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Coexpression cluster:C479: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.111472,0.217429,0.107302,0.19904,1.50281,0.574869,0.253108,0.324098,0.31878,0.00692657,0.524908,0.286323,0.442397,0.684702,2.6776,0.319274,0.43322,0.0591229,0.256938,0.176245,1.16734,0.176757,0.192508,0.589118,0.134089,0.304148,1.29742,0.558352,0.0865304,0.33292,0.162709,0.465029,0.393386,0.0955518,0.0681935,0.0638435,0.0667305,0.1987,0.453893,0.282055,0.0675531,0.152186,0.210363,0.283867,0.151936,0.125045,0.253928,0.169954,0.186425,0.0865963,0.315441,0.262847,0.63074,0.532773,0.671855,0.246686,0.298409,0.222594,0.0630426,0.221865,0.500944,0.255713,0.319823,0.409576,0.269358,1.75788,0.754286,1.10771,0.456006,0.950487,0.143869,0.144782,0.105378,0.670004,0.020227,0.390082,0.351133,0.395294,1.14905,0.130356,0.266362,0.408665,0.269087,0.0355014,0.622646,0.000236156,0.00447196,0.0123399,0.336397,1.20481,0.84263,0.598,1.20603,0.409701,0.288936,0.0539379,0.25404,0.517267,0.340143,0.0485661,0.794596,0.474756,0.512318,0.436368,0.371019,0.174162,0.422802,0.67874,0.133935,0.0770225,0.364924,0.509866,0.104228,0.183573,0.797061,0.23451,0.00333426,0.487455,0.986905,3.29611,0.662347,0.889041,0.195973,0.277756,0.90249,0.395934,0.248345,0.484077,0.701879,0.200186,2.48335,0.164582,0.715286,0.275188,0.854902,0.0111458,0.932181,0.191402,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,0.372477,0.216494,4.50825,1.49614,0.457994,0.178999,0.030735,0.0117055,0.598976,0.127482,0.255347,0.980005,0.864245,0.0779979,0.134125,0.116987,0.77808,0.582159,6.39744,0.118854,0.385896,0.740042,0.375051,0.252107,0.0689247
|tfbs_overrepresentation_jaspar=MA0003.1;0.00299983,MA0004.1;0.180726,MA0006.1;0.0840255,MA0007.1;0.168078,MA0009.1;0.561062,MA0014.1;0.00173807,MA0017.1;0.105116,MA0019.1;0.290278,MA0024.1;0.467291,MA0025.1;0.684106,MA0027.1;2.13512,MA0028.1;0.638033,MA0029.1;0.484339,MA0030.1;1.19426,MA0031.1;1.0728,MA0038.1;1.30951,MA0040.1;0.489524,MA0041.1;0.193578,MA0042.1;0.171628,MA0043.1;0.561349,MA0046.1;0.551181,MA0048.1;0.238801,MA0050.1;0.987319,MA0051.1;0.702073,MA0052.1;0.492957,MA0055.1;0.0875859,MA0056.1;0,MA0057.1;0.00684412,MA0058.1;0.119655,MA0059.1;0.118893,MA0060.1;0.319572,MA0061.1;0.107862,MA0063.1;0,MA0066.1;3.70517,MA0067.1;0.858361,MA0068.1;0.0158377,MA0069.1;0.547689,MA0070.1;0.537571,MA0071.1;0.22617,MA0072.1;0.533514,MA0073.1;2.88277e-06,MA0074.1;0.251422,MA0076.1;1.30941,MA0077.1;0.526569,MA0078.1;0.879874,MA0081.1;0.37884,MA0083.1;1.39355,MA0084.1;1.03923,MA0087.1;1.3161,MA0088.1;0.044646,MA0089.1;0,MA0090.1;0.427877,MA0091.1;2.31487,MA0092.1;0.475738,MA0093.1;0.0855877,MA0095.1;0,MA0098.1;0,MA0100.1;0.265855,MA0101.1;0.0872967,MA0103.1;0.27232,MA0105.1;0.0885831,MA0106.1;0.28721,MA0107.1;0.0527035,MA0108.2;0.415325,MA0109.1;0,MA0111.1;0.146643,MA0113.1;0.300221,MA0114.1;0.188951,MA0115.1;0.785493,MA0116.1;0.0541555,MA0117.1;0.595385,MA0119.1;2.35009,MA0122.1;0.619196,MA0124.1;0.746208,MA0125.1;0.667416,MA0130.1;0,MA0131.1;0.345226,MA0132.1;0,MA0133.1;0,MA0135.1;0.588754,MA0136.1;0.260607,MA0139.1;0.0220308,MA0140.1;0.224213,MA0141.1;0.117869,MA0142.1;0.39079,MA0143.1;0.300362,MA0144.1;1.06523,MA0145.1;0.605965,MA0146.1;0.000192711,MA0147.1;0.0556388,MA0148.1;0.198049,MA0149.1;0.21714,MA0062.2;1.11552,MA0035.2;1.85524,MA0039.2;3.52038e-06,MA0138.2;0.331323,MA0002.2;0.860866,MA0137.2;1.08925,MA0104.2;0.0336072,MA0047.2;0.761085,MA0112.2;1.73594,MA0065.2;0.252091,MA0150.1;0.828845,MA0151.1;0,MA0152.1;0.648673,MA0153.1;0.65174,MA0154.1;0.0854112,MA0155.1;0.345204,MA0156.1;2.20964,MA0157.1;0.962803,MA0158.1;0,MA0159.1;0.785302,MA0160.1;0.601097,MA0161.1;0,MA0162.1;0.000114726,MA0163.1;3.74282e-05,MA0164.1;0.310173,MA0080.2;0.605142,MA0018.2;0.288301,MA0099.2;3.4869,MA0079.2;4.84373e-06,MA0102.2;1.07547,MA0258.1;1.44838,MA0259.1;0.0592752,MA0442.1;0
}}
}}

Revision as of 19:12, 22 January 2013


Full id: C479_pleomorphic_mesothelioma_cholangiocellular_melanoma_Saos2_serous_glioblastoma



Phase1 CAGE Peaks

Hg19::chr11:66800552..66800553,+p@chr11:66800552..66800553
+
Hg19::chr1:224716846..224716914,+p4@CNIH3
Hg19::chr1:224716919..224716927,+p31@CNIH3
Hg19::chr1:224716955..224716961,+p30@CNIH3
Hg19::chr1:224716964..224716967,+p33@CNIH3
Hg19::chr20:44410265..44410286,-p@chr20:44410265..44410286
-
Hg19::chr2:147702122..147702148,-p@chr2:147702122..147702148
-
Hg19::chr2:147744107..147744108,-p@chr2:147744107..147744108
-
Hg19::chr2:154449717..154449762,-p3@ENST00000424322
Hg19::chr2:231825896..231825916,-p5@GPR55
Hg19::chr3:106393655..106393659,+p@chr3:106393655..106393659
+
Hg19::chr3:168808463..168808491,-p@chr3:168808463..168808491
-
Hg19::chr4:57931763..57931773,-p3@ENST00000512512
Hg19::chr4:57931786..57931797,-p2@ENST00000512512
Hg19::chr4:57931805..57931824,-p1@ENST00000512512
Hg19::chr6:55911444..55911446,-p@chr6:55911444..55911446
-
Hg19::chr6:56803369..56803378,-p@chr6:56803369..56803378
-
Hg19::chr6:56803379..56803390,-p@chr6:56803379..56803390
-
Hg19::chr6:56803460..56803471,-p@chr6:56803460..56803471
-
Hg19::chrX:31582142..31582159,+p@chrX:31582142..31582159
+


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
intralobular bile duct9.91e-411
acinus9.91e-411
intrahepatic bile duct9.91e-411
portal lobule9.91e-411
hepatic acinus9.91e-411
liver parenchyma1.40e-143
liver lobule1.40e-143
hepatic duct1.40e-143
liver1.99e-0919
digestive gland1.99e-0919
liver bud1.99e-0919
hepatic diverticulum2.82e-0822
liver primordium2.82e-0822
digestive tract diverticulum5.87e-0823
bile duct5.92e-086
digestive system duct5.92e-086
epithelial sac2.14e-0725
epithelium of foregut-midgut junction2.14e-0725
anatomical boundary2.14e-0725
hepatobiliary system2.14e-0725
foregut-midgut junction2.14e-0725
septum transversum2.14e-0725
sac3.78e-0726
Disease
Ontology termp-valuen
pleomorphic carcinoma6.62e-411
nervous system cancer3.31e-3011


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)
MA0003.10.00299983
MA0004.10.180726
MA0006.10.0840255
MA0007.10.168078
MA0009.10.561062
MA0014.10.00173807
MA0017.10.105116
MA0019.10.290278
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.638033
MA0029.10.484339
MA0030.11.19426
MA0031.11.0728
MA0038.11.30951
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.10.238801
MA0050.10.987319
MA0051.10.702073
MA0052.10.492957
MA0055.10.0875859
MA0056.10
MA0057.10.00684412
MA0058.10.119655
MA0059.10.118893
MA0060.10.319572
MA0061.10.107862
MA0063.10
MA0066.13.70517
MA0067.10.858361
MA0068.10.0158377
MA0069.10.547689
MA0070.10.537571
MA0071.10.22617
MA0072.10.533514
MA0073.12.88277e-06
MA0074.10.251422
MA0076.11.30941
MA0077.10.526569
MA0078.10.879874
MA0081.10.37884
MA0083.11.39355
MA0084.11.03923
MA0087.11.3161
MA0088.10.044646
MA0089.10
MA0090.10.427877
MA0091.12.31487
MA0092.10.475738
MA0093.10.0855877
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.10.0872967
MA0103.10.27232
MA0105.10.0885831
MA0106.10.28721
MA0107.10.0527035
MA0108.20.415325
MA0109.10
MA0111.10.146643
MA0113.10.300221
MA0114.10.188951
MA0115.10.785493
MA0116.10.0541555
MA0117.10.595385
MA0119.12.35009
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.0220308
MA0140.10.224213
MA0141.10.117869
MA0142.10.39079
MA0143.10.300362
MA0144.11.06523
MA0145.10.605965
MA0146.10.000192711
MA0147.10.0556388
MA0148.10.198049
MA0149.10.21714
MA0062.21.11552
MA0035.21.85524
MA0039.23.52038e-06
MA0138.20.331323
MA0002.20.860866
MA0137.21.08925
MA0104.20.0336072
MA0047.20.761085
MA0112.21.73594
MA0065.20.252091
MA0150.10.828845
MA0151.10
MA0152.10.648673
MA0153.10.65174
MA0154.10.0854112
MA0155.10.345204
MA0156.12.20964
MA0157.10.962803
MA0158.10
MA0159.10.785302
MA0160.10.601097
MA0161.10
MA0162.10.000114726
MA0163.13.74282e-05
MA0164.10.310173
MA0080.20.605142
MA0018.20.288301
MA0099.23.4869
MA0079.24.84373e-06
MA0102.21.07547
MA0258.11.44838
MA0259.10.0592752
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
FOS#235394.049079889002480.0001371204655711730.00179233095166304
FOSL1#806147.94271594327460.001408108119696510.00915699899831778
GATA2#262495.73521928009938.47144559106153e-060.000230824238477661
JUN#3725106.256414596168179.23595229958234e-073.96462647848779e-05
JUNB#3726710.71372143093742.10748306822698e-067.68249298996711e-05
JUND#372782.797865576748410.004383157975996010.0207747962720693
SETDB1#986948.06400523560210.001331741662951610.00883982252046546
STAT3#677463.155839499146270.0088383415222910.0335502326262694
USF2#739274.547269084774360.0005040821561941330.00444193691450887



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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