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Coexpression cluster:C338: Difference between revisions

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{{Coexpression_clusters
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5,0.966856,0.98457,0.895387,0.861161,0.96565,0.843024,0.937589,0.776723,0.900634,0.902029,0.572964,0.966275,0.967912,0.924426,0.93455,0.928392,0.823416,0.912021,0.961102,0.752669,0.944003,0.959307,0.88388,0.920745,0.818499,0.916934,0.955729,0.854622,0.796558,0.965476,0.942538,0.882452,0.88973,0.321251,0.922639,0.985184,0.976196,0.93853,0.621896,0.92256,0.721757,0.464426,0.465505,0.843852,0.601711,0.375742,0.465261,0.987343,0.967902,0.932162,0.905246,0.950985,0.907635,0.617443,0.689747,0.528266,0.770863,0.526692,0.714124,0.540576,0.59299,0.790252,0.730225,0.400269,0.544056,0.654923,0.345768,0.806647,0.925082,0.981202,0.978266,0.992019,0.823094,0.968602,0.964942,0.920377,0.946349,0.981974,0.963613,0.89105,0.977192,0.969202,0.79836,0.862604,0.927029,0.919395,0.978334,0.953003,0.988403,0.752174,0.938433,0.943398,0.750463,0.914402,0.909471,0.976488,0.977036,0.9616,0.86981,0.943748,0.671592,0.988875,0.944965,0.92863,0.680905,0.638772,0.986683,0.881725,0.859206,0.972306,0.566566,0.972015,0.700893,0.942327,0.888425,0.856193,0.936305,0.963217,0.926732,0.993801|tfbs_overrepresentation_for_novel_motifs=0.143948,0.000156471,0.0341358,0.614285,0.470143,1.0245,0.124514,0.816329,0.029561,0.000878771,0.0735689,0.454646,0.0155978,0.118408,0.247565,0.119736,0.265519,0.167515,0.0190937,0.0533521,0.137206,0.000309621,0.593527,1.48483,0.181578,0.162121,0.0374544,0.0823079,0.0243516,0.0286268,0.0647008,0.292383,0.0449239,0.0530511,0.0166732,0.000112303,0.016104,0.0872832,0.318658,0.0230867,0.194267,0.0584668,0.375119,0.747806,0.00679116,0.378189,0.1251,0.069095,0.458783,0.255039,0.509118,0.411096,0.258779,0.350976,0.475837,0.119953,0.262028,0.103222,0.00785258,0.102726,0.32323,0.397937,0.0888272,0.245859,0.136236,0.222166,0.551996,0.889382,1.41825,0.737624,0.0536708,0.096729,0.000368041,1.19411,0.00227848,0.0969051,0.0803799,0.234122,0.282332,0.395197,0.275055,0.245107,0.83575,0.572385,0.431067,1.68665e-05,0.00158588,0.0071081,0.186966,0.984017,0.634935,0.408872,0.304922,1.03416,0.0238196,0.151139,0.258701,0.337414,0.1899,0.0192233,0.543149,0.300686,0.886085,0.268157,0.214431,0.250761,0.256823,0.372628,0.181318,0.0202481,0.0373322,0.330971,0.569154,0.267371,0.592003,0.614529,3.23273e-06,0.0642305,0.220587,0.741282,3.04292,3.93258,0.604541,0.438712,0.691757,0.234645,0.384386,0.30868,0.503421,0.307146,0.409436,0.866477,0.515797,0.140501,0.646547,0.0606728,0.062374,0.0825583,0.608436,1.42699,1.03434,0.575287,0.122045,0.334687,0.215605,0.099088,1.75116,1.27059,0.208833,0.0092535,0.028005,0.000391854,0.409747,0.177897,0.126114,0.765951,1.00593,0.0909941,0.0482085,0.039044,0.574213,0.394694,0.281754,0.0400133,0.226459,0.833847,0.00783676,0.782249,0.00150999|tfbs_overrepresentation_jaspar=MA0003.1;9.96581e-10,MA0004.1;0.262334,MA0006.1;0.0232461,MA0007.1;0.0679494,MA0009.1;0.980907,MA0014.1;3.85575e-08,MA0017.1;0.904952,MA0019.1;1.44776,MA0024.1;0.294311,MA0025.1;0.487069,MA0027.1;1.90579,MA0028.1;0.027018,MA0029.1;0.831858,MA0030.1;0.812273,MA0031.1;0.252799,MA0038.1;0.792032,MA0040.1;0.841894,MA0041.1;0.0839596,MA0042.1;0.527061,MA0043.1;0.376179,MA0046.1;0.367181,MA0048.1;0.0141894,MA0050.1;0.528958,MA0051.1;0.391092,MA0052.1;0.316327,MA0055.1;3.51601e-06,MA0056.1;0,MA0057.1;0.0123933,MA0058.1;0.360926,MA0059.1;0.358486,MA0060.1;0.00534716,MA0061.1;0.0199515,MA0063.1;0,MA0066.1;0.126249,MA0067.1;0.649823,MA0068.1;0.00151483,MA0069.1;0.364099,MA0070.1;0.355189,MA0071.1;0.7003,MA0072.1;0.351626,MA0073.1;7.21317e-14,MA0074.1;0.39004,MA0076.1;0.0455123,MA0077.1;0.913763,MA0078.1;0.182227,MA0081.1;0.156318,MA0083.1;0.381987,MA0084.1;0.823032,MA0087.1;0.349692,MA0088.1;0.162232,MA0089.1;0,MA0090.1;0.188379,MA0091.1;0.076904,MA0092.1;0.221134,MA0093.1;0.251813,MA0095.1;0,MA0098.1;0,MA0100.1;0.133688,MA0101.1;0.482318,MA0103.1;0.0930326,MA0105.1;0.00206652,MA0106.1;0.14939,MA0107.1;0.0542121,MA0108.2;0.250614,MA0109.1;0,MA0111.1;0.4473,MA0113.1;0.933559,MA0114.1;0.0513379,MA0115.1;0.581155,MA0116.1;0.151824,MA0117.1;0.406527,MA0119.1;0.140833,MA0122.1;0.42795,MA0124.1;8.52331,MA0125.1;0.471774,MA0130.1;0,MA0131.1;0.193896,MA0132.1;0,MA0133.1;0,MA0135.1;1.03495,MA0136.1;0.406962,MA0139.1;0.00262644,MA0140.1;0.694107,MA0141.1;0.0395007,MA0142.1;0.651925,MA0143.1;0.934001,MA0144.1;0.25542,MA0145.1;0.000758083,MA0146.1;6.74825e-05,MA0147.1;0.156503,MA0148.1;0.611137,MA0149.1;0.0995233,MA0062.2;0.00301306,MA0035.2;0.339371,MA0039.2;2.99646e-09,MA0138.2;0.183007,MA0002.2;0.313072,MA0137.2;0.284824,MA0104.2;0.0879339,MA0047.2;0.142334,MA0112.2;0.0100703,MA0065.2;0.0132651,MA0150.1;0.408276,MA0151.1;0,MA0152.1;0.70943,MA0153.1;0.457467,MA0154.1;0.0251465,MA0155.1;0.0222112,MA0156.1;0.120803,MA0157.1;0.211768,MA0158.1;0,MA0159.1;0.0121148,MA0160.1;0.0939956,MA0161.1;0,MA0162.1;3.5882e-07,MA0163.1;9.03886e-07,MA0164.1;0.166704,MA0080.2;0.251956,MA0018.2;0.150204,MA0099.2;0.107829,MA0079.2;0,MA0102.2;0.858102,MA0258.1;0.41289,MA0259.1;0.0634142,MA0442.1;0}}
|full_id=C338_MCF7_immature_Adipocyte_Smooth_Osteoblast_Neutrophils_acute
|id=C338
}}

Latest revision as of 11:20, 17 September 2013


Full id: C338_MCF7_immature_Adipocyte_Smooth_Osteoblast_Neutrophils_acute



Phase1 CAGE Peaks

Hg19::chr12:19877370..19877371,+p1@ENST00000364015
Hg19::chr15:99652809..99652812,-p@chr15:99652809..99652812
-
Hg19::chr16:52643357..52643359,+p@chr16:52643357..52643359
+
Hg19::chr16:65818007..65818011,+p@chr16:65818007..65818011
+
Hg19::chr17:47026878..47026882,-p1@ENST00000364033
Hg19::chr1:224363656..224363657,-p1@ENST00000415453
Hg19::chr1:232967929..232967931,-p1@ENST00000384108
Hg19::chr20:62540306..62540310,+p1@ENST00000362935
Hg19::chr21:36532069..36532071,+p@chr21:36532069..36532071
+
Hg19::chr2:185290469..185290475,-p@chr2:185290469..185290475
-
Hg19::chr2:85955456..85955460,-p1@ENST00000362817
Hg19::chr3:102878803..102878807,+p1@ENST00000365052
Hg19::chr3:48521762..48521766,+p@chr3:48521762..48521766
+
Hg19::chr3:87414879..87414887,-p@chr3:87414879..87414887
-
Hg19::chr4:114341473..114341476,+p1@ENST00000384093
Hg19::chr4:147501199..147501202,+p1@ENST00000384453
Hg19::chr4:190630861..190630869,-p1@ENST00000365345
Hg19::chr4:88921388..88921392,+p1@ENST00000365130
Hg19::chr5:170937921..170937930,-p@chr5:170937921..170937930
-
Hg19::chr5:178311712..178311719,+p1@ENST00000383897
Hg19::chr6:10993746..10993752,-p@chr6:10993746..10993752
-
Hg19::chr6:13214286..13214295,+p1@RNU1-11P
Hg19::chr6:27285355..27285356,+p@chr6:27285355..27285356
+
Hg19::chr6:36607442..36607450,-p1@ENST00000459274
Hg19::chr7:122600140..122600142,-p@chr7:122600140..122600142
-
Hg19::chr7:129124342..129124347,+p1@ENST00000362976
Hg19::chr7:141427781..141427790,+p1@ENST00000390851
Hg19::chr7:53433749..53433755,+p1@RNU1-14P
Hg19::chr8:136754734..136754740,-p1@ENST00000362782
Hg19::chr8:23934667..23934672,-p1@ENST00000384472
Hg19::chr8:73918666..73918672,+p@chr8:73918666..73918672
+
Hg19::chr9:89645193..89645207,+p@chr9:89645193..89645207
+
Hg19::chrX:132372840..132372843,-p1@ENST00000365329
Hg19::chrX:41580123..41580127,-p@chrX:41580123..41580127
-


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><br><br>

Cell Type
Ontology termp-valuen
classical monocyte1.66e-0742
CD14-positive, CD16-negative classical monocyte1.66e-0742


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)
MA0003.19.96581e-10
MA0004.10.262334
MA0006.10.0232461
MA0007.10.0679494
MA0009.10.980907
MA0014.13.85575e-08
MA0017.10.904952
MA0019.11.44776
MA0024.10.294311
MA0025.10.487069
MA0027.11.90579
MA0028.10.027018
MA0029.10.831858
MA0030.10.812273
MA0031.10.252799
MA0038.10.792032
MA0040.10.841894
MA0041.10.0839596
MA0042.10.527061
MA0043.10.376179
MA0046.10.367181
MA0048.10.0141894
MA0050.10.528958
MA0051.10.391092
MA0052.10.316327
MA0055.13.51601e-06
MA0056.10
MA0057.10.0123933
MA0058.10.360926
MA0059.10.358486
MA0060.10.00534716
MA0061.10.0199515
MA0063.10
MA0066.10.126249
MA0067.10.649823
MA0068.10.00151483
MA0069.10.364099
MA0070.10.355189
MA0071.10.7003
MA0072.10.351626
MA0073.17.21317e-14
MA0074.10.39004
MA0076.10.0455123
MA0077.10.913763
MA0078.10.182227
MA0081.10.156318
MA0083.10.381987
MA0084.10.823032
MA0087.10.349692
MA0088.10.162232
MA0089.10
MA0090.10.188379
MA0091.10.076904
MA0092.10.221134
MA0093.10.251813
MA0095.10
MA0098.10
MA0100.10.133688
MA0101.10.482318
MA0103.10.0930326
MA0105.10.00206652
MA0106.10.14939
MA0107.10.0542121
MA0108.20.250614
MA0109.10
MA0111.10.4473
MA0113.10.933559
MA0114.10.0513379
MA0115.10.581155
MA0116.10.151824
MA0117.10.406527
MA0119.10.140833
MA0122.10.42795
MA0124.18.52331
MA0125.10.471774
MA0130.10
MA0131.10.193896
MA0132.10
MA0133.10
MA0135.11.03495
MA0136.10.406962
MA0139.10.00262644
MA0140.10.694107
MA0141.10.0395007
MA0142.10.651925
MA0143.10.934001
MA0144.10.25542
MA0145.10.000758083
MA0146.16.74825e-05
MA0147.10.156503
MA0148.10.611137
MA0149.10.0995233
MA0062.20.00301306
MA0035.20.339371
MA0039.22.99646e-09
MA0138.20.183007
MA0002.20.313072
MA0137.20.284824
MA0104.20.0879339
MA0047.20.142334
MA0112.20.0100703
MA0065.20.0132651
MA0150.10.408276
MA0151.10
MA0152.10.70943
MA0153.10.457467
MA0154.10.0251465
MA0155.10.0222112
MA0156.10.120803
MA0157.10.211768
MA0158.10
MA0159.10.0121148
MA0160.10.0939956
MA0161.10
MA0162.13.5882e-07
MA0163.19.03886e-07
MA0164.10.166704
MA0080.20.251956
MA0018.20.150204
MA0099.20.107829
MA0079.20
MA0102.20.858102
MA0258.10.41289
MA0259.10.0634142
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

No analysis results for this cluster

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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