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Coexpression cluster:C441: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.313352,0.647847,0.0904779,0.521108,0.528049,0.518467,0.226953,0.502803,0.26513,0.628972,0.47055,0.258748,0.611048,0.218743,0.245083,0.276011,0.401017,0.047482,0.0824365,0.621787,0.0905079,0.23024,0.506057,0.516065,0.368471,0.275879,2.87621,0.502604,0.250879,0.464564,0.141557,0.432083,0.0360115,0.620439,0.203464,0.443344,0.199614,0.520325,0.38935,0.0212383,0.776456,0.131762,0.428928,0.891523,0.00278846,0.106689,0.227736,0.148323,0.784143,0.251047,0.286755,0.236257,0.324106,0.49846,0.635443,0.220828,0.928082,0.197918,0.714228,0.197226,0.467239,0.22944,0.266076,0.377975,0.680025,0.349807,0.716956,1.06805,0.423263,0.911622,0.391938,0.520708,0.00448968,0.633615,0.0147578,0.160109,2.75023,0.364079,1.89457,3.80038,1.01006,0.377089,0.679423,0.511606,0.586887,0.0048652,0.00282308,0.257083,0.827525,1.1648,0.804514,0.562601,1.98223,0.627248,0.529799,0.376385,0.206847,0.483243,0.310601,1.19394,1.07407,0.441596,0.47839,0.404088,1.61802,0.15226,0.39086,0.216299,0.114869,0.0632414,0.656334,0.475985,0.0876862,0.161084,0.759328,2.17372,0.619971,0.434767,0.347912,0.354423,0.626054,0.823238,0.989456,0.25053,0.863933,0.364702,0.222409,0.450719,0.66511,0.378439,0.563221,0.143305,0.678365,0.248069,0.81669,0.938534,1.36399,0.168444,0.776656,1.61314,1.21607,0.741657,2.60931,1.20704,0.905716,0.192136,0.328551,1.45545,0.406714,0.0373053,0.280985,0.00728883,0.563563,0.759334,0.229091,0.940968,0.799018,0.0641085,0.115044,0.0993076,0.740521,0.547006,0.419845,0.331484,0.934619,0.241648,0.134701,0.225998,0.0386347
|tfbs_overrepresentation_jaspar=MA0003.1;0.000369852,MA0004.1;0.158412,MA0006.1;0.0694838,MA0007.1;0.449227,MA0009.1;0.526253,MA0014.1;0.0851404,MA0017.1;0.619077,MA0019.1;1.33677,MA0024.1;0.434294,MA0025.1;0.647545,MA0027.1;2.09389,MA0028.1;0.0770177,MA0029.1;1.14427,MA0030.1;0.441064,MA0031.1;1.00334,MA0038.1;0.22896,MA0040.1;0.456051,MA0041.1;0.508527,MA0042.1;0.149889,MA0043.1;1.30597,MA0046.1;0.516541,MA0048.1;0.0852241,MA0050.1;0.150446,MA0051.1;0.22589,MA0052.1;0.459414,MA0055.1;0.631633,MA0056.1;0,MA0057.1;0.317055,MA0058.1;0.101748,MA0059.1;0.101051,MA0060.1;0.0258987,MA0061.1;0.214431,MA0063.1;0,MA0066.1;0.22927,MA0067.1;0.820123,MA0068.1;0.514926,MA0069.1;0.51311,MA0070.1;0.503171,MA0071.1;0.201311,MA0072.1;0.499187,MA0073.1;0.260075,MA0074.1;0.225345,MA0076.1;0.110503,MA0077.1;0.49237,MA0078.1;0.30111,MA0081.1;0.101139,MA0083.1;0.532971,MA0084.1;0.999884,MA0087.1;1.24309,MA0088.1;0.848393,MA0089.1;0,MA0090.1;0.759616,MA0091.1;0.160096,MA0092.1;0.837387,MA0093.1;0.0708814,MA0095.1;0,MA0098.1;0,MA0100.1;0.239133,MA0101.1;0.25283,MA0103.1;0.501795,MA0105.1;0.020431,MA0106.1;1.32584,MA0107.1;0.041912,MA0108.2;0.383574,MA0109.1;0,MA0111.1;0.794681,MA0113.1;0.272101,MA0114.1;0.643657,MA0115.1;0.747865,MA0116.1;0.166035,MA0117.1;0.560027,MA0119.1;0.308642,MA0122.1;1.42642,MA0124.1;0.70896,MA0125.1;0.631059,MA0130.1;0,MA0131.1;0.315517,MA0132.1;0,MA0133.1;0,MA0135.1;0.553498,MA0136.1;0.234116,MA0139.1;0.622109,MA0140.1;0.199454,MA0141.1;0.329072,MA0142.1;1.68532,MA0143.1;0.74864,MA0144.1;0.140794,MA0145.1;0.950558,MA0146.1;0.0152175,MA0147.1;0.0444528,MA0148.1;0.518828,MA0149.1;0.192747,MA0062.2;0.0177333,MA0035.2;1.09434,MA0039.2;0.0613069,MA0138.2;0.816468,MA0002.2;0.459473,MA0137.2;0.0801516,MA0104.2;0.0256869,MA0047.2;0.250458,MA0112.2;0.033361,MA0065.2;0.0116842,MA0150.1;0.115337,MA0151.1;0,MA0152.1;0.20405,MA0153.1;0.615584,MA0154.1;0.142088,MA0155.1;0.26573,MA0156.1;0.0812668,MA0157.1;0.337287,MA0158.1;0,MA0159.1;0.386598,MA0160.1;0.18494,MA0161.1;0,MA0162.1;0.0235931,MA0163.1;0.155274,MA0164.1;0.770204,MA0080.2;0.0709213,MA0018.2;0.260646,MA0099.2;1.1153,MA0079.2;9.0745e-05,MA0102.2;1.03595,MA0258.1;0.032189,MA0259.1;0.403807,MA0442.1;0
}}
}}

Revision as of 19:10, 22 January 2013


Full id: C441_keratoacanthoma_skin_tongue_esophagus_cervical_salivary_Sebocyte



Phase1 CAGE Peaks

Hg19::chr10:8636368..8636400,-p@chr10:8636368..8636400
-
Hg19::chr12:3600112..3600125,+p6@PRMT8
Hg19::chr14:23777595..23777607,-p@chr14:23777595..23777607
-
Hg19::chr14:23777630..23777642,-p@chr14:23777630..23777642
-
Hg19::chr14:23777647..23777667,-p@chr14:23777647..23777667
-
Hg19::chr16:55600580..55600632,+p1@CAPNS2
Hg19::chr16:55600644..55600645,+p2@CAPNS2
Hg19::chr16:80586313..80586337,-p@chr16:80586313..80586337
-
Hg19::chr17:39672442..39672463,+p@chr17:39672442..39672463
+
Hg19::chr17:39674844..39674854,+p@chr17:39674844..39674854
+
Hg19::chr17:40324009..40324020,-p@chr17:40324009..40324020
-
Hg19::chr1:151826134..151826143,-p2@THEM5
Hg19::chr1:151826151..151826159,-p3@THEM5
Hg19::chr1:151826179..151826192,-p1@THEM5
Hg19::chr1:152572708..152572714,+p1@LCE3C
Hg19::chr1:236247199..236247215,-p@chr1:236247199..236247215
-
Hg19::chr20:10727793..10727802,+p@chr20:10727793..10727802
+
Hg19::chr9:97563025..97563035,+p@chr9:97563025..97563035
+
Hg19::chr9:97563078..97563086,+p@chr9:97563078..97563086
+
Hg19::chr9:97563106..97563117,+p@chr9:97563106..97563117
+
Hg19::chrX:69643154..69643183,+p1@GDPD2
Hg19::chrX:69643186..69643195,+p4@GDPD2


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:0035247peptidyl-arginine omega-N-methylation0.00691705418196945
GO:0019919peptidyl-arginine methylation, to asymmetrical-dimethyl arginine0.00691705418196945
GO:0035246peptidyl-arginine N-methylation0.00691705418196945
GO:0035241protein-arginine omega-N monomethyltransferase activity0.00691705418196945
GO:0018216peptidyl-arginine methylation0.00829997633890119
GO:0008469histone-arginine N-methyltransferase activity0.0103731380914246
GO:0016274protein-arginine N-methyltransferase activity0.0103731380914246
GO:0016273arginine N-methyltransferase activity0.0103731380914246
GO:0018195peptidyl-arginine modification0.0124455672994332
GO:0016571histone methylation0.0124455672994332
GO:0008889glycerophosphodiester phosphodiesterase activity0.0149772478673127
GO:0043393regulation of protein binding0.0149772478673127
GO:0008213protein amino acid alkylation0.0207279625682647
GO:0006479protein amino acid methylation0.0207279625682647
GO:0051098regulation of binding0.0257841692883749
GO:0042054histone methyltransferase activity0.0275901361221504
GO:0031424keratinization0.0275901361221504
GO:0006071glycerol metabolic process0.0275901361221504
GO:0019751polyol metabolic process0.0275901361221504
GO:0043414biopolymer methylation0.0275901361221504
GO:0016570histone modification0.0275901361221504
GO:0008276protein methyltransferase activity0.0275901361221504
GO:0009913epidermal cell differentiation0.0275901361221504
GO:0008170N-methyltransferase activity0.0275901361221504
GO:0016569covalent chromatin modification0.0275901361221504
GO:0048730epidermis morphogenesis0.0291732855349702
GO:0032259methylation0.0354271151573729
GO:0048729tissue morphogenesis0.0354271151573729
GO:0005886plasma membrane0.038525270902211
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0394621325759638
GO:0046982protein heterodimerization activity0.0465741722799623



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
surface2.32e-131
mammalian vulva2.62e-131
external female genitalia2.62e-131
tonsil4.23e-131
mucosa-associated lymphoid tissue4.23e-131
lymphoid tissue4.23e-131
tonsillar ring4.23e-131
zone of skin4.78e-134
surface structure6.17e-1399
orifice2.11e-1136
mouth4.01e-1029
stomodeum4.01e-1029
oral opening6.90e-0922
uterine cervix8.24e-096
neck of organ8.24e-096
skin epidermis1.14e-0715
outer epithelium1.14e-0715
enveloping layer of ectoderm1.14e-0715
open tracheal system trachea4.98e-072
Disease
Ontology termp-valuen
skin squamous cell carcinoma1.61e-131
keratoacanthoma1.61e-131
skin carcinoma2.15e-072
skin cancer2.15e-072
integumentary system cancer2.15e-072


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)
MA0003.10.000369852
MA0004.10.158412
MA0006.10.0694838
MA0007.10.449227
MA0009.10.526253
MA0014.10.0851404
MA0017.10.619077
MA0019.11.33677
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.0770177
MA0029.11.14427
MA0030.10.441064
MA0031.11.00334
MA0038.10.22896
MA0040.10.456051
MA0041.10.508527
MA0042.10.149889
MA0043.11.30597
MA0046.10.516541
MA0048.10.0852241
MA0050.10.150446
MA0051.10.22589
MA0052.10.459414
MA0055.10.631633
MA0056.10
MA0057.10.317055
MA0058.10.101748
MA0059.10.101051
MA0060.10.0258987
MA0061.10.214431
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.514926
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.10.260075
MA0074.10.225345
MA0076.10.110503
MA0077.10.49237
MA0078.10.30111
MA0081.10.101139
MA0083.10.532971
MA0084.10.999884
MA0087.11.24309
MA0088.10.848393
MA0089.10
MA0090.10.759616
MA0091.10.160096
MA0092.10.837387
MA0093.10.0708814
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.25283
MA0103.10.501795
MA0105.10.020431
MA0106.11.32584
MA0107.10.041912
MA0108.20.383574
MA0109.10
MA0111.10.794681
MA0113.10.272101
MA0114.10.643657
MA0115.10.747865
MA0116.10.166035
MA0117.10.560027
MA0119.10.308642
MA0122.11.42642
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.234116
MA0139.10.622109
MA0140.10.199454
MA0141.10.329072
MA0142.11.68532
MA0143.10.74864
MA0144.10.140794
MA0145.10.950558
MA0146.10.0152175
MA0147.10.0444528
MA0148.10.518828
MA0149.10.192747
MA0062.20.0177333
MA0035.21.09434
MA0039.20.0613069
MA0138.20.816468
MA0002.20.459473
MA0137.20.0801516
MA0104.20.0256869
MA0047.20.250458
MA0112.20.033361
MA0065.20.0116842
MA0150.10.115337
MA0151.10
MA0152.10.20405
MA0153.10.615584
MA0154.10.142088
MA0155.10.26573
MA0156.10.0812668
MA0157.10.337287
MA0158.10
MA0159.10.386598
MA0160.10.18494
MA0161.10
MA0162.10.0235931
MA0163.10.155274
MA0164.10.770204
MA0080.20.0709213
MA0018.20.260646
MA0099.21.1153
MA0079.29.0745e-05
MA0102.21.03595
MA0258.10.032189
MA0259.10.403807
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
SMC3#912653.419302919302920.01314679266670590.0466131816715812



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C441&oldid=2568952"