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Coexpression cluster:C786: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;4.34757,MA0004.1;0.380329,MA0006.1;0.236135,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;9.47886,MA0017.1;0.270554,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.25013,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;0.477043,MA0040.1;1.77386,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;3.17924,MA0048.1;0.830349,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.174262,MA0056.1;0,MA0057.1;0.46253,MA0058.1;0.293055,MA0059.1;0.79343,MA0060.1;0.138988,MA0061.1;1.80643,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.0911063,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;9.14535,MA0074.1;0.4723,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;0.55119,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.918839,MA0093.1;0.671378,MA0095.1;0,MA0098.1;0,MA0100.1;2.12878,MA0101.1;1.25862,MA0103.1;1.20737,MA0105.1;1.13797,MA0106.1;0.516528,MA0107.1;1.60878,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.885497,MA0113.1;0.532314,MA0114.1;0.51954,MA0115.1;1.06753,MA0116.1;0.536665,MA0117.1;0.865782,MA0119.1;0.277531,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;2.34656,MA0140.1;0.437738,MA0141.1;0.789887,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.163394,MA0145.1;0.14293,MA0146.1;0.0551603,MA0147.1;1.03863,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;5.63897,MA0138.2;0.569505,MA0002.2;0.407187,MA0137.2;0.255808,MA0104.2;1.36686,MA0047.2;0.504873,MA0112.2;2.25856,MA0065.2;0.340764,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.0494985,MA0155.1;2.72503,MA0156.1;0.257809,MA0157.1;0.612166,MA0158.1;0,MA0159.1;1.64451,MA0160.1;1.07255,MA0161.1;0,MA0162.1;2.00719,MA0163.1;3.94943,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;9.27936,MA0102.2;1.36707,MA0258.1;2.11165,MA0259.1;1.06648,MA0442.1;0
}}
}}

Revision as of 19:26, 22 January 2013


Full id: C786_liver_hepatocellular_placenta_hepatoblastoma_normal_Intestinal_Wilms



Phase1 CAGE Peaks

Hg19::chr10:72083650..72083662,-p7@LRRC20
Hg19::chr5:176514428..176514437,+p7@FGFR4
Hg19::chr8:21911054..21911086,+p9@EPB49
Hg19::chr8:21911140..21911149,+p40@EPB49
Hg19::chrX:132887732..132887744,-p9@GPC3
Hg19::chrX:133119565..133119581,-p4@GPC3
Hg19::chrX:133119584..133119595,-p5@GPC3
Hg19::chrX:133119601..133119627,-p1@GPC3
Hg19::chrX:152907882..152907906,+p2@DUSP9
Hg19::chrX:152911654..152911663,+p@chrX:152911654..152911663
+


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:0005007fibroblast growth factor receptor activity0.0390969097527538
GO:0008543fibroblast growth factor receptor signaling pathway0.0390969097527538
GO:0033549MAP kinase phosphatase activity0.0390969097527538
GO:0017017MAP kinase tyrosine/serine/threonine phosphatase activity0.0390969097527538
GO:0000188inactivation of MAPK activity0.0390969097527538
GO:0051017actin filament bundle formation0.0390969097527538
GO:0051693actin filament capping0.0390969097527538
GO:0051016barbed-end actin filament capping0.0390969097527538
GO:0030835negative regulation of actin filament depolymerization0.0390969097527538
GO:0030834regulation of actin filament depolymerization0.0390969097527538
GO:0030042actin filament depolymerization0.0390969097527538
GO:0043407negative regulation of MAP kinase activity0.0390969097527538
GO:0007015actin filament organization0.0469476316525681
GO:0008064regulation of actin polymerization and/or depolymerization0.0469476316525681
GO:0051261protein depolymerization0.0469476316525681
GO:0030832regulation of actin filament length0.0469476316525681
GO:0032535regulation of cellular component size0.0469476316525681
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0469476316525681
GO:0051129negative regulation of cellular component organization and biogenesis0.0469476316525681
GO:0051493regulation of cytoskeleton organization and biogenesis0.0469476316525681
GO:0033043regulation of organelle organization and biogenesis0.0469476316525681
GO:0006469negative regulation of protein kinase activity0.0469476316525681
GO:0033673negative regulation of kinase activity0.0469476316525681
GO:0051348negative regulation of transferase activity0.0469476316525681
GO:0008154actin polymerization and/or depolymerization0.0469476316525681
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.0469476316525681
GO:0007254JNK cascade0.0469476316525681
GO:0031098stress-activated protein kinase signaling pathway0.0473519937482128



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
embryonic stem cell1.52e-165
metabolising cell2.07e-0712
endopolyploid cell2.07e-0712
parenchymal cell2.07e-0712
polyploid cell2.07e-0712
hepatocyte2.07e-0712
Uber Anatomy
Ontology termp-valuen
liver1.51e-0919
digestive gland1.51e-0919
liver bud1.51e-0919
hepatic diverticulum3.71e-0822
liver primordium3.71e-0822
gut epithelium7.53e-0854
abdomen element8.95e-0854
abdominal segment element8.95e-0854
digestive tract diverticulum8.97e-0823
epithelial sac4.24e-0725
epithelium of foregut-midgut junction4.24e-0725
anatomical boundary4.24e-0725
hepatobiliary system4.24e-0725
foregut-midgut junction4.24e-0725
septum transversum4.24e-0725
abdominal segment of trunk8.09e-0760
abdomen8.09e-0760
sac8.42e-0726


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)
MA0003.14.34757
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.19.47886
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.11.77386
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.13.17924
MA0048.10.830349
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.174262
MA0056.10
MA0057.10.46253
MA0058.10.293055
MA0059.10.79343
MA0060.10.138988
MA0061.11.80643
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.19.14535
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.55119
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.918839
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.12.12878
MA0101.11.25862
MA0103.11.20737
MA0105.11.13797
MA0106.10.516528
MA0107.11.60878
MA0108.20.666881
MA0109.10
MA0111.10.885497
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.12.34656
MA0140.10.437738
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.14293
MA0146.10.0551603
MA0147.11.03863
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.25.63897
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.21.36686
MA0047.20.504873
MA0112.22.25856
MA0065.20.340764
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.12.72503
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.64451
MA0160.11.07255
MA0161.10
MA0162.12.00719
MA0163.13.94943
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.29.27936
MA0102.21.36707
MA0258.12.11165
MA0259.11.06648
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
FOXA1#316944.432567899754180.008915816386211960.0338209700551936
HEY1#2346283.232088834484570.0003859230867685430.00377816097291149
RXRA#625636.022385141739980.01138448209217310.0417231261264158



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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