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Coexpression cluster:C3345: Difference between revisions

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|ontology_enrichment_disease=DOID:162!9.23e-20!235;DOID:14566!1.04e-19!239;DOID:0050687!8.43e-13!143;DOID:305!3.77e-10!106;DOID:0050686!9.38e-10!137
|ontology_enrichment_disease=DOID:162!9.23e-20!235;DOID:14566!1.04e-19!239;DOID:0050687!8.43e-13!143;DOID:305!3.77e-10!106;DOID:0050686!9.38e-10!137
|ontology_enrichment_uberon=UBERON:0007023!4.28e-07!115
|ontology_enrichment_uberon=UBERON:0007023!4.28e-07!115
|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.0013899880098987!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189495754701463!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324146894347359!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321057799586121!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319563830072233!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460719655895192!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255283137693999!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.0076079466945839!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153754795339313!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387167420156707!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436286691382835!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000626459129533097!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433045275621196!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108460313450391!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127770583079887!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156369241310889!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186058280172724!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029361706683448!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268950401194176!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172510204722257!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00880632250117989!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766053246834997!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275851057523598!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239284416825926!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00202710008590874!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308434434240235!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245779933198675!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.00093867128860913!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054143038823126!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000719211250541309!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628260587563469!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247673730859998!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00613957893833134!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000645617171128428!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189766707238814!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328422423797911!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388211607987613!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109080028181233
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06475,0.0558058,0.0443426,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.0694567,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,0.0926491,0.21727,0.289306,0.119215,0.00138836,0.177967,0.0465298,0.057571,0.047591,0.0143259,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.0472142,0.0355833,0.125606,0.175094,0.0121461,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.00259914,0.0759837,0.286863,0.0122477,0.194941,0.218271,0.101607,5.85104e-05,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.00102368,0.0948451,0.00382477,0.0339656,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.188651,0.00340589,0.0182671,3.03264e-05,0.0546539,0.161789,0.0590944,5.73049e-07,0.00109188,0.218229,0.231073,0.407281,0.252227,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.0177337,0.36927,0.449036,0.407369,0.231447,0.544776,0.115047,0.37006,0.42622,0.448797,0.197484,0.396996,0.0107863,0.406019,0.381071,0.580441,0.276075,0.432035,0.722159,0.0886602,0.48809,0.153829,0.0217093,0.522904,0.0608227,0.151996,0.227104,0.518585,0.617852,0.38649,0.284625,0.504757,0.55194,0.0437169,0.28907,0.164197,0.128922,0.00506733,0.574635,0.478174,0.336276,0.468444,0.0366482,0.119142,0.243383,0.777351,0.390974,0.73485,0.683217,0.161598,0.751174,0.277094,0.496032,0.799185,0.37357,0.78509,0.477353,0.199161,0.399222,0.185744,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.0997241,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.78,0.24884,0.408413,0.165147,0.322213,0.656109,0.33942,0.61031,0.387276,0.0391112,0.221908,0.00120002,0.222037,0.416621,0.416292,0.462712,0.148994,0.579431,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.178743,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.15059,0.0867777,0.159081,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.0254647,0.601877,0.307334,0.459728,0.283463,0.0517073,0.472935,0.399569,0.273281,0.368095,0.275089,0.0858306,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.0627969,0.52832,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.0139948,0.19104,0.163057,0.0260582,0.208013,0.0900729,0.0953646,0.166124,0.0348699,0.378361,0.255516,0.20753,0.119514,0.00111175,0.193601,0.00215229,0.222977,0.000913176,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.00178627,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.00242972,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.00316602,0.115972,0.0022686,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.000163687,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.0257187,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.0133429,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 13:36, 5 September 2012


Full id: C3345_acute_hepatoblastoma_Myoblast_tridermal_Reticulocytes_seminal_neuroepithelioma



Phase1 CAGE Peaks

Hg19::chr12:95867863..95867874,+p3@METAP2
Hg19::chr12:95867884..95867904,+p2@METAP2
Hg19::chr12:95867919..95867951,+p1@METAP2


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>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism4.28e-07115
Disease
Ontology termp-valuen
cancer9.23e-20235
disease of cellular proliferation1.04e-19239
cell type cancer8.43e-13143
carcinoma3.77e-10106
organ system cancer9.38e-10137


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
BCLAF1#9774321.65264761012189.8473954032885e-050.0013899880098987
CCNT2#90536.336201576962630.003930750035764890.0189495754701463
E2F1#186934.907389214879320.008460985347239390.0324146894347359
E2F6#187635.017155731697390.00791769806886330.0321057799586121
EGR1#195834.988179094810140.008056488137383440.0319563830072233
ELF1#199734.258097958807540.01295179875054610.0460719655895192
ELK4#2005316.2356816584680.0002336043955745990.00255283137693999
ETS1#211339.728760922202340.001085840092584840.0076079466945839
GABPB1#255337.067683836182170.002832212825417420.0153754795339313
GATA1#2623313.56030814380040.0004009615963782630.00387167420156707
GATA2#2624312.7449317335540.0004829527704283790.00436286691382835
GTF2B#2959331.94382993432423.06634405746243e-050.000626459129533097
GTF2F1#2962312.73966087675770.0004835525047438590.00433045275621196
HMGN3#932438.178547723350590.001827766942164210.0108460313450391
IRF1#365937.63716375356390.002244692747297240.0127770583079887
JUND#372736.994663941871030.002921845042734990.0156369241310889
MAX#414936.452555509007120.003721913834265510.0186058280172724
MYC#460935.22228187160940.007020843755740150.029361706683448
NFKB1#479035.488063424193840.006049381815655430.0268950401194176
PAX5#507936.669565531177830.003370290999677260.0172510204722257
POU2F2#545239.106124057742520.001324165192682130.00880632250117989
REST#597839.650028716128020.001112636247114590.00766053246834997
SIN3A#2594235.408884726815140.006318961977991520.0275851057523598
SIX5#147912317.0867153554590.0002004060546325010.00239284416825926
SMARCB1#6598318.25271578115740.000164397760679890.00202710008590874
SMC3#9126315.04493284493280.0002935825420371870.00308434434240235
SP1#666735.69838137814090.005403962701712170.0245779933198675
SP2#6668326.15353049384465.58768218891694e-050.00093867128860913
TAF7#6879311.43306940492390.0006690181981945830.0054143038823126
TAL1#6886329.86861667744023.75103522793067e-050.000719211250541309
TCF12#6938310.63446490218640.0008313523990202070.00628260587563469
TFAP2A#7020316.5186343730450.0002218033880766340.00247673730859998
TFAP2C#7022310.80922860986020.0007916746575753130.00613957893833134
THAP1#55145331.36914460285133.23800758564397e-050.000645617171128428
USF1#739136.361499277207960.00388404057290560.0189766707238814
YY1#752834.911170749853860.008441455341808260.0328422423797911
ZNF143#7702313.50087655222790.0004062804962997170.00388211607987613
ZNF263#1012738.221841637010680.001799043925565870.0109080028181233



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.