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Coexpression cluster:C807: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.0347211,0.273994,0.404877,0.237701,0.403356,0.474413,0.434224,0.138703,0.0921938,0.375531,0.515448,1.16754,0.46359,0.666154,0.256724,0.68716,0.191625,0.116269,0.178097,0.752779,0.111654,0.396189,0.233338,0.314616,0.537051,0.310025,0.39419,0.240354,0.281506,0.355553,0.722879,0.165252,0.108961,0.20845,0.200804,0.20579,0.404426,0.186493,0.125439,0.207288,0.903115,0.031261,0.235234,0.235672,0.301189,0.47544,0.365597,0.116302,0.240465,0.550604,0.486559,0.468946,0.797754,0.947672,0.466348,1.96373,0.435652,0.0825677,0.434711,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.144996,0.0579262,0.945703,0.104203,0.0955465,0.0867529,0.644006,0.709631,0.309107,0.380738,0.659298,1.23725,1.39374,0.89511,0.0102458,0.70174,0.0795497,0.575506,1.4989,1.12715,0.868602,0.739223,0.509773,0.238337,1.02531,0.368981,0.780743,0.579925,0.524614,0.187593,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.637089,0.7752,0.772599,0.741574,0.384185,1.07963,0.204477,0.0136871,0.354459,0.624851,0.173291,0.937551,1.4047,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,1.02842,0.869279,0.358161,2.27323,0.50181,1.13991,0.260985,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,0.971618,0.052013,0.0287097,0.869654,0.414185,1.2007,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.931981,0.473159,0.02648
|tfbs_overrepresentation_jaspar=MA0003.1;0.00190472,MA0004.1;0.380329,MA0006.1;1.23783,MA0007.1;0.952442,MA0009.1;0.828613,MA0014.1;0.0036779,MA0017.1;0.270554,MA0019.1;1.29263,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.697761,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;0.477043,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;0.817858,MA0048.1;0.0613414,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.0662377,MA0056.1;0,MA0057.1;0.211138,MA0058.1;0.293055,MA0059.1;0.291897,MA0060.1;0.138988,MA0061.1;0.377096,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.0911063,MA0069.1;1.90569,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;2.20556,MA0074.1;0.4723,MA0076.1;0.828432,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;0.0309101,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.995927,MA0092.1;0.347826,MA0093.1;0.238771,MA0095.1;0,MA0098.1;0,MA0100.1;0.49029,MA0101.1;0.241637,MA0103.1;0.646502,MA0105.1;0.0508589,MA0106.1;0.516528,MA0107.1;0.529721,MA0108.2;0.666881,MA0109.1;0,MA0111.1;1.59097,MA0113.1;0.532314,MA0114.1;0.174997,MA0115.1;1.06753,MA0116.1;0.182037,MA0117.1;0.865782,MA0119.1;0.760742,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.716757,MA0140.1;0.437738,MA0141.1;0.290336,MA0142.1;2.61279,MA0143.1;0.532484,MA0144.1;0.491079,MA0145.1;0.0359093,MA0146.1;0.0551603,MA0147.1;0.543675,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;0.0109452,MA0138.2;0.569505,MA0002.2;0.129981,MA0137.2;0.710884,MA0104.2;0.428616,MA0047.2;0.504873,MA0112.2;0.0329985,MA0065.2;0.147044,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.185581,MA0155.1;0.12484,MA0156.1;0.257809,MA0157.1;0.612166,MA0158.1;0,MA0159.1;0.544949,MA0160.1;0.417847,MA0161.1;0,MA0162.1;0.0377269,MA0163.1;0.0728181,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;0.00464855,MA0102.2;1.36707,MA0258.1;0.155735,MA0259.1;0.560522,MA0442.1;0
}}
}}

Revision as of 19:27, 22 January 2013


Full id: C807_neuroectodermal_renal_leiomyoma_Smooth_neuroblastoma_Aortic_Melanocyte



Phase1 CAGE Peaks

Hg19::chr11:69466307..69466329,+p@chr11:69466307..69466329
+
Hg19::chr11:69466430..69466446,+p@chr11:69466430..69466446
+
Hg19::chr11:69466577..69466634,+p@chr11:69466577..69466634
+
Hg19::chr11:69467214..69467238,+p5@CCND1
Hg19::chr11:69467344..69467411,+p2@CCND1
Hg19::chr11:69467416..69467438,+p7@CCND1
Hg19::chr11:69467457..69467532,+p3@CCND1
Hg19::chr11:69467977..69467992,+p@chr11:69467977..69467992
+
Hg19::chr11:69468195..69468212,+p@chr11:69468195..69468212
+
Hg19::chr11:69468466..69468480,+p@chr11:69468466..69468480
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
organism subdivision7.87e-20264
trunk4.59e-17199
epithelial tube1.24e-15117
multi-cellular organism4.86e-15656
mesenchyme1.43e-14160
entire embryonic mesenchyme1.43e-14160
unilaminar epithelium3.02e-14148
vasculature6.38e-1478
vascular system6.38e-1478
artery6.62e-1442
arterial blood vessel6.62e-1442
arterial system6.62e-1442
trunk mesenchyme7.15e-14122
vessel2.46e-1368
epithelial tube open at both ends9.44e-1359
blood vessel9.44e-1359
blood vasculature9.44e-1359
vascular cord9.44e-1359
multilaminar epithelium1.25e-1283
epithelium6.78e-12306
systemic artery7.69e-1233
systemic arterial system7.69e-1233
cell layer7.78e-12309
epithelial vesicle2.58e-1178
surface structure2.86e-1199
dense mesenchyme tissue3.46e-1173
somite3.70e-1171
presomitic mesoderm3.70e-1171
presumptive segmental plate3.70e-1171
dermomyotome3.70e-1171
trunk paraxial mesoderm3.70e-1171
paraxial mesoderm8.93e-1172
presumptive paraxial mesoderm8.93e-1172
splanchnic layer of lateral plate mesoderm1.26e-1083
anatomical system2.04e-10624
anatomical cluster3.45e-10373
anatomical group3.70e-10625
skeletal muscle tissue4.37e-1062
striated muscle tissue4.37e-1062
myotome4.37e-1062
muscle tissue1.45e-0964
musculature1.45e-0964
musculature of body1.45e-0964
multi-tissue structure5.67e-09342
anatomical conduit1.43e-08240
organ component layer1.76e-0866
aorta1.82e-0721
aortic system1.82e-0721
cardiovascular system4.65e-07109
integument6.15e-0746
integumental system6.15e-0746
blood vessel smooth muscle6.99e-0710
arterial system smooth muscle6.99e-0710
artery smooth muscle tissue6.99e-0710
aorta smooth muscle tissue6.99e-0710
circulatory system7.70e-07112
skin of body8.83e-0741
Disease
Ontology termp-valuen
cell type cancer6.17e-07143


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)
MA0003.10.00190472
MA0004.10.380329
MA0006.11.23783
MA0007.10.952442
MA0009.10.828613
MA0014.10.0036779
MA0017.10.270554
MA0019.11.29263
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.697761
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.11.90569
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.12.20556
MA0074.10.4723
MA0076.10.828432
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.995927
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.646502
MA0105.10.0508589
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.11.59097
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.12.61279
MA0143.10.532484
MA0144.10.491079
MA0145.10.0359093
MA0146.10.0551603
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.0109452
MA0138.20.569505
MA0002.20.129981
MA0137.20.710884
MA0104.20.428616
MA0047.20.504873
MA0112.20.0329985
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.185581
MA0155.10.12484
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.0377269
MA0163.10.0728181
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.00464855
MA0102.21.36707
MA0258.10.155735
MA0259.10.560522
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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