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Coexpression cluster:C1314: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,1.01544,1.06849,0.889639,0.336106,0.236034,0.127969,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.585619,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.323162,1.01199,0.0393783,0.468392,0.66382,0.542147,0.0909286,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,1.35522,0.861462,0.684675,0.826413,1.24834,3.5342,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,1.65925,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,1.66144,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,1.40818,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.308967,1.07915,0.258882,1.59875,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,1.94435,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.0799681,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.262822,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;2.69832,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;1.41984,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;2.56931,MA0072.1;1.00572,MA0073.1;0.0569999,MA0074.1;1.58758,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;1.29635,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;2.74425,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.830067,MA0106.1;0.70837,MA0107.1;0.857383,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;2.32368,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;1.22729,MA0035.2;0.621793,MA0039.2;0.35955,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;1.18263,MA0150.1;0.484557,MA0151.1;0,MA0152.1;1.52275,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.978497,MA0163.1;0.273773,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.476723,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:51, 22 January 2013


Full id: C1314_bile_lung_hepatoma_Hepatocyte_Mast_choriocarcinoma_giant



Phase1 CAGE Peaks

Hg19::chr10:5138470..5138477,+p@chr10:5138470..5138477
+
Hg19::chr10:5138548..5138561,+p@chr10:5138548..5138561
+
Hg19::chr2:209118767..209118804,-p6@IDH1
Hg19::chr2:209118811..209118822,-p12@IDH1
Hg19::chr2:209118837..209118850,-p9@IDH1
Hg19::chr5:133945416..133945452,-p@chr5:133945416..133945452
-


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>

Cell Type
Ontology termp-valuen
metabolising cell2.14e-0912
endopolyploid cell2.14e-0912
parenchymal cell2.14e-0912
polyploid cell2.14e-0912
hepatocyte2.14e-0912
epithelial cell2.64e-07253
endodermal cell6.47e-0758
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract6.00e-10118
endoderm-derived structure9.24e-10160
endoderm9.24e-10160
presumptive endoderm9.24e-10160
digestive system5.63e-09145
digestive tract5.63e-09145
primitive gut5.63e-09145
larynx1.52e-089
epithelium of foregut-midgut junction3.34e-0725
anatomical boundary3.34e-0725
hepatobiliary system3.34e-0725
foregut-midgut junction3.34e-0725
septum transversum3.34e-0725
hepatic diverticulum3.96e-0722
liver primordium3.96e-0722
liver8.16e-0719
digestive gland8.16e-0719
liver bud8.16e-0719
Disease
Ontology termp-valuen
carcinoma1.15e-13106
cancer5.98e-12235
disease of cellular proliferation2.19e-11239
cell type cancer2.64e-11143


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.12.69832
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.11.41984
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.12.56931
MA0072.11.00572
MA0073.10.0569999
MA0074.11.58758
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.12.74425
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.12.32368
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.21.22729
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.21.18263
MA0150.10.484557
MA0151.10
MA0152.11.52275
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.978497
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.476723
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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
ESRRA#21013241.9201570680631.74384396582811e-079.57043194677468e-06
FOSL2#235538.465100302280850.003598315634615090.0182190568945346
FOXA1#316947.387613166256970.0008562625545346090.00644566851182356
FOXA2#3170416.42030916844353.8126130114368e-050.000719135796101585
GATA1#262336.780154071900220.006765763983348560.0287438321058024
GTF2F1#296236.369830438378830.008068208196303160.0319119710590307
HNF4A#3172311.56614518147680.001463487150085730.00937585170333725
HNF4G#3174314.37671126322340.0007769772937197380.00608935401311689
NANOG#79923314.62238924050630.000739456292883380.00582545642094345
NR3C1#290837.486511665586520.00510866965984070.0237563716373883
RXRA#6256310.03730856956660.002205419116789220.012704454889043
SMC3#912637.522466422466420.005039540716828550.0234788148692893
SRF#672236.89858913108390.00644245168930370.0279978034278957
TCF12#693835.317232451093210.013367345733860.0472380124889559
TCF7L2#693435.385088281568670.01290488779931040.0463981539821046
TFAP2A#702038.259317186522480.003860738477055590.0190427725420425
TFAP2C#702235.404614304930110.01277576166695870.0460591588503402
ZNF143#770236.750438276113950.006850259204468580.0290343014104742



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:C1314&oldid=2569825"