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Coexpression cluster:C285: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.16826972862577,0.126186423124351,0.0937756414473559,0.158716988307714,0.0856043003192711,0.0924647000597185,0.187330388394593,0.143777404502777,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.913280645454497,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0592523085472017,0.0342736005912748,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C285_cervical_Hep2_small_colon_temporal_duodenum_bronchogenic|gostat_on_coexpression_clusters=GO:0043085!positive regulation of catalytic activity!0.00666478581887981!842;79092;8527$GO:0032147!activation of protein kinase activity!0.0144788471296079!79092;8527$GO:0046982!protein heterodimerization activity!0.0159147723705919!7163;8527$GO:0050790!regulation of catalytic activity!0.0159147723705919!842;79092;8527$GO:0065009!regulation of a molecular function!0.0159147723705919!842;79092;8527$GO:0045860!positive regulation of protein kinase activity!0.0159147723705919!79092;8527$GO:0033674!positive regulation of kinase activity!0.0159147723705919!79092;8527$GO:0051347!positive regulation of transferase activity!0.0159147723705919!79092;8527$GO:0042803!protein homodimerization activity!0.0163259198672619!7163;8527$GO:0004035!alkaline phosphatase activity!0.020550845677255!248$GO:0050700!CARD domain binding!0.023967518948923!79092$GO:0045859!regulation of protein kinase activity!0.023967518948923!79092;8527$GO:0043549!regulation of kinase activity!0.023967518948923!79092;8527$GO:0051338!regulation of transferase activity!0.023967518948923!79092;8527$GO:0046339!diacylglycerol metabolic process!0.023967518948923!8527$GO:0008635!caspase activation via cytochrome c!0.0288826181170591!842$GO:0007250!activation of NF-kappaB-inducing kinase!0.0362320546560548!79092$GO:0042802!identical protein binding!0.0404723163106256!7163;8527$GO:0046983!protein dimerization 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22,0.941428,0.150572,0.602904,0.907781,0.957262,0.363136,0.787543,0.630062,0.0148306,0.628428,0.809351,0.00413098,0.695701,0.873454,0.517253,0.491702,0.646361,0.755421,0.429683,0.886378,0.261361,0.769558,0.395901,0.0142093,0.89899,0.989753,0.988143,0.964885,0.742483,0.968954,0.0774622,0.561881,0.9597,0.83803,0.879888,0.927709,0.860322,0.243428,0.881266,0.982524,0.377469,0.281824,0.503656,0.73123,0.00287325,0.409338,0.958382,0.377648,0.959395,0.145921,0.932684,0.000172309,0.770935,0.249714,0.534249,0.462063,0.779493,0.740157,0.821594,0.773211,0.925334,0.852347,0.669282,0.107017,0.21598,0.890561,0.330953,0.923211,0.973867,0.987365,0.266878,0.0803396|tfbs_overrepresentation_for_novel_motifs=0.0723752,0.207544,0.0679442,0.181912,0.704287,1.10053,0.553214,0.444928,0.031383,0.00729029,0.152126,1.07468,0.0413739,0.247783,1.72933,0.795611,0.190529,0.306359,0.321954,0.158764,0.586638,0.402489,0.390579,0.254309,0.457321,0.104369,0.215442,1.0621,0.00933964,0.274676,0.0329202,0.613044,0.22913,0.434385,0.0928033,0.0118798,0.00544639,0.181438,1.63409,0.00626734,0.355517,0.286816,0.641756,0.448405,0.648076,0.421273,0.262008,0.142557,0.226133,0.270499,0.111246,0.275618,0.6495,0.265995,0.380448,0.0717921,0.479151,0.21545,0.98193,0.214391,0.241178,0.264719,0.279106,0.173629,0.285645,0.153548,0.451923,0.777092,0.207217,0.629532,0.0259242,0.468057,0.000386771,0.37887,0.013551,0.133187,0.188887,0.16364,0.205134,0.232808,0.338761,1.57321,1.00441,0.0848179,0.338961,0.000311961,0.0935582,0.0443834,0.124382,0.869816,0.530781,0.318564,0.224958,1.1458,0.0461856,2.37692,0.194547,0.253831,0.795386,0.00376418,1.29211,0.630274,0.249978,0.192812,0.147065,0.0375094,0.183029,0.522762,0.0225263,0.0387327,0.376132,0.248074,0.339033,0.160677,2.12731,1.44216,0.00222151,2.7984,0.904638,0.415158,0.973057,0.123128,0.0469096,0.620975,0.585292,1.52139,0.91988,0.228277,1.04723,0.0660166,0.319081,0.135573,0.417824,2.09467,0.541892,0.23357,2.75879,1.06428,0.505486,1.30792,0.919291,0.473972,0.925152,2.79878,2.7498,1.20401,0.429776,1.15268,0.831365,0.125052,0.117577,2.45956e-05,0.319367,0.0709782,0.076425,0.656947,0.116136,0.237608,0.457463,0.200717,0.472954,0.305602,0.20463,0.205147,2.12274,0.284293,0.00211785,0.259248,0.00172248|tfbs_overrepresentation_jaspar=MA0003.1;0.00019307,MA0004.1;0.359809,MA0006.1;0.0449853,MA0007.1;0.327168,MA0009.1;1.43212,MA0014.1;0.00851051,MA0017.1;3.03229,MA0019.1;0.318355,MA0024.1;0.617045,MA0025.1;0.390923,MA0027.1;1.78493,MA0028.1;0.144251,MA0029.1;0.228475,MA0030.1;3.41444,MA0031.1;3.86886,MA0038.1;0.263954,MA0040.1;0.232423,MA0041.1;0.393391,MA0042.1;0.0364729,MA0043.1;1.43296,MA0046.1;0.280609,MA0048.1;0.510682,MA0050.1;1.83749,MA0051.1;0.934746,MA0052.1;0.235047,MA0055.1;1.35064,MA0056.1;0,MA0057.1;0.0195776,MA0058.1;0.0813231,MA0059.1;0.0177841,MA0060.1;0.00128055,MA0061.1;0.019829,MA0063.1;0,MA0066.1;0.264449,MA0067.1;1.3452,MA0068.1;0.0618261,MA0069.1;0.761408,MA0070.1;0.269786,MA0071.1;0.480128,MA0072.1;0.266579,MA0073.1;2.30108e-06,MA0074.1;0.0743125,MA0076.1;0.0209784,MA0077.1;0.261111,MA0078.1;0.120524,MA0081.1;0.0805829,MA0083.1;0.294032,MA0084.1;2.84721,MA0087.1;1.34527,MA0088.1;0.0197864,MA0089.1;0,MA0090.1;1.52402,MA0091.1;0.041012,MA0092.1;0.126121,MA0093.1;0.26662,MA0095.1;0,MA0098.1;0,MA0100.1;0.0821839,MA0101.1;0.132959,MA0103.1;0.659218,MA0105.1;0.00129462,MA0106.1;0.313513,MA0107.1;0.0198386,MA0108.2;0.177698,MA0109.1;0,MA0111.1;0.0269095,MA0113.1;0.334147,MA0114.1;1.18092,MA0115.1;1.20568,MA0116.1;1.96819,MA0117.1;1.53259,MA0119.1;0.359999,MA0122.1;0.336089,MA0124.1;0.444822,MA0125.1;0.376666,MA0130.1;0,MA0131.1;0.130054,MA0132.1;0,MA0133.1;0,MA0135.1;0.310984,MA0136.1;0.272187,MA0139.1;0.618365,MA0140.1;0.0602746,MA0141.1;1.33124,MA0142.1;0.160525,MA0143.1;0.334372,MA0144.1;2.53827,MA0145.1;0.0285078,MA0146.1;0.0892594,MA0147.1;0.0684386,MA0148.1;5.33036,MA0149.1;0.207563,MA0062.2;0.00457874,MA0035.2;0.21705,MA0039.2;0.0482878,MA0138.2;0.121158,MA0002.2;1.04619,MA0137.2;1.90307,MA0104.2;0.0311865,MA0047.2;5.76957,MA0112.2;0.0813703,MA0065.2;0.469626,MA0150.1;0.742352,MA0151.1;0,MA0152.1;1.27354,MA0153.1;0.363372,MA0154.1;1.55858,MA0155.1;0.00826551,MA0156.1;0.154795,MA0157.1;4.28487,MA0158.1;0,MA0159.1;0.287644,MA0160.1;0.759309,MA0161.1;0,MA0162.1;9.43263e-05,MA0163.1;0.0756869,MA0164.1;1.71662,MA0080.2;0.129336,MA0018.2;0.650185,MA0099.2;0.0628256,MA0079.2;1.71891e-13,MA0102.2;0.74655,MA0258.1;0.749389,MA0259.1;0.307246,MA0442.1;0}}
|full_id=C285_cervical_Hep2_small_colon_temporal_duodenum_bronchogenic
|id=C285
}}

Latest revision as of 11:13, 17 September 2013


Full id: C285_cervical_Hep2_small_colon_temporal_duodenum_bronchogenic



Phase1 CAGE Peaks

Hg19::chr10:99550654..99550658,-p@chr10:99550654..99550658
-
Hg19::chr11:72957611..72957646,+p@chr11:72957611..72957646
+
Hg19::chr13:114748246..114748260,-p@chr13:114748246..114748260
-
Hg19::chr16:15596148..15596153,+p7@C16orf45
Hg19::chr17:78152310..78152314,+p10@CARD14
Hg19::chr17:78152323..78152332,+p3@CARD14
Hg19::chr18:33766737..33766750,-p@chr18:33766737..33766750
-
Hg19::chr18:5521372..5521391,-p@chr18:5521372..5521391
-
Hg19::chr1:15850650..15850657,-p9@CASP9
Hg19::chr1:197411581..197411608,+p@chr1:197411581..197411608
+
Hg19::chr1:207326648..207326670,+p@chr1:207326648..207326670
+
Hg19::chr2:233320827..233320853,+p2@ALPI
Hg19::chr2:233320855..233320886,+p1@ALPI
Hg19::chr2:233323059..233323070,+p@chr2:233323059..233323070
+
Hg19::chr2:233324192..233324197,+p@chr2:233324192..233324197
+
Hg19::chr2:234296792..234296806,+p13@DGKD
Hg19::chr2:933319..933328,-p@chr2:933319..933328
-
Hg19::chr2:933356..933367,-p@chr2:933356..933367
-
Hg19::chr4:173883976..173883983,+p@chr4:173883976..173883983
+
Hg19::chr4:173883984..173884005,+p@chr4:173883984..173884005
+
Hg19::chr4:173884006..173884018,+p@chr4:173884006..173884018
+
Hg19::chr4:173884019..173884038,+p@chr4:173884019..173884038
+
Hg19::chr4:173884042..173884047,+p@chr4:173884042..173884047
+
Hg19::chr5:370139..370155,+p@chr5:370139..370155
+
Hg19::chr5:370156..370169,+p@chr5:370156..370169
+
Hg19::chr5:37249149..37249162,+p@chr5:37249149..37249162
+
Hg19::chr5:58571500..58571517,-p1@uc003jsd.1
Hg19::chr6:1111683..1111701,+p@chr6:1111683..1111701
+
Hg19::chr6:134664463..134664474,+p@chr6:134664463..134664474
+
Hg19::chr6:134718844..134718848,+p@chr6:134718844..134718848
+
Hg19::chr6:152084749..152084760,+p@chr6:152084749..152084760
+
Hg19::chr6:152084846..152084856,+p@chr6:152084846..152084856
+
Hg19::chr6:152084870..152084873,+p@chr6:152084870..152084873
+
Hg19::chr6:152084876..152084885,+p@chr6:152084876..152084885
+
Hg19::chr6:152084890..152084896,+p@chr6:152084890..152084896
+
Hg19::chr6:64276121..64276143,-p@chr6:64276121..64276143
-
Hg19::chr6:64276192..64276203,-p@chr6:64276192..64276203
-
Hg19::chr6:87797935..87797943,-p2@CGA
Hg19::chr8:80963618..80963643,-p15@TPD52
Hg19::chr8:80963645..80963656,-p22@TPD52
Hg19::chr8:80963666..80963669,-p37@TPD52
Hg19::chr8:80963673..80963679,-p29@TPD52
Hg19::chrX:2420841..2420865,-p4@DHRSX
Hg19::chrX:2420871..2420883,-p6@DHRSX
Hg19::chrX:57619447..57619495,+p2@ZXDB


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

GO IDGO nameFDR corrected p-value
GO:0043085positive regulation of catalytic activity0.00666478581887981
GO:0032147activation of protein kinase activity0.0144788471296079
GO:0046982protein heterodimerization activity0.0159147723705919
GO:0050790regulation of catalytic activity0.0159147723705919
GO:0065009regulation of a molecular function0.0159147723705919
GO:0045860positive regulation of protein kinase activity0.0159147723705919
GO:0033674positive regulation of kinase activity0.0159147723705919
GO:0051347positive regulation of transferase activity0.0159147723705919
GO:0042803protein homodimerization activity0.0163259198672619
GO:0004035alkaline phosphatase activity0.020550845677255
GO:0050700CARD domain binding0.023967518948923
GO:0045859regulation of protein kinase activity0.023967518948923
GO:0043549regulation of kinase activity0.023967518948923
GO:0051338regulation of transferase activity0.023967518948923
GO:0046339diacylglycerol metabolic process0.023967518948923
GO:0008635caspase activation via cytochrome c0.0288826181170591
GO:0007250activation of NF-kappaB-inducing kinase0.0362320546560548
GO:0042802identical protein binding0.0404723163106256
GO:0046983protein dimerization activity0.0404723163106256



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
larynx9.93e-1279
upper respiratory tract5.23e-6019
respiratory primordium6.65e-3038
endoderm of foregut6.65e-3038
segment of respiratory tract4.03e-2447
respiratory tract5.96e-2154
respiratory system3.49e-1574
foregut7.56e-1387
organ segment2.37e-1198
subdivision of digestive tract2.95e-09118
digestive system1.93e-07145
digestive tract1.93e-07145
primitive gut1.93e-07145
primordium9.78e-07160
Disease
Ontology termp-valuen
carcinoma2.37e-16106
cell type cancer5.90e-12143
cancer1.45e-08235
disease of cellular proliferation2.27e-08239


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)
MA0003.10.00019307
MA0004.10.359809
MA0006.10.0449853
MA0007.10.327168
MA0009.11.43212
MA0014.10.00851051
MA0017.13.03229
MA0019.10.318355
MA0024.10.617045
MA0025.10.390923
MA0027.11.78493
MA0028.10.144251
MA0029.10.228475
MA0030.13.41444
MA0031.13.86886
MA0038.10.263954
MA0040.10.232423
MA0041.10.393391
MA0042.10.0364729
MA0043.11.43296
MA0046.10.280609
MA0048.10.510682
MA0050.11.83749
MA0051.10.934746
MA0052.10.235047
MA0055.11.35064
MA0056.10
MA0057.10.0195776
MA0058.10.0813231
MA0059.10.0177841
MA0060.10.00128055
MA0061.10.019829
MA0063.10
MA0066.10.264449
MA0067.11.3452
MA0068.10.0618261
MA0069.10.761408
MA0070.10.269786
MA0071.10.480128
MA0072.10.266579
MA0073.12.30108e-06
MA0074.10.0743125
MA0076.10.0209784
MA0077.10.261111
MA0078.10.120524
MA0081.10.0805829
MA0083.10.294032
MA0084.12.84721
MA0087.11.34527
MA0088.10.0197864
MA0089.10
MA0090.11.52402
MA0091.10.041012
MA0092.10.126121
MA0093.10.26662
MA0095.10
MA0098.10
MA0100.10.0821839
MA0101.10.132959
MA0103.10.659218
MA0105.10.00129462
MA0106.10.313513
MA0107.10.0198386
MA0108.20.177698
MA0109.10
MA0111.10.0269095
MA0113.10.334147
MA0114.11.18092
MA0115.11.20568
MA0116.11.96819
MA0117.11.53259
MA0119.10.359999
MA0122.10.336089
MA0124.10.444822
MA0125.10.376666
MA0130.10
MA0131.10.130054
MA0132.10
MA0133.10
MA0135.10.310984
MA0136.10.272187
MA0139.10.618365
MA0140.10.0602746
MA0141.11.33124
MA0142.10.160525
MA0143.10.334372
MA0144.12.53827
MA0145.10.0285078
MA0146.10.0892594
MA0147.10.0684386
MA0148.15.33036
MA0149.10.207563
MA0062.20.00457874
MA0035.20.21705
MA0039.20.0482878
MA0138.20.121158
MA0002.21.04619
MA0137.21.90307
MA0104.20.0311865
MA0047.25.76957
MA0112.20.0813703
MA0065.20.469626
MA0150.10.742352
MA0151.10
MA0152.11.27354
MA0153.10.363372
MA0154.11.55858
MA0155.10.00826551
MA0156.10.154795
MA0157.14.28487
MA0158.10
MA0159.10.287644
MA0160.10.759309
MA0161.10
MA0162.19.43263e-05
MA0163.10.0756869
MA0164.11.71662
MA0080.20.129336
MA0018.20.650185
MA0099.20.0628256
MA0079.21.71891e-13
MA0102.20.74655
MA0258.10.749389
MA0259.10.307246
MA0442.10



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
CEBPB#1051142.479912594701050.0008753074883893530.00652926496535217
GATA3#262584.842047352392180.0002100809335598130.00244518473420855
NR3C1#290882.661870814430760.009192961431128360.0347674705379546
STAT3#6774122.80519066590780.0007801882787431220.00611268444438506



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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