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Coexpression cluster:C3590: Difference between revisions

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|full_id=C3590_teratocarcinoma_medulla_putamen_locus_astrocytoma_retina_caudate
|full_id=C3590_teratocarcinoma_medulla_putamen_locus_astrocytoma_retina_caudate
|id=C3590
|id=C3590
|ontology_enrichment_celltype=CL:0000055!1.64e-14!180;CL:0000393!2.79e-10!60;CL:0000211!2.79e-10!60;CL:0000192!4.24e-10!42;CL:0000514!4.24e-10!42;CL:0000183!3.93e-09!59;CL:0000187!2.23e-08!54;CL:0000359!1.42e-07!32;CL:0000057!1.51e-07!75;CL:0002539!2.66e-07!10;CL:0000680!3.67e-07!57;CL:0000056!3.67e-07!57;CL:0000355!3.67e-07!57;CL:0002620!8.25e-07!23
|ontology_enrichment_celltype=CL:0000192!8.73e-09!43;CL:0000514!8.73e-09!43;CL:0002539!4.35e-08!10;CL:0002620!2.31e-07!23;CL:0000393!2.75e-07!61;CL:0000211!2.75e-07!61;CL:0000057!4.85e-07!76;CL:0000359!8.57e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.23e-35!94;UBERON:0001016!1.23e-35!94;UBERON:0005743!2.26e-35!86;UBERON:0001017!2.90e-33!82;UBERON:0003075!2.82e-32!86;UBERON:0007284!2.82e-32!86;UBERON:0001049!5.06e-30!57;UBERON:0005068!5.06e-30!57;UBERON:0006241!5.06e-30!57;UBERON:0007135!5.06e-30!57;UBERON:0002346!1.36e-29!90;UBERON:0002616!8.13e-27!59;UBERON:0000955!8.66e-27!69;UBERON:0006238!8.66e-27!69;UBERON:0000025!3.31e-25!194;UBERON:0004111!1.55e-22!241;UBERON:0003056!1.64e-22!61;UBERON:0000033!1.84e-21!123;UBERON:0002780!6.03e-21!41;UBERON:0001890!6.03e-21!41;UBERON:0006240!6.03e-21!41;UBERON:0000477!6.31e-21!286;UBERON:0004121!1.01e-20!169;UBERON:0007023!2.49e-20!115;UBERON:0000153!2.89e-20!129;UBERON:0007811!2.89e-20!129;UBERON:0003080!6.12e-20!42;UBERON:0000924!1.73e-19!173;UBERON:0006601!1.73e-19!173;UBERON:0000119!4.24e-19!312;UBERON:0000483!4.42e-19!309;UBERON:0002020!3.32e-18!34;UBERON:0003528!3.32e-18!34;UBERON:0001893!7.14e-18!34;UBERON:0000468!8.36e-18!659;UBERON:0002791!2.98e-17!33;UBERON:0001869!4.44e-17!32;UBERON:0002049!8.46e-16!79;UBERON:0007798!8.46e-16!79;UBERON:0000475!1.03e-15!365;UBERON:0000467!5.34e-15!625;UBERON:0000480!8.55e-15!626;UBERON:0000055!1.36e-13!69;UBERON:0001981!1.16e-12!60;UBERON:0007500!1.16e-12!60;UBERON:0004537!1.16e-12!60;UBERON:0006965!1.16e-12!60;UBERON:0000956!2.22e-12!25;UBERON:0000203!2.22e-12!25;UBERON:0001009!3.68e-12!113;UBERON:0000481!8.16e-12!347;UBERON:0003076!1.97e-11!15;UBERON:0003057!1.97e-11!15;UBERON:0004535!2.09e-11!110;UBERON:0002619!2.44e-11!22;UBERON:0001950!1.39e-10!20;UBERON:0004872!2.95e-10!84;UBERON:0004732!4.07e-10!13;UBERON:0000922!5.23e-10!612;UBERON:0000947!6.31e-10!21;UBERON:0010191!6.31e-10!21;UBERON:0001637!1.43e-09!42;UBERON:0003509!1.43e-09!42;UBERON:0004572!1.43e-09!42;UBERON:0004733!2.23e-09!12;UBERON:0002028!2.23e-09!12;UBERON:0007277!2.23e-09!12;UBERON:0001135!1.30e-08!15;UBERON:0004573!5.24e-08!33;UBERON:0004571!5.24e-08!33;UBERON:0002050!6.87e-08!605;UBERON:0005423!6.87e-08!605;UBERON:0000923!1.07e-07!604;UBERON:0005291!1.07e-07!604;UBERON:0006598!1.07e-07!604;UBERON:0002532!1.07e-07!604;UBERON:0002308!1.74e-07!9;UBERON:0000125!1.74e-07!9;UBERON:0000064!1.84e-07!219;UBERON:0003914!1.91e-07!118;UBERON:0004237!2.66e-07!10;UBERON:0004695!2.66e-07!10;UBERON:0002111!2.66e-07!10;UBERON:0004178!2.66e-07!10;UBERON:0002385!3.87e-07!63;UBERON:0001015!3.87e-07!63;UBERON:0000383!3.87e-07!63;UBERON:0002680!3.98e-07!9;UBERON:0001895!3.98e-07!9;UBERON:0010092!3.98e-07!9;UBERON:0001134!5.18e-07!61;UBERON:0002036!5.18e-07!61;UBERON:0003082!5.18e-07!61;UBERON:0002420!6.05e-07!9;UBERON:0007245!6.05e-07!9;UBERON:0010009!6.05e-07!9;UBERON:0010011!6.05e-07!9;UBERON:0000454!6.05e-07!9
|ontology_enrichment_uberon=UBERON:0003075!9.74e-37!82;UBERON:0007284!9.74e-37!82;UBERON:0001016!1.12e-33!89;UBERON:0002346!2.16e-33!86;UBERON:0001017!3.70e-33!81;UBERON:0001049!1.58e-32!56;UBERON:0005068!1.58e-32!56;UBERON:0006241!1.58e-32!56;UBERON:0007135!1.58e-32!56;UBERON:0000073!3.01e-30!53;UBERON:0002616!3.01e-30!53;UBERON:0000477!6.14e-29!373;UBERON:0010314!1.27e-27!132;UBERON:0000955!4.49e-27!68;UBERON:0006238!4.49e-27!68;UBERON:0000025!4.38e-26!192;UBERON:0003056!9.33e-25!61;UBERON:0010371!1.04e-22!104;UBERON:0004111!2.27e-21!240;UBERON:0002780!2.95e-21!41;UBERON:0001890!2.95e-21!41;UBERON:0003080!2.95e-21!41;UBERON:0006240!2.95e-21!41;UBERON:0000483!2.49e-19!306;UBERON:0004121!2.58e-19!171;UBERON:0000924!2.58e-19!171;UBERON:0006601!2.58e-19!171;UBERON:0007023!5.61e-19!114;UBERON:0000119!6.56e-19!309;UBERON:0003528!9.07e-19!34;UBERON:0002020!9.07e-19!34;UBERON:0001893!2.73e-18!34;UBERON:0001869!1.72e-17!32;UBERON:0002791!3.59e-17!32;UBERON:0011216!1.12e-15!223;UBERON:0000468!3.44e-15!656;UBERON:0000467!3.09e-14!624;UBERON:0000480!4.52e-14!625;UBERON:0000481!1.11e-13!342;UBERON:0002049!2.49e-13!78;UBERON:0007798!2.49e-13!78;UBERON:0000956!1.05e-12!25;UBERON:0000203!1.05e-12!25;UBERON:0003076!1.24e-12!15;UBERON:0003057!1.24e-12!15;UBERON:0000055!5.09e-12!68;UBERON:0007500!5.33e-12!59;UBERON:0001981!5.33e-12!59;UBERON:0004537!5.33e-12!59;UBERON:0006965!5.33e-12!59;UBERON:0002619!1.64e-11!22;UBERON:0004732!2.98e-11!13;UBERON:0000947!4.51e-11!21;UBERON:0010191!4.51e-11!21;UBERON:0001950!1.18e-10!20;UBERON:0001009!1.84e-10!112;UBERON:0004733!1.88e-10!12;UBERON:0002028!1.88e-10!12;UBERON:0007277!1.88e-10!12;UBERON:0000923!1.97e-10!560;UBERON:0010316!1.97e-10!560;UBERON:0005291!1.97e-10!560;UBERON:0006598!1.97e-10!560;UBERON:0010317!1.97e-10!560;UBERON:0002532!1.97e-10!560;UBERON:0000922!2.24e-10!592;UBERON:0001637!2.87e-10!42;UBERON:0003509!2.87e-10!42;UBERON:0004572!2.87e-10!42;UBERON:0002050!3.24e-10!564;UBERON:0004535!9.72e-10!109;UBERON:0001135!1.05e-09!15;UBERON:0004872!1.13e-09!83;UBERON:0005423!1.03e-08!581;UBERON:0004573!1.65e-08!33;UBERON:0004571!1.65e-08!33;UBERON:0000064!3.78e-08!218;UBERON:0004237!4.35e-08!10;UBERON:0004695!4.35e-08!10;UBERON:0002111!4.35e-08!10;UBERON:0004178!4.35e-08!10;UBERON:0002680!5.78e-08!9;UBERON:0001895!5.78e-08!9;UBERON:0010092!5.78e-08!9;UBERON:0000125!9.69e-08!9;UBERON:0002308!9.69e-08!9;UBERON:0002420!3.23e-07!9;UBERON:0007245!3.23e-07!9;UBERON:0010009!3.23e-07!9;UBERON:0010011!3.23e-07!9;UBERON:0000454!3.23e-07!9;UBERON:0003914!5.25e-07!117
|tf_chipseq_enrich=MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.00085714662559809!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000737007664881203!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374666917990336!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542018397341122!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00196855090776552!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328826658626352
|tf_chipseq_enrich=MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.00085714662559809!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000737007664881203!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374666917990336!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542018397341122!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00196855090776552!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328826658626352
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74211,0.160149,0.123526,0.0906475,0.0558058,0.0443426,0.166024,0.009894,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.00956472,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00049486,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.00136406,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0370461,0.145116,0.206454,0.00206897,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.00771936,0.172982,0.0661495,0.000654973,0.0626744,0.191335,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.252227,0.0360851,0.412187,0.131093,0.0434602,0.00935312,0.418146,0.36927,0.449036,0.407369,0.231447,0.18653,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.00417723,0.432035,0.722159,0.390366,0.48809,0.0334527,0.443185,0.522904,0.0608227,0.00127936,0.227104,0.518585,0.00310917,0.38649,0.284625,0.156746,0.04783,0.0437169,0.28907,0.0142854,0.462688,0.287881,0.0556235,0.478174,0.336276,0.0263888,0.00355636,0.119142,0.243383,0.777351,0.390974,0.149257,0.683217,0.161598,0.164332,0.021206,0.150692,0.21803,0.37357,0.454657,0.0282154,0.78384,0.746954,0.43491,0.20342,0.200493,0.20558,0.0505073,0.25656,0.0189087,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.0556238,0.181415,0.282286,0.78,0.24884,0.0978616,0.516511,0.322213,0.28903,0.33942,0.0156581,0.387276,0.169614,0.0248202,0.537348,0.222037,0.416621,0.416292,0.462712,0.382478,0.057399,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.0628556,0.373557,0.000122849,0.0980968,0.365487,0.534741,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.00977892,0.00438156,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,0.0323359,0.0135408,0.508064,0.250964,0.383276,0.0243456,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,2.66103e-06,0.472935,0.399569,0.0413011,0.368095,0.275089,0.384593,0.00444763,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.0193657,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.00177656,0.000130607,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.00651011,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.00178627,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.0701861,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.000773769,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,6.66781e-05,0.258496,0.00371613,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.0129343,0.13108,0.256963,0.222798,0.000975743,0.176789,0.0969345,0.202137,0.310405,0.280943,0.00206803,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.00312563,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.00339727,0.0981146,0.00210274,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.0687209,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.00172878,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271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}}
}}

Revision as of 15:14, 19 October 2012


Full id: C3590_teratocarcinoma_medulla_putamen_locus_astrocytoma_retina_caudate



Phase1 CAGE Peaks

Hg19::chr16:77822451..77822469,+p2@VAT1L
Hg19::chr16:77822475..77822492,+p1@VAT1L
Hg19::chr16:77822511..77822522,+p3@VAT1L


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
neural plate9.74e-3782
presumptive neural plate9.74e-3782
nervous system1.12e-3389
neurectoderm2.16e-3386
central nervous system3.70e-3381
neural tube1.58e-3256
neural rod1.58e-3256
future spinal cord1.58e-3256
neural keel1.58e-3256
regional part of nervous system3.01e-3053
regional part of brain3.01e-3053
anatomical cluster6.14e-29373
structure with developmental contribution from neural crest1.27e-27132
brain4.49e-2768
future brain4.49e-2768
tube4.38e-26192
pre-chordal neural plate9.33e-2561
ecto-epithelium1.04e-22104
anatomical conduit2.27e-21240
regional part of forebrain2.95e-2141
forebrain2.95e-2141
anterior neural tube2.95e-2141
future forebrain2.95e-2141
epithelium2.49e-19306
ectoderm-derived structure2.58e-19171
ectoderm2.58e-19171
presumptive ectoderm2.58e-19171
adult organism5.61e-19114
cell layer6.56e-19309
brain grey matter9.07e-1934
gray matter9.07e-1934
telencephalon2.73e-1834
cerebral hemisphere1.72e-1732
regional part of telencephalon3.59e-1732
organ system subdivision1.12e-15223
multi-cellular organism3.44e-15656
anatomical system3.09e-14624
anatomical group4.52e-14625
multi-tissue structure1.11e-13342
vasculature2.49e-1378
vascular system2.49e-1378
cerebral cortex1.05e-1225
pallium1.05e-1225
posterior neural tube1.24e-1215
chordal neural plate1.24e-1215
vessel5.09e-1268
epithelial tube open at both ends5.33e-1259
blood vessel5.33e-1259
blood vasculature5.33e-1259
vascular cord5.33e-1259
regional part of cerebral cortex1.64e-1122
segmental subdivision of nervous system2.98e-1113
aorta4.51e-1121
aortic system4.51e-1121
neocortex1.18e-1020
circulatory system1.84e-10112
segmental subdivision of hindbrain1.88e-1012
hindbrain1.88e-1012
presumptive hindbrain1.88e-1012
germ layer1.97e-10560
germ layer / neural crest1.97e-10560
embryonic tissue1.97e-10560
presumptive structure1.97e-10560
germ layer / neural crest derived structure1.97e-10560
epiblast (generic)1.97e-10560
embryo2.24e-10592
artery2.87e-1042
arterial blood vessel2.87e-1042
arterial system2.87e-1042
embryonic structure3.24e-10564
cardiovascular system9.72e-10109
smooth muscle tissue1.05e-0915
splanchnic layer of lateral plate mesoderm1.13e-0983
developing anatomical structure1.03e-08581
systemic artery1.65e-0833
systemic arterial system1.65e-0833
organ part3.78e-08218
blood vessel smooth muscle4.35e-0810
arterial system smooth muscle4.35e-0810
artery smooth muscle tissue4.35e-0810
aorta smooth muscle tissue4.35e-0810
regional part of metencephalon5.78e-089
metencephalon5.78e-089
future metencephalon5.78e-089
neural nucleus9.69e-089
nucleus of brain9.69e-089
basal ganglion3.23e-079
nuclear complex of neuraxis3.23e-079
aggregate regional part of brain3.23e-079
collection of basal ganglia3.23e-079
cerebral subcortex3.23e-079
epithelial tube5.25e-07117


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
MAFK#7975327.10073313782995.02195559325033e-050.00085714662559809
NANOG#79923329.24477848101273.99627955670032e-050.000737007664881203
SRF#6722313.79717826216780.0003806615025800190.00374666917990336
TAF7#6879311.43306940492390.0006690181981945830.00542018397341122
TRIM28#10155318.59052504526250.0001555969297255280.00196855090776552
YY1#752834.911170749853860.008441455341808260.0328826658626352



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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