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Coexpression cluster:C414: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0737355,0.0218471,0.0704497,2.73427,2.75286,0.446495,0.193858,1.34275,0.0173141,0.00181707,0.127781,0.223608,0.00986189,0.18622,0.75795,0.222896,0.359143,0.137813,0.310345,0.173055,0.528893,0.0794402,0.14085,1.14313,0.0918928,0.239737,0.230183,0.139567,0.200446,0.351258,0.115556,0.389116,0.260815,0.139529,0.158665,0.0722915,0.356842,0.448243,0.131632,0.0139095,0.64612,0.346812,0.0999099,0.193557,0.644463,0.0845678,0.194588,0.38574,0.266098,0.0544697,0.250009,0.202536,0.121746,0.453481,0.587358,0.188158,0.452131,0.166937,0.089928,0.166299,0.423157,0.196176,0.0791041,0.336984,0.208359,0.834297,0.667509,1.01514,0.991173,0.859886,0.0999006,0.41347,0.572194,0.585564,0.046819,0.0398214,0.587161,0.323653,0.37794,1.03959,0.322532,0.336133,0.208117,0.210347,0.539768,0.00700751,0.0847843,0.185475,0.741627,1.11136,0.753896,0.516018,1.04021,0.113524,0.437541,0.29887,0.791347,0.438691,0.749501,0.00368621,1.74987,0.398316,1.10755,0.362101,0.301097,0.125207,0.349366,0.18395,0.306554,0.0472968,0.075464,0.431643,0.240351,0.133204,0.70928,0.353647,0.0299643,0.1149,0.830218,0.279389,0.578146,0.267369,0.442338,1.16038,0.812657,1.5605,0.555018,0.407146,0.616494,0.552006,0.516623,0.373998,0.629526,0.612237,0.765929,0.171747,0.112299,0.432429,0.726382,1.55835,1.16239,0.691851,0.190777,0.43571,0.302448,0.161608,0.289694,1.40098,0.105021,0.26801,0.0121652,0.0143922,0.516957,0.0157334,0.569975,0.888975,0.714117,1.10353,0.635627,0.0781127,0.690731,0.500787,0.377296,0.079602,1.52719,0.207576,0.0231383,0.563058,0.00300171
|tfbs_overrepresentation_jaspar=MA0003.1;5.08933e-08,MA0004.1;0.130779,MA0006.1;0.194765,MA0007.1;0.120068,MA0009.1;0.480543,MA0014.1;0.000238896,MA0017.1;0.0687354,MA0019.1;0.227177,MA0024.1;0.391254,MA0025.1;0.599238,MA0027.1;2.03861,MA0028.1;1.23143,MA0029.1;1.0498,MA0030.1;0.397801,MA0031.1;1.63324,MA0038.1;0.569682,MA0040.1;0.412311,MA0041.1;0.437147,MA0042.1;0.778983,MA0043.1;0.480818,MA0046.1;0.47108,MA0048.1;0.402406,MA0050.1;0.781212,MA0051.1;1.07026,MA0052.1;0.41557,MA0055.1;0.121215,MA0056.1;0,MA0057.1;0.118248,MA0058.1;0.0802423,MA0059.1;0.0796335,MA0060.1;0.645628,MA0061.1;0.536938,MA0063.1;0,MA0066.1;0.196017,MA0067.1;0.769322,MA0068.1;0.105313,MA0069.1;0.467738,MA0070.1;0.458064,MA0071.1;0.50749,MA0072.1;0.454189,MA0073.1;3.93678e-11,MA0074.1;0.561594,MA0076.1;2.10067,MA0077.1;0.44756,MA0078.1;0.263604,MA0081.1;0.07971,MA0083.1;1.22186,MA0084.1;0.947429,MA0087.1;0.452083,MA0088.1;0.0164834,MA0089.1;0,MA0090.1;0.315775,MA0091.1;0.413133,MA0092.1;2.36527,MA0093.1;0.198309,MA0095.1;0,MA0098.1;0,MA0100.1;0.205224,MA0101.1;1.18678,MA0103.1;0.049017,MA0105.1;0.0974258,MA0106.1;1.85907,MA0107.1;0.85764,MA0108.2;0.342362,MA0109.1;0,MA0111.1;0.102187,MA0113.1;0.236174,MA0114.1;0.0284198,MA0115.1;0.697973,MA0116.1;0.126338,MA0117.1;0.513502,MA0119.1;0.25231,MA0122.1;0.53644,MA0124.1;0.659634,MA0125.1;0.583056,MA0130.1;0,MA0131.1;0.277285,MA0132.1;0,MA0133.1;0,MA0135.1;0.507125,MA0136.1;0.200538,MA0139.1;0.0510937,MA0140.1;0.503284,MA0141.1;0.0788154,MA0142.1;0.319458,MA0143.1;0.236302,MA0144.1;0.48115,MA0145.1;0.963103,MA0146.1;0.0058386,MA0147.1;0.129769,MA0148.1;0.446835,MA0149.1;0.162171,MA0062.2;0.516277,MA0035.2;0.50217,MA0039.2;3.44083e-05,MA0138.2;0.264522,MA0002.2;0.896123,MA0137.2;0.481909,MA0104.2;0.0784157,MA0047.2;1.16012,MA0112.2;0.0502653,MA0065.2;0.126603,MA0150.1;0.636869,MA0151.1;0,MA0152.1;0.513688,MA0153.1;0.567879,MA0154.1;0.0935732,MA0155.1;0.000517058,MA0156.1;0.840015,MA0157.1;1.46654,MA0158.1;0,MA0159.1;0.0320844,MA0160.1;0.470272,MA0161.1;0,MA0162.1;0.000165262,MA0163.1;0.00408849,MA0164.1;0.245213,MA0080.2;0.438824,MA0018.2;0.225392,MA0099.2;0.514256,MA0079.2;8.29828e-12,MA0102.2;0.983247,MA0258.1;0.239173,MA0259.1;0.138164,MA0442.1;0
}}
}}

Revision as of 19:09, 22 January 2013


Full id: C414_cholangiocellular_testis_gall_pagetoid_mesothelioma_thyroid_osteoclastoma



Phase1 CAGE Peaks

Hg19::chr11:73874637..73874639,+p@chr11:73874637..73874639
+
Hg19::chr11:77795673..77795689,-p@chr11:77795673..77795689
-
Hg19::chr13:88008760..88008795,+p@chr13:88008760..88008795
+
Hg19::chr13:98605781..98605792,+p34@IPO5
Hg19::chr15:32969649..32969656,+p14@SCG5
Hg19::chr15:32976526..32976537,+p7@SCG5
Hg19::chr18:1099004..1099011,+p@chr18:1099004..1099011
+
Hg19::chr18:514455..514467,+p@chr18:514455..514467
+
Hg19::chr1:207059144..207059147,+p@chr1:207059144..207059147
+
Hg19::chr21:45826350..45826387,+p22@TRPM2
Hg19::chr2:158155402..158155409,-p3@ENST00000410472
Hg19::chr2:158155450..158155474,-p1@ENST00000410472
Hg19::chr2:234545393..234545403,+p3@UGT1A10
Hg19::chr2:234545407..234545408,+p9@UGT1A10
Hg19::chr2:234545437..234545446,+p4@UGT1A10
Hg19::chr2:234545708..234545716,+p5@UGT1A10
Hg19::chr3:98275000..98275016,-p@chr3:98275000..98275016
-
Hg19::chr4:166513744..166513789,+p@chr4:166513744..166513789
+
Hg19::chr4:166513830..166513834,+p@chr4:166513830..166513834
+
Hg19::chr4:33469231..33469240,+p@chr4:33469231..33469240
+
Hg19::chr5:52786654..52786665,-p@chr5:52786654..52786665
-
Hg19::chr6:32522809..32522827,-p@chr6:32522809..32522827
-
Hg19::chr6:32522832..32522842,-p@chr6:32522832..32522842
-
Hg19::chr6:32549685..32549701,-p13@HLA-DRB1
Hg19::chr7:91788143..91788146,-p@chr7:91788143..91788146
-


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:0047631ADP-ribose diphosphatase activity0.029669747316823
GO:0016486peptide hormone processing0.0346106294482937



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
metabolising cell6.76e-1812
endopolyploid cell6.76e-1812
parenchymal cell6.76e-1812
polyploid cell6.76e-1812
hepatocyte6.76e-1812
Uber Anatomy
Ontology termp-valuen
intralobular bile duct5.42e-1951
acinus5.42e-1951
intrahepatic bile duct5.42e-1951
portal lobule5.42e-1951
hepatic acinus5.42e-1951
liver parenchyma2.39e-663
liver lobule2.39e-663
hepatic duct2.39e-663
bile duct4.27e-346
digestive system duct4.27e-346
biliary system2.62e-239
biliary tree2.62e-239
biliary bud2.62e-239
parenchyma1.22e-1415
liver6.95e-1219
duct6.95e-1219
digestive gland6.95e-1219
liver bud6.95e-1219
hepatic diverticulum1.80e-1022
liver primordium1.80e-1022
digestive tract diverticulum4.42e-1023
epithelial sac2.15e-0925
epithelium of foregut-midgut junction2.15e-0925
anatomical boundary2.15e-0925
hepatobiliary system2.15e-0925
foregut-midgut junction2.15e-0925
septum transversum2.15e-0925
sac4.34e-0926
exocrine gland7.41e-0831
exocrine system7.41e-0831
endocrine gland4.03e-0735


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)
MA0003.15.08933e-08
MA0004.10.130779
MA0006.10.194765
MA0007.10.120068
MA0009.10.480543
MA0014.10.000238896
MA0017.10.0687354
MA0019.10.227177
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.11.23143
MA0029.11.0498
MA0030.10.397801
MA0031.11.63324
MA0038.10.569682
MA0040.10.412311
MA0041.10.437147
MA0042.10.778983
MA0043.10.480818
MA0046.10.47108
MA0048.10.402406
MA0050.10.781212
MA0051.11.07026
MA0052.10.41557
MA0055.10.121215
MA0056.10
MA0057.10.118248
MA0058.10.0802423
MA0059.10.0796335
MA0060.10.645628
MA0061.10.536938
MA0063.10
MA0066.10.196017
MA0067.10.769322
MA0068.10.105313
MA0069.10.467738
MA0070.10.458064
MA0071.10.50749
MA0072.10.454189
MA0073.13.93678e-11
MA0074.10.561594
MA0076.12.10067
MA0077.10.44756
MA0078.10.263604
MA0081.10.07971
MA0083.11.22186
MA0084.10.947429
MA0087.10.452083
MA0088.10.0164834
MA0089.10
MA0090.10.315775
MA0091.10.413133
MA0092.12.36527
MA0093.10.198309
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.11.18678
MA0103.10.049017
MA0105.10.0974258
MA0106.11.85907
MA0107.10.85764
MA0108.20.342362
MA0109.10
MA0111.10.102187
MA0113.10.236174
MA0114.10.0284198
MA0115.10.697973
MA0116.10.126338
MA0117.10.513502
MA0119.10.25231
MA0122.10.53644
MA0124.10.659634
MA0125.10.583056
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.200538
MA0139.10.0510937
MA0140.10.503284
MA0141.10.0788154
MA0142.10.319458
MA0143.10.236302
MA0144.10.48115
MA0145.10.963103
MA0146.10.0058386
MA0147.10.129769
MA0148.10.446835
MA0149.10.162171
MA0062.20.516277
MA0035.20.50217
MA0039.23.44083e-05
MA0138.20.264522
MA0002.20.896123
MA0137.20.481909
MA0104.20.0784157
MA0047.21.16012
MA0112.20.0502653
MA0065.20.126603
MA0150.10.636869
MA0151.10
MA0152.10.513688
MA0153.10.567879
MA0154.10.0935732
MA0155.10.000517058
MA0156.10.840015
MA0157.11.46654
MA0158.10
MA0159.10.0320844
MA0160.10.470272
MA0161.10
MA0162.10.000165262
MA0163.10.00408849
MA0164.10.245213
MA0080.20.438824
MA0018.20.225392
MA0099.20.514256
MA0079.28.29828e-12
MA0102.20.983247
MA0258.10.239173
MA0259.10.138164
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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