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Coexpression cluster:C1240: Difference between revisions

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{{Coexpression_clusters
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of transcription, DNA-dependent!0.0437259851098411!7643;90649$GO:0006351!transcription, DNA-dependent!0.0437259851098411!7643;90649$GO:0032774!RNA biosynthetic process!0.0437259851098411!7643;90649$GO:0003677!DNA binding!0.0437259851098411!7643;90649$GO:0045449!regulation of transcription!0.0437259851098411!7643;90649$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0437259851098411!7643;90649$GO:0006350!transcription!0.0437259851098411!7643;90649$GO:0010468!regulation of gene expression!0.0437259851098411!7643;90649$GO:0031323!regulation of cellular metabolic process!0.0437259851098411!7643;90649$GO:0019222!regulation of metabolic process!0.0437259851098411!7643;90649$GO:0016070!RNA metabolic process!0.0437259851098411!7643;90649$GO:0008270!zinc ion 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0.172653,0.0924531,0.120918,0.593272,0.507382,0.425328,0.384398,0.462521,0.387627,0.179489,0.214126,0.143317,0.261663,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.558766,0.545381,0.630108,0.299959,0.509613,0.498355,0.406059,0.452427,0.56256,0.494497,0.366448,0.540845,0.511559,0.280842,0.335456,0.416632,0.404559,0.545676,0.467154,0.600528,0.249647,0.43669,0.446356,0.248584,0.397145,0.390152,0.537963,0.540199,0.488863,0.342785,0.447064,0.20487,0.603936,0.449548,0.41929,0.209566,0.189123,0.588995,0.355645,0.332105,0.522124,0.158122,0.521096,0.220023,0.444217,0.363335,0.329186,0.432735,0.493369,0.416144,0.648861|tfbs_overrepresentation_for_novel_motifs=0.392069,1.50607,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,1.19284,0.0544999,0.497563,0.647852,0.184039,0.592674,0.341795,0.956905,0.827563,0.28906,0.19568,3.59641,0.384762,0.498384,0.520063,0.338096,0.430372,0.670692,1.52633,1.28759,1.63811,0.459534,1.1974,0.864517,0.257226,0.546594,0.309012,0.0934825,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,0.541549,0.340293,0.494995,0.415364,0.60533,0.486696,2.40896,0.346342,0.684981,0.617179,2.43245,0.941629,1.09491,0.595623,0.350547,0.562713,0.459282,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.310394,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.73028,0.343884,0.277058,0.566252,0.924148,0.715799,1.92468,1.41651,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,2.63462,0.507004,1.22894,0.304323,0.039977,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,2.48084,0.886402,1.12733,0.76179,1.01492,0.47854,1.14174,0.633392,1.28996,1.37933,2.06018,1.28879,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,1.16062,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.877715,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.0992692|tfbs_overrepresentation_jaspar=MA0003.1;0.00215847,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.187674,MA0017.1;0.991615,MA0019.1;0.652951,MA0024.1;3.33297,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.382278,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;2.46167,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;2.61656,MA0061.1;0.198335,MA0063.1;0,MA0066.1;1.47685,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.000265001,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.252594,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;1.17914,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;1.9963,MA0113.1;0.665691,MA0114.1;0.741402,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;1.59899,MA0144.1;0.254954,MA0145.1;0.581146,MA0146.1;1.54462,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.128723,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.262665,MA0065.2;0.996317,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.911393,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.0015479,MA0102.2;1.51913,MA0258.1;1.27333,MA0259.1;0.289405,MA0442.1;0}}
|full_id=C1240_testicular_iPS_HES3GFP_H9_teratocarcinoma_non_gall
|id=C1240
}}

Latest revision as of 11:40, 17 September 2013


Full id: C1240_testicular_iPS_HES3GFP_H9_teratocarcinoma_non_gall



Phase1 CAGE Peaks

Hg19::chr19:20188776..20188826,+p1@ZNF90
Hg19::chr19:20216874..20216879,+p@chr19:20216874..20216879
+
Hg19::chr19:20230445..20230450,+p@chr19:20230445..20230450
+
Hg19::chr19:20278012..20278034,+p1@ZNF486
Hg19::chr19:20349233..20349273,-p@chr19:20349233..20349273
-
Hg19::chr19:20607694..20607718,-p3@ZNF826P
Hg19::chr19:20607724..20607748,-p1@ZNF826P


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:0006355regulation of transcription, DNA-dependent0.0437259851098411
GO:0006351transcription, DNA-dependent0.0437259851098411
GO:0032774RNA biosynthetic process0.0437259851098411
GO:0003677DNA binding0.0437259851098411
GO:0045449regulation of transcription0.0437259851098411
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0437259851098411
GO:0006350transcription0.0437259851098411
GO:0010468regulation of gene expression0.0437259851098411
GO:0031323regulation of cellular metabolic process0.0437259851098411
GO:0019222regulation of metabolic process0.0437259851098411
GO:0016070RNA metabolic process0.0437259851098411
GO:0008270zinc ion binding0.0437259851098411



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>

Cell Type
Ontology termp-valuen
neural cell1.90e-0825
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.03e-10171
ectoderm1.03e-10171
presumptive ectoderm1.03e-10171
nervous system1.10e-1089
central nervous system3.08e-1081
neurectoderm1.03e-0986
neural plate1.64e-0882
presumptive neural plate1.64e-0882
structure with developmental contribution from neural crest3.10e-08132
ecto-epithelium1.06e-07104
neural tube7.35e-0756
neural rod7.35e-0756
future spinal cord7.35e-0756
neural keel7.35e-0756


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.991615
MA0019.10.652951
MA0024.13.33297
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.12.46167
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.12.61656
MA0061.10.198335
MA0063.10
MA0066.11.47685
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.9963
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.11.59899
MA0144.10.254954
MA0145.10.581146
MA0146.11.54462
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.996317
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.0015479
MA0102.21.51913
MA0258.11.27333
MA0259.10.289405
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
GATA2#262435.462113600094570.01328368362592780.0469789250011268
NFYA#480037.896677442784510.004740525698894690.0223297746467104
NFYB#480137.182768537229910.00619473990889960.0273758067678909
PBX3#5090515.65322334767443.84090498614029e-060.00012547396804739
SP1#666754.070272412957780.002549206128991580.0141127240342302
TAF7#687958.166478146374229.23676943912675e-050.00134337691610216



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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