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Coexpression cluster:C4222: Difference between revisions

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|full_id=C4222_Fibroblast_Mast_Smooth_mesenchymal_Myoblast_Preadipocyte_basal
|full_id=C4222_Fibroblast_Mast_Smooth_mesenchymal_Myoblast_Preadipocyte_basal
|id=C4222
|id=C4222
|ontology_enrichment_celltype=CL:0000055!2.08e-32!180;CL:0000057!1.60e-19!75;CL:0000680!1.40e-15!57;CL:0000056!1.40e-15!57;CL:0000355!1.40e-15!57;CL:0000187!3.77e-14!54;CL:0000393!1.26e-13!60;CL:0000211!1.26e-13!60;CL:0000192!3.09e-13!42;CL:0000514!3.09e-13!42;CL:0000359!7.65e-13!32;CL:0000183!4.23e-11!59;CL:0002620!2.04e-10!23;CL:0000222!7.42e-10!119;CL:0002321!1.76e-09!248;CL:0000220!4.76e-09!246;CL:0002371!2.03e-08!591;CL:0000144!2.36e-08!625;CL:0000034!4.26e-07!444;CL:0000048!4.60e-07!430;CL:0000548!7.70e-07!679;CL:0000004!7.70e-07!679;CL:0000255!7.70e-07!679;CL:0000723!8.58e-07!436
|ontology_enrichment_celltype=CL:0000057!2.61e-20!76;CL:0000680!6.77e-15!58;CL:0000056!6.77e-15!58;CL:0000355!6.77e-15!58;CL:0000187!1.38e-13!55;CL:0000393!2.58e-13!61;CL:0000211!2.58e-13!61;CL:0000359!8.50e-13!32;CL:0000192!1.45e-12!43;CL:0000514!1.45e-12!43;CL:0000055!1.76e-12!106;CL:0000183!6.15e-11!59;CL:0002620!3.02e-10!23;CL:0002321!3.79e-09!250;CL:0000222!4.99e-09!121;CL:0002371!1.41e-08!588;CL:0000048!1.85e-07!427;CL:0000034!2.31e-07!441;CL:0000723!3.85e-07!433;CL:0000548!5.03e-07!679;CL:0000255!5.03e-07!679
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!1.08e-23!83;UBERON:0002329!1.08e-23!83;UBERON:0003077!1.08e-23!83;UBERON:0003059!1.08e-23!83;UBERON:0007282!1.08e-23!83;UBERON:0009618!1.08e-23!83;UBERON:0007285!1.08e-23!83;UBERON:0004290!1.80e-18!70;UBERON:0000486!9.25e-16!82;UBERON:0001134!1.13e-14!61;UBERON:0002036!1.13e-14!61;UBERON:0003082!1.13e-14!61;UBERON:0002385!1.07e-13!63;UBERON:0001015!1.07e-13!63;UBERON:0000383!1.07e-13!63;UBERON:0000475!1.12e-12!365;UBERON:0002049!2.61e-12!79;UBERON:0007798!2.61e-12!79;UBERON:0001637!3.32e-12!42;UBERON:0003509!3.32e-12!42;UBERON:0004572!3.32e-12!42;UBERON:0003102!7.65e-12!95;UBERON:0004872!2.01e-11!84;UBERON:0005256!2.11e-11!143;UBERON:0004573!4.60e-11!33;UBERON:0004571!4.60e-11!33;UBERON:0002199!4.85e-11!45;UBERON:0002416!4.85e-11!45;UBERON:0001981!1.37e-10!60;UBERON:0007500!1.37e-10!60;UBERON:0004537!1.37e-10!60;UBERON:0006965!1.37e-10!60;UBERON:0000055!1.46e-10!69;UBERON:0000490!9.53e-10!138;UBERON:0002097!1.90e-09!40;UBERON:0004535!2.71e-08!110;UBERON:0002100!3.53e-08!216;UBERON:0001009!4.13e-08!113;UBERON:0000119!2.50e-07!312;UBERON:0000481!3.26e-07!347;UBERON:0000483!5.45e-07!309;UBERON:0000947!7.95e-07!21;UBERON:0010191!7.95e-07!21;UBERON:0003129!9.13e-07!11
|ontology_enrichment_uberon=UBERON:0007524!1.23e-18!73;UBERON:0003077!3.32e-18!72;UBERON:0007285!3.32e-18!72;UBERON:0002329!4.11e-18!71;UBERON:0003059!4.11e-18!71;UBERON:0007282!4.11e-18!71;UBERON:0004290!4.11e-18!71;UBERON:0009618!4.11e-18!71;UBERON:0000486!2.00e-15!83;UBERON:0007503!1.39e-14!78;UBERON:0001134!3.46e-14!62;UBERON:0002036!3.46e-14!62;UBERON:0003082!3.46e-14!62;UBERON:0002385!2.38e-13!64;UBERON:0001015!2.38e-13!64;UBERON:0000383!2.38e-13!64;UBERON:0003102!8.94e-13!99;UBERON:0001637!1.22e-12!42;UBERON:0003509!1.22e-12!42;UBERON:0004572!1.22e-12!42;UBERON:0000490!3.73e-12!148;UBERON:0002049!1.47e-11!78;UBERON:0007798!1.47e-11!78;UBERON:0004573!3.23e-11!33;UBERON:0004571!3.23e-11!33;UBERON:0002199!3.67e-11!46;UBERON:0002416!3.67e-11!46;UBERON:0004872!8.32e-11!83;UBERON:0007500!2.69e-10!59;UBERON:0001981!2.69e-10!59;UBERON:0004537!2.69e-10!59;UBERON:0006965!2.69e-10!59;UBERON:0003104!4.09e-10!160;UBERON:0009142!4.09e-10!160;UBERON:0000055!5.71e-10!68;UBERON:0005256!1.01e-09!122;UBERON:0002097!1.33e-09!41;UBERON:0000119!2.98e-08!309;UBERON:0000483!6.77e-08!306;UBERON:0004535!8.96e-08!109;UBERON:0000481!1.00e-07!342;UBERON:0001009!1.14e-07!112;UBERON:0000475!3.25e-07!264;UBERON:0000947!9.12e-07!21;UBERON:0010191!9.12e-07!21
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190507031873984!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115508191522287!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280241020767785!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326349613576221!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323165729488047!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917192070234268!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463577541967951!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015447747820857!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00437763447238062!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392251228879535!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128407441438887!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187007100421849!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00721416184241965!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029524860117002!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000739226781123318!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472174014973764!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.0088367085340913!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277533146902501!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239997797726909!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00375764713307699!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000648215975152522!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190793148673011!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330168959045432!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109672162352425
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95,0.0300692,0.131551,0.0445237,0.052362,6.26508e-09,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.0377931,0.137332,0.0145999,0.0656973,0.00188014,0.000131656,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.0694567,0.02609,0.0394698,0.0596469,0.0178982,0.122476,0.108872,0.000241884,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.00335855,0.00203513,0.190048,0.131088,0.00176415,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,2.39266e-05,0.141463,0.000891578,0.0103864,0.0889592,9.91491e-15,0.0458479,0.0473033,0.094881,0.445524,3.73309e-12,0.00307881,0.109194,0.000391885,0.131452,0.687347,0.448776,0.051838,0.000176849,0.0500365,0.061829,7.60655e-05,0.000147224,0.144075,0.0340203,0.0741807,0.00447267,0.739716,0.655293,0.00204117,0.00514993,0.000310064,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.00103374,0.00583965,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.297678,0.206454,0.218192,0.00608582,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,3.76086e-07,0.114242,0.0929549,0.172425,0.104948,0.00217546,0.057168,0.234298,0.00296278,0.286863,0.152372,0.0203723,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,2.24667e-10,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.0200941,0.137219,0.00238639,0.251466,0.288096,0.11903,0.0838874,0.00806892,0.113145,0.112651,0.186638,0.174776,0.00464715,0.264079,0.249049,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.00423976,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.0169521,0.218229,0.231073,0.0020598,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.0162067,0.231447,0.18653,0.43956,0.37006,0.42622,0.448797,0.0209277,3.79347e-09,0.36145,0.406019,0.381071,0.580441,0.0863135,0.11074,0.722159,0.390366,0.48809,0.00559336,0.443185,0.522904,0.0199034,0.871256,0.227104,0.518585,0.617852,0.0135352,0.284625,0.504757,0.55194,0.729153,0.28907,0.164197,0.462688,0.287881,0.0556235,0.478174,4.64145e-06,0.468444,0.258219,0.119142,0.243383,0.777351,0.390974,0.73485,0.683217,0.161598,0.751174,0.644754,0.0323708,0.799185,0.37357,0.78509,0.477353,0.452741,0.746954,0.771991,0.20342,0.200493,0.20558,0.300504,0.00348292,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.446891,0.616388,0.01635,0.000926901,0.322213,0.656109,0.33942,0.00285083,0.387276,0.0391112,0.0816402,0.537348,0.222037,0.416621,0.416292,0.0252635,0.0457685,0.579431,0.204817,0.452428,0.138871,0.308032,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.0805711,0.0393909,0.0980968,0.365487,0.534741,0.39088,0.363192,0.00266072,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,9.09657e-05,0.000553931,0.00285094,0.0795725,0.0527347,0.00604105,0.15059,0.386538,0.508064,0.250964,0.383276,0.0243456,0.504711,0.220231,0.00608438,0.196976,0.191517,0.463751,0.00258603,0.307334,0.459728,0.283463,0.0517073,0.135386,0.399569,0.273281,0.0114705,0.275089,0.384593,0.00444763,0.0105648,0.339729,0.197805,0.0153645,0.387069,0.332774,0.00107377,0.299887,0.0814305,0.205413,0.00105378,0.0779009,0.276869,0.205298,3.8422e-10,0.18966,0.036838,0.188263,0.0719199,0.00386277,1.26386e-06,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.000872573,0.252184,1.06858e-05,0.255516,0.00176345,0.119514,0.179412,0.193601,0.00215229,0.00221755,0.341681,0.310674,0.21801,0.0015337,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.0023439,0.27872,0.00376943,0.131118,0.20837,5.77125e-07,5.05887e-15,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.00404853,0.201602,0.350452,0.154941,0.000318033,0.0986735,0.108462,0.0595618,0.21593,0.000752649,0.220319,0.195218,0.124213,0.259632,2.52161e-06,0.00113527,0.159884,7.46043e-07,0.150733,0.217112,0.00801612,0.00121059,0.185335,0.0723291,0.0367308,0.00371613,0.00166408,2.24734e-10,0.207559,0.010576,0.193031,0.249101,0.115972,0.0273485,0.246105,0.173026,0.200432,0.139785,0.197112,0.0315594,0.156465,0.00899301,0.256963,0.00221189,0.172134,0.176789,0.000163687,0.202137,0.00649151,0.0437875,0.218161,0.0822373,0.0219487,0.106739,0.0536053,2.70035e-05,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.211332,0.187731,0.0025753,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,7.83704e-05,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.0687209,0.141729,0.0037817,0.255956,0.200105,0.0280973,0.29837,0.253509,0.177664,0.00482769,0.264413,0.000422974,0.160658,0.206239,0.19924,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}}
}}

Revision as of 15:46, 19 October 2012


Full id: C4222_Fibroblast_Mast_Smooth_mesenchymal_Myoblast_Preadipocyte_basal



Phase1 CAGE Peaks

Hg19::chr2:33824285..33824308,-p2@FAM98A
Hg19::chr2:33824309..33824326,-p3@FAM98A
Hg19::chr2:33824336..33824378,-p1@FAM98A


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>


Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue1.23e-1873
paraxial mesoderm3.32e-1872
presumptive paraxial mesoderm3.32e-1872
somite4.11e-1871
presomitic mesoderm4.11e-1871
presumptive segmental plate4.11e-1871
dermomyotome4.11e-1871
trunk paraxial mesoderm4.11e-1871
multilaminar epithelium2.00e-1583
epithelial vesicle1.39e-1478
skeletal muscle tissue3.46e-1462
striated muscle tissue3.46e-1462
myotome3.46e-1462
muscle tissue2.38e-1364
musculature2.38e-1364
musculature of body2.38e-1364
surface structure8.94e-1399
artery1.22e-1242
arterial blood vessel1.22e-1242
arterial system1.22e-1242
unilaminar epithelium3.73e-12148
vasculature1.47e-1178
vascular system1.47e-1178
systemic artery3.23e-1133
systemic arterial system3.23e-1133
integument3.67e-1146
integumental system3.67e-1146
splanchnic layer of lateral plate mesoderm8.32e-1183
epithelial tube open at both ends2.69e-1059
blood vessel2.69e-1059
blood vasculature2.69e-1059
vascular cord2.69e-1059
mesenchyme4.09e-10160
entire embryonic mesenchyme4.09e-10160
vessel5.71e-1068
trunk mesenchyme1.01e-09122
skin of body1.33e-0941
cell layer2.98e-08309
epithelium6.77e-08306
cardiovascular system8.96e-08109
multi-tissue structure1.00e-07342
circulatory system1.14e-07112
organism subdivision3.25e-07264
aorta9.12e-0721
aortic system9.12e-0721


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
CCNT2#90536.336201576962630.003930750035764890.0190507031873984
CEBPB#105137.971147625824820.001974187055288560.0115508191522287
CTCF#1066435.360256373075030.0064925092527670.0280241020767785
E2F1#186934.907389214879320.008460985347239390.0326349613576221
E2F6#187635.017155731697390.00791769806886330.0323165729488047
EBF1#187938.9064668465690.00141523283560980.00917192070234268
ELF1#199734.258097958807540.01295179875054610.0463577541967951
GABPB1#255337.067683836182170.002832212825417420.015447747820857
GATA2#2624312.7449317335540.0004829527704283790.00437763447238062
HDAC2#3066313.41562023662630.0004140761399857210.00392251228879535
IRF1#365937.63716375356390.002244692747297240.0128407441438887
MAX#414936.452555509007120.003721913834265510.0187007100421849
MXI1#460139.96157162875930.001011470541259020.00721416184241965
MYC#460935.22228187160940.007020843755740150.029524860117002
NANOG#79923329.24477848101273.99627955670032e-050.000739226781123318
NRF1#4899312.21027944771090.0005492172401020010.00472174014973764
POU2F2#545239.106124057742520.001324165192682130.0088367085340913
SIN3A#2594235.408884726815140.006318961977991520.0277533146902501
SIX5#147912317.0867153554590.0002004060546325010.00239997797726909
SRF#6722313.79717826216780.0003806615025800190.00375764713307699
THAP1#55145331.36914460285133.23800758564397e-050.000648215975152522
USF1#739136.361499277207960.00388404057290560.0190793148673011
YY1#752834.911170749853860.008441455341808260.0330168959045432
ZNF263#1012738.221841637010680.001799043925565870.0109672162352425



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.