271,0.405542090685568,0,0,0,0.385817102887059,0.474783455904965,0.440530790736559,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0502991463552631,0.186670330086339,0.152608620485698,0.198488304874285,0,0,0.181616767436814,0.275752932992257,0.24205504664276,0.0534545700183436,0,0,0,0,0,0,0,0,0,0,0,0,0,0.190397841472823,0.0824244927467616,0,0,0.08106578238155,0,0,0.0948420448069823,0,0,0.0713662365134967,0.087969206950705,0.0882151269915992,0,0,0.135578961919851,0,0,0,0.175213663176675,0.260548024905462,0.289024004143484,0.196914560204395,0.232827633528851,0.116080565920249,0,0.120818431757809,0,0.10360579629716,0.122845985799448,0,0,0,0.0799298460338426,0,0.182196659508327,0.091620887334261,0.0651586387455666,0.0570765567424092,0.0273432540435293,0.17357587122559,0.0427037663627782,0,0.356390593312032,0,0,0.1360670709359,0.165580161042293,0,0.158054039799331,0.226378124863029,0.128035554111004,0.0962157777662699,0.350871951395953,0.154458903240703,0.15829986032434,0.204169432998994,0.11699192718931,0.180493200633673,0.164246578501346,0.291106098816871,0.172365003954154,0.354525021943001,0.0890103343787787,0.102624439496886,0.233000982852579,0.11469646534793,0.213836757070759,0,0,0,0.0499826791869596,0.0540496261796572,0.0860269859063006,0.181359100908638,0.0977156115525172,0.13512544777972,0,0.20459956312869,0,0.165650208579294,0.186418478780918,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.128119866952565,0,0,0,0,0,0,0.343308609582855,0.165458487625984,0.0482120461578062,0.0585651160278124,0.165240025483351,0.219885287597619,0,0,0,0,0,0,0.0736108385273246,0.0147783357041213,0.0372505621677013,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0594409392973691,0.0172117523345547,0,0.219430880434753,0.050087155848042,0,0,0,0,0.107573223228122,0.033221095912122,0,0,0.0674967599784259,0,0.174773300386913,0,0.290763855624295,0,0,0,0.242315926110442,0.267591342710514,0,0.222382892024854,0.20855662473171,0.0715362608323278,0,0,0,0,0.246075866847322,0.325591254117777,0.521120611938458,0.365221866270533,0.652958241502116,0,0,0,0.0256728428633096,0,0.0907193436021567,0.324319419287666,0.434373218281285,0.252491876641462,0.215699486225762,0,0,0,0.221212197891035,0.0982634576619174,0.156675748297206,0,0,0,0,0,0,0,0.0718400352871927,0.1749941830566,0.365686486934294,0.326876421299287,0.179711634111168,0.179467695646126,0.327558653292253,0,0.248230446868769,0.0709836812024541,0.148542981396699,0.181630511148827,0.140549822362013,0,0.0793645050922885,0.0767600769151731,0.0897740605496476,0.189286314149658,0.144067467090408,0,0.112649387005267,0,0,0.119471955332098,0,0.0211494138237492,0.317975544424619,0,0,0,0,0,0.0381527044137606,0,0,0.099145253918139,0,0,0,0,0,0,0,0,0.110593802369687,0.0663237790710398,0.128877225231348,0.0560798888033103,0.288557537691078,0.236810113610532,0.199920462594552,0.132300728608495,0,0,0,0.0800184682686384,0.165791835868262,0.212087596895138,0,0.0410533852141233,0,0,0.0738371582016079,0.00172995875103598,0,0,0.129173874305484,0,0.318834865254947,0,0,0.0718350632709503,0.105352457754613,0.091886618011139,0,0,0,0,0.125370020962594,0,0.03302520229664,0.194686839862908,0,0,0.121131878925007,0.029754832101131,0,0,0.00574771177646025,0.11721277736131,0.107784894264258,0.157131307928642,0.0918790352528284,0.089157897260001,0,0.213072052700123,0.167413666000157,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.122532772993059,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0664648991865313,0,0,0.147266263057341,0,0,0.0291184785323036,0.696931914130656,0.561571962403592,0,0,0,0.510548002448886,0,0,0.179363157398504,0,0.457312177667757,0,0.172711625852638,0,0.222886870436488,0,0,0.294319102417383,0.574433761210532,0.476561809887893,0,0,0,0,0,0,0.361000824172266,0.0935499597594456,0.460924642071274,0.275482132507796,0.429485832199853,0.366001365528124,0.593335708088471,0.486973302682347,0.546693642831245,0,0,0.0621683679383978,0.0468626006398675,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0831434490344895,0,0,0,0,0,0,0,0.00305227085273996,0.00675529078143561,0.205910519014322,0,0.458504226770148,0,0,0,0.0659606055603839,0,0.833490232932968,0.119233744361939,0,0,0,0,0,0,0,0.104404778877955,0,0,0,0.17121583204563,0.0245978506987986,0,0,0,0.110915157511936,0,0.286238922103287,0.0849975826884634,0.078715799182705,0.427737423403669,0,0.0334876163089719,0.0407118925007903,0.203964919649634,0,0.00451588186005951,0.447225262270001,0,0.0508638757203747,0,0.168526753451332,0.151802208584906,0.135839332955708,0.110236269607548,0.331486901773341,0.373848528348823,0,0.110594224770766,0,0.264309401882715,0.331589670039496,0,0,0,0.0400413846955684,0.0547535628453514,0.216654170591784,0,0,0,0,0.0767324847848016,0,0.773064759532031,0.551164907732114,0.0647398703344467,0.105537049972849,0.147223260029563,0,0,0.369248041846374,0,0,0,0.000207530855688414,0.0661775500679038,0.123586669401688,0.234186964128339,0.11042019958172,0,0.188365813972295,0.270497510320477,0.17016354871382,0,0,0.0683298683982573,0.046616925903038,0,0,0.805541091283198,0.689282175287128,0.0983073219796616,0,0,0,0,0,0,0,0,0,0,0,0,0,0.734827094095294,0.982391454701085,0.761720075967582,0.517675704141427,0.507406355636883,0.313961293154471,0.0795885447315708,0.0943092468000965,0,0,0.101577454368654,0.141526227140634,0.110536533650711,0.113445166687003,0.166556393082458,0.180574486347811,0.162834543034241,0.123659379089237,0,0.163662235871164,0.119587535934552,0.117561082617775,0.171862516091862,0.169642199129735,0.161309027678618,0.117445612912116,0.262311622187397,0.254674973982594,0.182341901105911,0.0607951148206197,0.330903729395183,0.148254195206626,0.0725618668317725,0.138267461602633,0.13057957785286,0.317202040184978,0.255285902718873,0.307536067226092,0.265192765499538,0,0.167909928645134,0.0843766322300271,0.113522313399568,0.225339726908717,0.0904423417827262,0.347072977964867,0.186749169737715,0.16903989043601,0.0861048924880567,0.184710572801466,0.141709355787741,0.224214349798037,0.149563140589838,0.128861217532784,0.0153559535005846,0.635080283775389,0,0,0,0.517627198438788,0.27654204250204,0.0050998347804051,0,0,0,0,0.139697176867509,0,0,0.214703965888745,0.220512297725122,0.0634331720967665,0.281673635973099,0,0,0,0,0.20602424662604,0.0636048451378017,0,0.231814006190654,0.115428755346868,0.327107204075249,0.666894682962691,0.596863148182169,0.651499702204598,0.919405271944104,0.210162025788965,0.795701871654021,0.385193981212532,0,0,0,0,0.246194219601905,0,0,0.031493427513643,0.147184609291298,0,0,0.152768865150507,0,0.418306546581682,0.690673585056427,0.818261764693817,0.452731904542776,0.993137903723866,0,0.516369810879999,0.067634117395718,0,0.541386467982503,0.525561252659395,0.0538106037540985,0.0890788809625826,0,0,0,0.646019547388952,0.31225446797703,0.0485170957947049,0.0275678337088124,0.118586233508558,0.493706318277504,0,0.281751001695877,0,0.169601464072093,0.0843723556258797,0.26388840311137,0.00485702030137637,0,0.10208351176708,0,0,0,0,0.0537261859220301,0.0988652163614907,0.153323010348428,0,0.0358192171234274,0.096440547233681,0,0,0,0,0.000420622854112769,0,0.0847238323803794,0.111136349399877,0,0.0468619933380315,0.0464741249455258,0.190248357112215,0.114586195761373,0,0.0858467613960337,0.167411066169369,0.394368951680851,0.167716906896504,0.785391246817935,0.445627302118986,0.405975931859538,0.267086169465202,0,0,0,0,0,0,0,0,0.398641293102342,0.0696269099253994,0.254889762925146,0.903821961030411,0.12901067229319,0.325512595891034,0,0.189150011450774,0.157720048453017,0.165944337293556,0.0518077165209662,0.0806184284061465,0.185948442440047,0.109746296935809,0,0.0670015771248572,0.103106967823645,0.58883244086171,0.383125036123224,0,0.092743246865863,0,0,0.125935033097091,0,0.00344520641702123,0,0,0,0,0.124719478691449,0,0.118809236324772,0,0,0,0,0.108430025043595,0,0.0685403199460521,0
|full_id=C284_parietal_occipital_medial_temporal_olfactory_locus_hippocampus
|full_id=C284_parietal_occipital_medial_temporal_olfactory_locus_hippocampus
|id=C284
|id=C284

Revision as of 15:38, 12 September 2012


Full id: C284_parietal_occipital_medial_temporal_olfactory_locus_hippocampus



Phase1 CAGE Peaks

Hg19::chr5:71411518..71411547,+p@chr5:71411518..71411547
+
Hg19::chr5:71479565..71479587,+p@chr5:71479565..71479587
+
Hg19::chr5:71482436..71482488,+p@chr5:71482436..71482488
+
Hg19::chr5:71489985..71489998,+p@chr5:71489985..71489998
+
Hg19::chr5:71490424..71490435,+p@chr5:71490424..71490435
+
Hg19::chr5:71490449..71490460,+p@chr5:71490449..71490460
+
Hg19::chr5:71490491..71490500,+p@chr5:71490491..71490500
+
Hg19::chr5:71490523..71490532,+p@chr5:71490523..71490532
+
Hg19::chr5:71490598..71490608,+p@chr5:71490598..71490608
+
Hg19::chr5:71490621..71490632,+p@chr5:71490621..71490632
+
Hg19::chr5:71490679..71490694,+p@chr5:71490679..71490694
+
Hg19::chr5:71490722..71490725,+p@chr5:71490722..71490725
+
Hg19::chr5:71490729..71490756,+p@chr5:71490729..71490756
+
Hg19::chr5:71490789..71490815,+p9@MAP1B
Hg19::chr5:71490821..71490833,+p19@MAP1B
Hg19::chr5:71490856..71490870,+p15@MAP1B
Hg19::chr5:71490880..71490891,+p23@MAP1B
Hg19::chr5:71490899..71490911,+p17@MAP1B
Hg19::chr5:71490923..71490924,+p56@MAP1B
Hg19::chr5:71490983..71491006,+p10@MAP1B
Hg19::chr5:71491080..71491109,+p14@MAP1B
Hg19::chr5:71491131..71491143,+p18@MAP1B
Hg19::chr5:71491157..71491183,+p6@MAP1B
Hg19::chr5:71491656..71491681,+p34@MAP1B
Hg19::chr5:71491821..71491840,+p@chr5:71491821..71491840
+
Hg19::chr5:71491859..71491877,+p@chr5:71491859..71491877
+
Hg19::chr5:71491884..71491904,+p@chr5:71491884..71491904
+
Hg19::chr5:71492510..71492528,+p@chr5:71492510..71492528
+
Hg19::chr5:71493786..71493803,+p36@MAP1B
Hg19::chr5:71493818..71493848,+p24@MAP1B
Hg19::chr5:71494196..71494211,+p33@MAP1B
Hg19::chr5:71494295..71494313,+p25@MAP1B
Hg19::chr5:71494567..71494578,+p@chr5:71494567..71494578
+
Hg19::chr5:71494879..71494901,+p@chr5:71494879..71494901
+
Hg19::chr5:71495032..71495074,+p@chr5:71495032..71495074
+
Hg19::chr5:71495080..71495197,+p@chr5:71495080..71495197
+
Hg19::chr5:71495203..71495271,+p@chr5:71495203..71495271
+
Hg19::chr5:71495849..71495883,+p@chr5:71495849..71495883
+
Hg19::chr5:71499530..71499550,+p@chr5:71499530..71499550
+
Hg19::chr5:71500942..71500967,+p@chr5:71500942..71500967
+
Hg19::chr5:71501161..71501215,+p@chr5:71501161..71501215
+
Hg19::chr5:71501221..71501269,+p@chr5:71501221..71501269
+
Hg19::chr5:71501410..71501437,+p@chr5:71501410..71501437
+
Hg19::chr5:71502973..71503023,+p29@MAP1B
Hg19::chr5:71503222..71503286,+p22@MAP1B
Hg19::chr5:71503803..71503818,+p4@MAP1B


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
non-terminally differentiated cell1.18e-18180
fibroblast6.45e-1175
neurectodermal cell2.33e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.90e-3494
nervous system1.90e-3494
central nervous system3.18e-3482
neural tube1.90e-2957
neural rod1.90e-2957
future spinal cord1.90e-2957
neural keel1.90e-2957
brain7.03e-2969
future brain7.03e-2969
neural plate3.87e-2786
presumptive neural plate3.87e-2786
organism subdivision3.48e-26365
regional part of brain7.81e-2659
neurectoderm1.79e-2590
ectoderm-derived structure9.80e-25169
regional part of forebrain5.05e-2441
forebrain5.05e-2441
future forebrain5.05e-2441
ectoderm7.60e-24173
presumptive ectoderm7.60e-24173
anterior neural tube7.75e-2442
epithelium9.07e-22309
gray matter1.52e-2134
brain grey matter1.52e-2134
tube1.65e-21194
head1.68e-21123
cell layer1.79e-21312
telencephalon4.08e-2134
regional part of telencephalon1.61e-2033
pre-chordal neural plate2.36e-2061
cerebral hemisphere3.29e-2032
anatomical conduit5.31e-20241
anterior region of body2.54e-19129
craniocervical region2.54e-19129
anatomical cluster7.13e-19286
cerebral cortex2.46e-1625
pallium2.46e-1625
multi-cellular organism6.54e-16659
regional part of cerebral cortex1.24e-1422
multi-tissue structure1.70e-14347
adult organism1.17e-13115
neocortex2.51e-1320
anatomical system2.22e-12625
anatomical group4.29e-12626
embryo2.37e-10612
embryonic structure2.21e-09605
developing anatomical structure2.21e-09605
organ part3.06e-09219
germ layer3.18e-09604
embryonic tissue3.18e-09604
presumptive structure3.18e-09604
epiblast (generic)3.18e-09604
posterior neural tube6.77e-0715
chordal neural plate6.77e-0715
somite8.45e-0783
paraxial mesoderm8.45e-0783
presomitic mesoderm8.45e-0783
presumptive segmental plate8.45e-0783
trunk paraxial mesoderm8.45e-0783
presumptive paraxial mesoderm8.45e-0783


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
BATF#10538136.883726593477112.6472925649547e-081.82495437750035e-06
BCL11A#53335138.01745470319334.37388609720519e-093.55213289351487e-07
BCLAF1#9774136.119226498512691.04077750403072e-076.08951046181871e-06
EBF1#1879152.904282667359469.4924302550943e-050.00137424441836955
EP300#2033152.208894041159740.001838804530295620.0108824676341329
ETS1#2113132.749432434535440.0005486577962926620.00473642516010988
IRF4#3662136.193231846253789.05832488493346e-085.34789368376238e-06
MEF2A#4205135.297000039682015.41291926535482e-072.50918719553658e-05
NFKB1#4790151.789585899193640.01371857254973410.0483108203298271
POU2F2#5452142.771429061052070.0002883198911356910.003063882896858
SPI1#6688142.4969680243330.000836818081469730.00631340342488023
SRF#6722133.899202552351771.57387285244086e-050.000368303174627091
TCF12#6938112.543024215740230.003013407161694680.01600311352386
ZBTB33#100091510.32545381412436.165442395064e-127.92020465311302e-10



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

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