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Coexpression cluster:C570: Difference between revisions

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{{Coexpression_clusters
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0.0326141,0.161988,0.406925,0.158025,0.652741,0.746477,1.47569e-05,0.0833218,0.173214,0.00901372,0.78067,0.738453,0.310488,0.712596,0.0863248,0.472747,0.56823,0.164088,0.610746,0.0137353,0.626829,0.188899,0.30561,0.248678,0.220147,0.234688,0.699044,0.200901,0.59256,0.494883,0.018821,0.457901,0.279289,0.72675,0.00257697,0.000455993,0.685986,0.507062,0.21748,0.859567,0.654357,5.29016e-05,0.0769537,0.581622,0.72894,0.506174,0.662625,0.664864,0.32996,0.473473,0.221428,0.342918,0.367157,0.129464,0.557795,0.681406,0.451473,0.481816,0.742427,0.778356,0.0198107,0.118994,0.192307,0.114259,0.017066,0.596464,0.000129951,0.469901,0.388788,0.634865,0.278057,0.419455,0.338949,0.0043227,0.102214,0.730872,0.367255,0.0341071,0.452288,0.254606,0.255313,0.00206644,0.351578,0.198874,0.255153,0.153167,0.480972,0.0397954,0.670087,0.758074,0.674028,0.363759,0.42349,0.0495549,0.0333413,0.296723,0.445268,0.306508,0.344935,0.520488,0.00369598,0.213844,0.308984,0.0904162,0.180997,0.00809293,0.344397,0.120234,0.835001,0.195235,0.557415,0.803818,0.0224269,0.696022,0.400059,0.12357,0.206183,0.647685,0.263796,0.487191,0.529302,0.240004,0.127493,0.694264,0.538145,0.762813,0.0618684,0.140829,0.730672,0.391272,0.479646,0.685494,0.677093,0.259979,0.104869,0.784325,0.616883,0.741876,0.0975675,0.164579,0.744519,0.352603,0.415815,0.380706,0.332077,0.265928,0.0146031,0.502951,0.325254,0.81416,0.43333,0.388184,0.643716,0.232132,0.726332,0.788647,0.707691,0.219641|tfbs_overrepresentation_for_novel_motifs=0.157827,1.36836,0.464859,0.718081,0.789854,0.25764,0.318839,0.215354,2.86029,0.268189,0.234283,0.355038,0.156166,0.309388,0.393521,0.431887,0.511522,0.0927064,0.689727,0.306606,0.152859,2.16144,0.251588,0.387475,0.542899,0.374311,0.309883,0.249905,0.127478,0.509928,0.622094,1.34484,0.260283,0.0409179,0.340569,0.785985,0.102549,0.258546,0.622505,0.0503272,0.338389,0.205653,3.82991,0.123709,0.90499,0.173971,0.319738,0.226038,3.65327,0.400978,0.386472,0.329494,1.29462,0.615394,0.758742,0.311792,0.130259,0.2852,0.509529,0.284391,0.582323,0.321692,0.212582,0.48664,0.336598,0.456015,0.843028,1.20113,0.535417,1.04233,0.19602,0.836913,0.0158491,0.756844,0.150647,0.580064,2.14805,0.471562,0.532468,0.18023,0.0470011,0.48568,0.336303,0.219253,0.70821,0.588509,0.149619,1.56962,0.408949,1.29895,0.932961,0.68283,1.37726,0.270867,0.12599,0.290488,0.684177,0.599297,0.412954,0.229879,0.626127,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,1.49731,0.18443,0.115618,0.48378,0.591605,2.05965,0.241506,0.886618,0.333119,0.0943916,0.619973,0.453946,0.0803321,0.748992,0.406842,0.255485,0.345739,0.993708,1.19002,0.313614,0.564749,0.78949,0.0864157,0.683478,0.219902,0.803201,0.908,0.945426,0.757411,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,0.845643,0.596045,0.447394,0.278424,0.432737,1.59165,2.46528,0.266036,1.19009,0.0298174,0.683836,0.443914,0.321292,1.07219,1.02262,0.116843,0.184652,0.164414,0.867287,0.66649,0.531753,0.499061,0.46162,0.335644,0.905857,0.317742,4.97089|tfbs_overrepresentation_jaspar=MA0003.1;1.16699,MA0004.1;0.670242,MA0006.1;0.124371,MA0007.1;1.85633,MA0009.1;0.644692,MA0014.1;0.111471,MA0017.1;2.77077,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;0.252793,MA0042.1;0.227947,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.957021,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;0.19033,MA0056.1;0,MA0057.1;0.0733461,MA0058.1;0.5014,MA0059.1;0.964661,MA0060.1;0.0584466,MA0061.1;1.08093,MA0063.1;0,MA0066.1;0.860141,MA0067.1;0.948938,MA0068.1;0.0313753,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;0.0227426,MA0074.1;0.850035,MA0076.1;0.178863,MA0077.1;0.608956,MA0078.1;0.402443,MA0081.1;0.166796,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.369952,MA0089.1;0,MA0090.1;0.554239,MA0091.1;0.240316,MA0092.1;0.211423,MA0093.1;0.397767,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;0.403202,MA0103.1;1.80818,MA0105.1;0.329208,MA0106.1;0.355999,MA0107.1;1.0064,MA0108.2;0.492699,MA0109.1;0,MA0111.1;0.199239,MA0113.1;0.370073,MA0114.1;2.63575,MA0115.1;0.874839,MA0116.1;0.607827,MA0117.1;0.680135,MA0119.1;0.471628,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;0.418384,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;0.327047,MA0139.1;0.364861,MA0140.1;0.286995,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.0738381,MA0145.1;1.26426,MA0146.1;4.39497,MA0147.1;0.617362,MA0148.1;1.31921,MA0149.1;4.87439,MA0062.2;0.0439512,MA0035.2;0.286421,MA0039.2;0.311281,MA0138.2;0.403517,MA0002.2;1.16356,MA0137.2;0.138998,MA0104.2;0.462925,MA0047.2;0.914023,MA0112.2;2.87571,MA0065.2;3.56208,MA0150.1;0.5439,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.820684,MA0155.1;0.837529,MA0156.1;0.140505,MA0157.1;0.442323,MA0158.1;0,MA0159.1;1.53699,MA0160.1;0.743405,MA0161.1;0,MA0162.1;0.0485277,MA0163.1;0.473291,MA0164.1;0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|full_id=C570_oral_Prostate_Esophageal_Mammary_Corneal_Keratinocyte_Small
|id=C570
|ontology_enrichment_celltype=CL:0000066!1.63e-25!254;CL:0000063!9.94e-17!578;CL:0000012!2.44e-15!682;CL:0000548!3.26e-15!679;CL:0000004!3.26e-15!679;CL:0000255!3.26e-15!679;CL:0002076!8.78e-13!43;CL:0000223!1.56e-11!59;CL:0000003!1.43e-09!722;CL:0002077!4.77e-08!33;CL:0002368!2.23e-07!13
|ontology_enrichment_disease=DOID:162!1.65e-16!235;DOID:0050687!1.86e-16!143;DOID:305!1.27e-15!106;DOID:14566!2.72e-15!239
|ontology_enrichment_uberon=
}}

Latest revision as of 11:26, 17 September 2013


Full id: C570_oral_Prostate_Esophageal_Mammary_Corneal_Keratinocyte_Small



Phase1 CAGE Peaks

Hg19::chr16:87865215..87865228,-p@chr16:87865215..87865228
-
Hg19::chr16:87865535..87865593,-p5@SLC7A5
Hg19::chr16:87865862..87865890,-p3@SLC7A5
Hg19::chr16:87865969..87865982,-p11@SLC7A5
Hg19::chr16:87866311..87866331,-p4@SLC7A5
Hg19::chr16:87868136..87868180,-p@chr16:87868136..87868180
-
Hg19::chr16:87870180..87870274,-p@chr16:87870180..87870274
-
Hg19::chr16:87871480..87871532,-p@chr16:87871480..87871532
-
Hg19::chr16:87872354..87872372,-p@chr16:87872354..87872372
-
Hg19::chr16:87872373..87872412,-p@chr16:87872373..87872412
-
Hg19::chr16:87873374..87873400,-p@chr16:87873374..87873400
-
Hg19::chr16:87873403..87873438,-p@chr16:87873403..87873438
-
Hg19::chr16:87874679..87874710,-p@chr16:87874679..87874710
-
Hg19::chr16:87874738..87874767,-p@chr16:87874738..87874767
-
Hg19::chr16:87885379..87885431,-p@chr16:87885379..87885431
-
Hg19::chr16:87903102..87903120,-p1@SLC7A5


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell2.14e-25253
animal cell1.61e-14679
eukaryotic cell1.61e-14679
endo-epithelial cell1.79e-1342
endodermal cell4.52e-1258
native cell3.25e-09722
ecto-epithelial cell1.24e-0734
respiratory epithelial cell2.44e-0713
Disease
Ontology termp-valuen
cancer4.10e-16235
cell type cancer4.71e-16143
disease of cellular proliferation4.59e-15239
carcinoma9.36e-15106


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)
MA0003.11.16699
MA0004.10.670242
MA0006.10.124371
MA0007.11.85633
MA0009.10.644692
MA0014.10.111471
MA0017.12.77077
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.957021
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.19033
MA0056.10
MA0057.10.0733461
MA0058.10.5014
MA0059.10.964661
MA0060.10.0584466
MA0061.11.08093
MA0063.10
MA0066.10.860141
MA0067.10.948938
MA0068.10.0313753
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.0227426
MA0074.10.850035
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.166796
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.369952
MA0089.10
MA0090.10.554239
MA0091.10.240316
MA0092.10.211423
MA0093.10.397767
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.403202
MA0103.11.80818
MA0105.10.329208
MA0106.10.355999
MA0107.11.0064
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.12.63575
MA0115.10.874839
MA0116.10.607827
MA0117.10.680135
MA0119.10.471628
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.364861
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.0738381
MA0145.11.26426
MA0146.14.39497
MA0147.10.617362
MA0148.11.31921
MA0149.14.87439
MA0062.20.0439512
MA0035.20.286421
MA0039.20.311281
MA0138.20.403517
MA0002.21.16356
MA0137.20.138998
MA0104.20.462925
MA0047.20.914023
MA0112.22.87571
MA0065.23.56208
MA0150.10.5439
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.820684
MA0155.10.837529
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.11.53699
MA0160.10.743405
MA0161.10
MA0162.10.0485277
MA0163.10.473291
MA0164.10.380804
MA0080.20.126365
MA0018.20.357181
MA0099.20.292649
MA0079.20.139596
MA0102.21.16862
MA0258.13.75465
MA0259.10.640339
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
POLR2A#5430162.147453176558074.88536678567824e-060.000151132352408012
SIN3A#25942113.718608249685411.49176951969046e-050.000353526019666331
SIX5#14791255.339598548580940.001736587159380960.0106881623159048
SP1#6667134.629934869739484.9106978951726e-083.16390115653258e-06
ZBTB33#100091121.7694984581121.16503414517696e-131.81604479236024e-11



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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