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Coexpression cluster:C557: Difference between revisions

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{{Coexpression_clusters
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coagulation!0.00126852059183336!57088;948$GO:0050817!coagulation!0.00126852059183336!57088;948$GO:0007599!hemostasis!0.00126852059183336!57088;948$GO:0050878!regulation of body fluid levels!0.00126852059183336!57088;948$GO:0042060!wound healing!0.00126852059183336!57088;948$GO:0017128!phospholipid scramblase activity!0.00484368389615771!57088$GO:0017121!phospholipid scrambling!0.00484368389615771!57088$GO:0004115!3',5'-cyclic-AMP phosphodiesterase activity!0.00730233978810365!5142$GO:0009611!response to wounding!0.00730233978810365!57088;948$GO:0007009!plasma membrane organization and biogenesis!0.0110150024093571!57088$GO:0009605!response to external stimulus!0.0132790655320293!57088;948$GO:0005626!insoluble fraction!0.0141174333515346!5142$GO:0005548!phospholipid transporter activity!0.0208393166100831!57088$GO:0000267!cell fraction!0.0209698967234201!5142;948$GO:0065008!regulation of biological quality!0.0218046051086361!57088;948$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase 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6723,0.118381,0.306508,0.344935,0.520488,0.460196,0.213844,0.308984,0.393893,0.180997,0.538507,0.704612,0.845895,0.537704,0.662929,0.557415,0.803818,0.210671,0.696022,0.747563,0.848907,0.78972,0.647685,0.530923,0.805592,0.529302,0.607047,0.127493,0.694264,0.835246,0.762813,0.619716,0.481329,0.377361,0.74112,0.0287015,0.321688,0.677093,0.828783,0.830671,0.784325,0.616883,0.741876,0.407853,0.0638244,0.395887,0.129812,0.415815,0.380706,0.868972,0.633803,0.235786,0.815071,0.325254,0.501416,0.111474,0.738828,0.643716,0.598522,0.726332,0.788647,0.707691,0.219641|tfbs_overrepresentation_for_novel_motifs=0.157827,0.0158194,0.152819,0.718081,1.28612,0.25764,0.318839,1.23744,0.058273,0.438851,0.234283,0.355038,0.0400361,0.309388,0.393521,0.431887,0.511522,0.0927064,0.171822,0.0115332,0.464958,0.0268886,0.251588,0.387475,0.18461,0.374311,0.131361,0.249905,0.127478,0.113679,0.217756,1.34484,0.0750467,0.15896,0.104423,0.405974,0.102549,0.258546,0.299553,0.0503272,0.338389,0.205653,0.097714,0.123709,0.00483408,0.173971,0.319738,0.226038,0.541305,0.400978,0.386472,0.329494,0.0752075,0.615394,0.758742,0.838357,0.407898,0.2852,0.0270825,0.284391,0.582323,0.321692,0.465207,0.48664,0.336598,0.456015,0.843028,1.20113,0.535417,1.04233,0.570382,0.22329,0.0732084,0.756844,0.150647,0.0336796,0.120629,0.471562,0.532468,0.532279,0.400226,0.48568,0.893218,0.219253,0.70821,0.00751148,0.0552506,0.10849,0.408949,1.29895,0.932961,0.68283,1.37726,0.270867,0.12599,0.0858933,0.385004,1.45968,0.412954,0.020964,0.0899484,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,0.306566,0.18443,0.115618,0.160439,3.59827,0.149112,0.241506,0.886618,0.101627,0.0385455,0.216858,0.453946,0.275094,1.77152,0.406842,0.255485,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.0864157,0.683478,0.219902,0.803201,0.342946,0.945426,0.101403,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,1.45285,0.447394,0.278424,1.10486,1.59165,0.203207,0.0770919,0.0134468,0.00537053,2.75655,0.0546497,0.321292,1.07219,0.394947,0.116843,0.543,0.955335,0.867287,0.66649,0.531753,0.166635,0.46162,1.60088,0.530837,0.317742,0.0156497|tfbs_overrepresentation_jaspar=MA0003.1;0.000203219,MA0004.1;0.238283,MA0006.1;0.124371,MA0007.1;0.223897,MA0009.1;0.644692,MA0014.1;0.024058,MA0017.1;0.150184,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;0.0172925,MA0050.1;0.228625,MA0051.1;1.53688,MA0052.1;0.574006,MA0055.1;0.00174802,MA0056.1;0,MA0057.1;0.0158853,MA0058.1;1.54187,MA0059.1;1.53659,MA0060.1;0.0584466,MA0061.1;0.395503,MA0063.1;0,MA0066.1;0.321498,MA0067.1;0.948938,MA0068.1;0.128042,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.787225,MA0072.1;0.616162,MA0073.1;1.88779e-05,MA0074.1;0.316991,MA0076.1;0.178863,MA0077.1;0.608956,MA0078.1;0.402443,MA0081.1;0.499456,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.20753,MA0089.1;0,MA0090.1;0.189305,MA0091.1;0.240316,MA0092.1;0.607109,MA0093.1;0.12631,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;0.403202,MA0103.1;0.118522,MA0105.1;0.0621554,MA0106.1;0.355999,MA0107.1;0.598395,MA0108.2;0.492699,MA0109.1;0,MA0111.1;0.199239,MA0113.1;0.370073,MA0114.1;0.0814649,MA0115.1;0.874839,MA0116.1;0.0861811,MA0117.1;0.680135,MA0119.1;0.155538,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;0.0410754,MA0140.1;0.7823,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.928804,MA0145.1;0.23881,MA0146.1;0.00119685,MA0147.1;0.0881384,MA0148.1;0.257816,MA0149.1;0.764418,MA0062.2;0.168482,MA0035.2;1.42445,MA0039.2;0.00138827,MA0138.2;0.403517,MA0002.2;0.434729,MA0137.2;0.430142,MA0104.2;0.0580852,MA0047.2;0.345656,MA0112.2;0.0357356,MA0065.2;0.0416912,MA0150.1;0.185024,MA0151.1;0,MA0152.1;1.44602,MA0153.1;0.738108,MA0154.1;0.0124644,MA0155.1;0.0948197,MA0156.1;0.433955,MA0157.1;1.1256,MA0158.1;0,MA0159.1;0.0884959,MA0160.1;0.26995,MA0161.1;0,MA0162.1;0.0005964,MA0163.1;0.000243345,MA0164.1;0.380804,MA0080.2;0.397909,MA0018.2;0.357181,MA0099.2;1.44708,MA0079.2;5.64518e-08,MA0102.2;1.16862,MA0258.1;0.242841,MA0259.1;0.0929051,MA0442.1;0}}
|full_id=C557_Lymphatic_Endothelial_mesothelioma_pleomorphic_Cardiac_lung_aorta
|id=C557
}}

Latest revision as of 11:25, 17 September 2013


Full id: C557_Lymphatic_Endothelial_mesothelioma_pleomorphic_Cardiac_lung_aorta



Phase1 CAGE Peaks

Hg19::chr11:108794408..108794422,+p@chr11:108794408..108794422
+
Hg19::chr11:108794429..108794441,+p@chr11:108794429..108794441
+
Hg19::chr11:108794468..108794473,+p@chr11:108794468..108794473
+
Hg19::chr12:46807404..46807413,+p@chr12:46807404..46807413
+
Hg19::chr1:66723029..66723041,+p54@PDE4B
Hg19::chr2:170930109..170930110,+p3@AL833423
Hg19::chr3:145968814..145968846,-p2@PLSCR4
Hg19::chr4:114238302..114238314,+p67@ANK2
Hg19::chr6:84849274..84849294,+p@chr6:84849274..84849294
+
Hg19::chr7:79998842..79998855,+p25@CD36
Hg19::chr7:79998864..79998896,+p12@CD36
Hg19::chr7:79998905..79998917,+p26@CD36
Hg19::chr7:79998932..79998956,+p17@CD36
Hg19::chr7:79999026..79999038,+p31@CD36
Hg19::chr9:13446440..13446456,+p2@ENST00000428006
Hg19::chr9:13446472..13446510,+p1@ENST00000428006


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:0007596blood coagulation0.00126852059183336
GO:0050817coagulation0.00126852059183336
GO:0007599hemostasis0.00126852059183336
GO:0050878regulation of body fluid levels0.00126852059183336
GO:0042060wound healing0.00126852059183336
GO:0017128phospholipid scramblase activity0.00484368389615771
GO:0017121phospholipid scrambling0.00484368389615771
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.00730233978810365
GO:0009611response to wounding0.00730233978810365
GO:0007009plasma membrane organization and biogenesis0.0110150024093571
GO:0009605response to external stimulus0.0132790655320293
GO:0005626insoluble fraction0.0141174333515346
GO:0005548phospholipid transporter activity0.0208393166100831
GO:0000267cell fraction0.0209698967234201
GO:0065008regulation of biological quality0.0218046051086361
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0233904230898605
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0233904230898605
GO:0006950response to stress0.0295632196082685
GO:0005200structural constituent of cytoskeleton0.0377855298244911
GO:0005319lipid transporter activity0.0405219551907834



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>


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)
MA0003.10.000203219
MA0004.10.238283
MA0006.10.124371
MA0007.10.223897
MA0009.10.644692
MA0014.10.024058
MA0017.10.150184
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
MA0048.10.0172925
MA0050.10.228625
MA0051.11.53688
MA0052.10.574006
MA0055.10.00174802
MA0056.10
MA0057.10.0158853
MA0058.11.54187
MA0059.11.53659
MA0060.10.0584466
MA0061.10.395503
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.128042
MA0069.10.630852
MA0070.10.620368
MA0071.10.787225
MA0072.10.616162
MA0073.11.88779e-05
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.499456
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.20753
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.607109
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.403202
MA0103.10.118522
MA0105.10.0621554
MA0106.10.355999
MA0107.10.598395
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.0814649
MA0115.10.874839
MA0116.10.0861811
MA0117.10.680135
MA0119.10.155538
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.0410754
MA0140.10.7823
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.928804
MA0145.10.23881
MA0146.10.00119685
MA0147.10.0881384
MA0148.10.257816
MA0149.10.764418
MA0062.20.168482
MA0035.21.42445
MA0039.20.00138827
MA0138.20.403517
MA0002.20.434729
MA0137.20.430142
MA0104.20.0580852
MA0047.20.345656
MA0112.20.0357356
MA0065.20.0416912
MA0150.10.185024
MA0151.10
MA0152.11.44602
MA0153.10.738108
MA0154.10.0124644
MA0155.10.0948197
MA0156.10.433955
MA0157.11.1256
MA0158.10
MA0159.10.0884959
MA0160.10.26995
MA0161.10
MA0162.10.0005964
MA0163.10.000243345
MA0164.10.380804
MA0080.20.397909
MA0018.20.357181
MA0099.21.44708
MA0079.25.64518e-08
MA0102.21.16862
MA0258.10.242841
MA0259.10.0929051
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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