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Coexpression cluster:C595: Difference between revisions

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{{Coexpression_clusters
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of bilateral symmetry!0.0312453970958568!7547$GO:0009799!determination of symmetry!0.0312453970958568!7547$GO:0007368!determination of left/right symmetry!0.0312453970958568!7547$GO:0003705!RNA polymerase II transcription factor activity, enhancer 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4658,0.0940786,0.419307,0.460081,0.719638,0.41248,0.245823,0.307708,0.528985,0.666362,0.747244,0.572915,0.504664,0.437157,0.716425,0.611134,0.621945,0.399385,0.311607,0.844055,0.229398,0.707863,0.348894,0.676528,0.110317,0.240791,0.241466,0.559235,0.333781,0.187694,0.241313,0.854523,0.195481,0.117716,0.278812,0.735636,0.650372,0.345521,0.403299,0.282135,0.477978,0.00468619,0.424456,0.29046,0.327384,0.497947,0.438989,0.201933,0.047809,0.374626,0.170712,0.515655,0.681219,0.826788,0.815334,0.628334,0.534283,0.451142,0.771969,0.672536,0.724882,0.829964,0.768195,0.623948,0.811363,0.453963,0.506604,0.583424,0.321002,0.670761,0.815591,0.740494,0.136849,0.459605,0.70766,0.718304,0.457962,0.661914,0.653454,0.230823,0.810793,0.762623,0.593207,0.719076,0.388139,0.00435223,0.721773,0.687969,0.395855,0.361878,0.851225,0.242842,0.214706,0.794497,0.308457,0.00123398,0.412853,0.715967,0.619978,0.574957,0.0350713,0.42771,0.684335,0.0771899|tfbs_overrepresentation_for_novel_motifs=0.514064,0.00572335,0.167518,0.760633,0.847893,1.38695,0.899058,0.517403,0.0669953,0.0781644,0.252096,0.3759,0.177832,0.329255,0.137951,0.153757,1.32362,0.692936,0.431744,0.351904,0.16756,0.213423,0.26993,0.135481,0.581509,1.80933,0.9801,0.268197,0.856732,0.131814,0.235027,0.568576,0.0851517,0.180835,0.116543,6.39416,0.740892,0.27709,1.64746,0.0583135,0.370199,0.222502,0.118046,0.136946,0.565712,2.3669,0.901103,0.682582,0.394038,1.38293,0.407934,0.349819,0.224172,0.639823,0.784252,0.331716,0.143846,0.304469,0.13168,0.303639,0.606437,0.341844,0.512045,1.27004,0.357077,1.20368,0.869007,1.22829,0.559029,1.06908,0.212516,0.532685,0.219458,0.782342,0.0450471,0.155706,0.139392,0.494371,0.556046,0.196113,0.0546605,0.50868,0.356776,0.897002,0.733386,0.00154893,0.580891,0.871857,0.430803,1.32629,0.95934,0.70782,0.584068,1.04207,0.139351,0.0967938,0.427968,0.623577,0.434875,0.108128,1.65474,0.578851,0.618385,0.538198,1.18153,0.248535,0.523764,0.326366,0.20048,0.403142,1.5876,0.61581,0.163638,0.259545,0.912801,0.113572,0.0496749,0.234099,0.476505,0.0908333,0.77444,0.428661,0.75254,0.959954,1.02031,0.495057,3.32915,0.588683,0.815183,1.62016,0.708473,0.237246,0.828971,0.363559,0.971853,0.283882,0.230408,0.740422,0.930667,1.77777,1.3781,0.894557,0.890389,0.620293,0.469857,0.297516,0.454976,1.61933,0.219968,1.02878,0.0167889,0.108176,0.708834,0.489782,0.341434,1.09904,0.41656,0.129698,0.581613,0.530833,0.893382,2.78047,1.36699,1.02668,0.48429,0.356103,0.580438,0.89656,0.023093|tfbs_overrepresentation_jaspar=MA0003.1;0.0972587,MA0004.1;0.256222,MA0006.1;0.137644,MA0007.1;0.241375,MA0009.1;0.669377,MA0014.1;0.0115261,MA0017.1;0.16476,MA0019.1;0.38027,MA0024.1;0.570967,MA0025.1;0.796882,MA0027.1;2.25966,MA0028.1;0.148561,MA0029.1;0.588958,MA0030.1;0.578277,MA0031.1;0.518602,MA0038.1;0.904297,MA0040.1;0.594421,MA0041.1;1.36862,MA0042.1;0.687159,MA0043.1;0.669676,MA0046.1;0.659066,MA0048.1;0.0212749,MA0050.1;0.688784,MA0051.1;0.896276,MA0052.1;0.598036,MA0055.1;0.120131,MA0056.1;0,MA0057.1;2.31304,MA0058.1;0.182945,MA0059.1;0.182001,MA0060.1;1.8362,MA0061.1;0.43901,MA0063.1;0,MA0066.1;0.341645,MA0067.1;0.975379,MA0068.1;0.147451,MA0069.1;0.655419,MA0070.1;0.644843,MA0071.1;0.308534,MA0072.1;0.640598,MA0073.1;5.00938,MA0074.1;0.337035,MA0076.1;0.194691,MA0077.1;0.633326,MA0078.1;0.424186,MA0081.1;0.18212,MA0083.1;0.676499,MA0084.1;1.15904,MA0087.1;0.63829,MA0088.1;0.662469,MA0089.1;0,MA0090.1;0.205547,MA0091.1;0.258318,MA0092.1;0.647316,MA0093.1;0.139688,MA0095.1;0,MA0098.1;0,MA0100.1;2.51026,MA0101.1;0.141917,MA0103.1;0.131472,MA0105.1;2.1572,MA0106.1;0.37688,MA0107.1;0.650533,MA0108.2;0.515791,MA0109.1;0,MA0111.1;0.617603,MA0113.1;0.39123,MA0114.1;0.0920489,MA0115.1;0.900969,MA0116.1;1.61784,MA0117.1;0.705104,MA0119.1;0.170362,MA0122.1;1.73183,MA0124.1;0.860724,MA0125.1;0.779672,MA0130.1;0,MA0131.1;0.440395,MA0132.1;0,MA0133.1;0,MA0135.1;0.698212,MA0136.1;0.347318,MA0139.1;0.0481205,MA0140.1;0.30631,MA0141.1;0.180729,MA0142.1;3.14454,MA0143.1;2.69221,MA0144.1;0.284854,MA0145.1;0.00981909,MA0146.1;0.0580435,MA0147.1;0.0991954,MA0148.1;0.758022,MA0149.1;0.298252,MA0062.2;0.0512998,MA0035.2;0.305721,MA0039.2;0.0386601,MA0138.2;0.425279,MA0002.2;0.220677,MA0137.2;0.465392,MA0104.2;0.0667907,MA0047.2;0.366327,MA0112.2;0.0445156,MA0065.2;0.0514203,MA0150.1;0.201098,MA0151.1;0,MA0152.1;0.311809,MA0153.1;0.763487,MA0154.1;0.0723831,MA0155.1;0.11478,MA0156.1;0.154615,MA0157.1;0.46471,MA0158.1;0,MA0159.1;0.0995776,MA0160.1;0.288813,MA0161.1;0,MA0162.1;0.0243066,MA0163.1;0.0128736,MA0164.1;0.402162,MA0080.2;0.432036,MA0018.2;0.378086,MA0099.2;0.312108,MA0079.2;1.22888,MA0102.2;1.1957,MA0258.1;0.569952,MA0259.1;0.104286,MA0442.1;0}}
|full_id=C595_teratocarcinoma_HES3GFP_H9_testicular_Wilms_hepatoblastoma_neuroblastoma
|id=C595
}}

Latest revision as of 11:26, 17 September 2013


Full id: C595_teratocarcinoma_HES3GFP_H9_testicular_Wilms_hepatoblastoma_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr12:75760714..75760729,+p1@GLIPR1L1
Hg19::chr15:75052999..75053003,-p@chr15:75052999..75053003
-
Hg19::chr18:11261018..11261023,-p@chr18:11261018..11261023
-
Hg19::chr1:63220075..63220077,+p@chr1:63220075..63220077
+
Hg19::chr22:35029651..35029657,-p@chr22:35029651..35029657
-
Hg19::chr22:35029659..35029670,-p@chr22:35029659..35029670
-
Hg19::chr6:10417399..10417415,-p32@TFAP2A
Hg19::chr6:10417454..10417460,-p40@TFAP2A
Hg19::chr6:3222149..3222154,+p@chr6:3222149..3222154
+
Hg19::chr8:70963473..70963506,-p@chr8:70963473..70963506
-
Hg19::chrX:136648643..136648711,+p2@ZIC3
Hg19::chrX:136648735..136648747,+p9@ZIC3
Hg19::chrX:136648753..136648767,+p5@ZIC3
Hg19::chrX:136648768..136648781,+p6@ZIC3
Hg19::chrX:136648807..136648822,+p8@ZIC3


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:0009855determination of bilateral symmetry0.0312453970958568
GO:0009799determination of symmetry0.0312453970958568
GO:0007368determination of left/right symmetry0.0312453970958568
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0351417582722758



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>

Cell Type
Ontology termp-valuen
embryonic stem cell3.12e-625
germ line cell1.85e-287
germ cell1.85e-287
neuron5.60e-196
neuroblast5.60e-196
electrically signaling cell5.60e-196
neuronal stem cell2.13e-148
melanocyte6.74e-1210
melanoblast6.74e-1210
neurecto-epithelial cell3.30e-1020
neurectodermal cell2.42e-0959
pigment cell1.18e-0814
columnar/cuboidal epithelial cell1.29e-0727
ectodermal cell1.36e-0772
Uber Anatomy
Ontology termp-valuen
testis5.92e-258
male reproductive organ2.99e-1811
gonad8.38e-1521
indifferent external genitalia8.38e-1521
indifferent gonad8.38e-1521
gonad primordium8.38e-1521
external genitalia3.95e-1422
male organism2.91e-0922
male reproductive system2.91e-0922
Disease
Ontology termp-valuen
germ cell and embryonal cancer3.80e-2022
germ cell cancer3.80e-2022


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)
MA0003.10.0972587
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.0115261
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.904297
MA0040.10.594421
MA0041.11.36862
MA0042.10.687159
MA0043.10.669676
MA0046.10.659066
MA0048.10.0212749
MA0050.10.688784
MA0051.10.896276
MA0052.10.598036
MA0055.10.120131
MA0056.10
MA0057.12.31304
MA0058.10.182945
MA0059.10.182001
MA0060.11.8362
MA0061.10.43901
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.15.00938
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.662469
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.647316
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.12.51026
MA0101.10.141917
MA0103.10.131472
MA0105.12.1572
MA0106.10.37688
MA0107.10.650533
MA0108.20.515791
MA0109.10
MA0111.10.617603
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.11.61784
MA0117.10.705104
MA0119.10.170362
MA0122.11.73183
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.10.180729
MA0142.13.14454
MA0143.12.69221
MA0144.10.284854
MA0145.10.00981909
MA0146.10.0580435
MA0147.10.0991954
MA0148.10.758022
MA0149.10.298252
MA0062.20.0512998
MA0035.20.305721
MA0039.20.0386601
MA0138.20.425279
MA0002.20.220677
MA0137.20.465392
MA0104.20.0667907
MA0047.20.366327
MA0112.20.0445156
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.0723831
MA0155.10.11478
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.10.0243066
MA0163.10.0128736
MA0164.10.402162
MA0080.20.432036
MA0018.20.378086
MA0099.20.312108
MA0079.21.22888
MA0102.21.1957
MA0258.10.569952
MA0259.10.104286
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
BCL3#60236.909420560747660.008495119184903560.0324265104547401
POU5F1#5460244.72522686025410.0009078211302340520.00660848477176512



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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