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Coexpression cluster:C495: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0413820215904058,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.29065969745981,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C495_mesothelioma_Preadipocyte_Smooth_Multipotent_Placental_Sertoli_Adipocyte|gostat_on_coexpression_clusters=GO:0004687!myosin light chain kinase activity!0.0435818046170126!4638$GO:0005010!insulin-like growth factor receptor activity!0.0435818046170126!3480$GO:0043548!phosphoinositide 3-kinase binding!0.0435818046170126!3480$GO:0043560!insulin receptor substrate binding!0.0435818046170126!3480$GO:0030238!male sex determination!0.0435818046170126!3480$GO:0042346!positive regulation of NF-kappaB import into nucleus!0.0435818046170126!387$GO:0048009!insulin-like growth factor receptor signaling pathway!0.0435818046170126!3480$GO:0042993!positive regulation of transcription factor import into nucleus!0.0435818046170126!387$GO:0042307!positive regulation of protein import into nucleus!0.0435818046170126!387$GO:0046824!positive regulation of nucleocytoplasmic transport!0.0435818046170126!387$GO:0051222!positive regulation of protein transport!0.0435818046170126!387$GO:0042802!identical protein binding!0.0435818046170126!3480;7164$GO:0042345!regulation of NF-kappaB import into nucleus!0.0435818046170126!387$GO:0042348!NF-kappaB import into nucleus!0.0435818046170126!387$GO:0000287!magnesium ion binding!0.0465671813510537!387;4638$GO:0000086!G2/M transition of mitotic cell cycle!0.0465671813510537!7164$GO:0051262!protein tetramerization!0.0465671813510537!3480$GO:0007530!sex determination!0.0465671813510537!3480$GO:0042990!regulation of transcription factor import into nucleus!0.0465671813510537!387$GO:0042991!transcription factor import into nucleus!0.0465671813510537!387$GO:0043450!alkene biosynthetic process!0.0465671813510537!84909$GO:0019370!leukotriene biosynthetic process!0.0465671813510537!84909$GO:0042306!regulation of protein import into nucleus!0.0465671813510537!387$GO:0033157!regulation of intracellular protein transport!0.0465671813510537!387|id=C495|ontology_enrichment_celltype=CL:0000077!5.37e-22!19;CL:0000213!4.33e-08!58;CL:0000215!4.33e-08!58;CL:0000076!1.52e-07!63|ontology_enrichment_disease=|ontology_enrichment_uberon=|pathway_enrichment=0.000339245429383648;0.0429484713599698;2;116;Vascular smooth muscle contraction (KEGG):04270!1.16148822114083e-05;0.00245074014660715;3;200;Focal adhesion (KEGG):04510!0.000134337357082296;0.0212588867582733;2;73;Adherens junction (KEGG):04520!9.48585957389088e-07;0.000600454911027293;3;87;MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544!9.65003594215768e-06;0.00245074014660715;3;188;Focal Adhesion 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,0.263718,0.0757346,0.23618,0.931383,0.211841,0.490545,0.311197,0.2603,0.163791,0.128236,0.635814,0.429714,0.421435,0.268517,0.182187,0.363943,0.0952386,0.331306,0.27764,0.259872,0.551494,0.691633,0.261104,1.10065,0.236404,0.369868,0.235655,0.519357,0.270343,0.35087,0.426924,0.284296,0.397545,0.774525,1.12911,0.473932,0.971498,0.470686,1.02248,1.69907,0.689771,0.101827,0.0900341,0.38945,0.412445,1.18754,0.141103,1.24363,0.426001,1.4157,0.647925,0.642096,0.0759684,0.356951,0.0147967,0.352635,1.2264,0.863265,0.617268,0.497892,0.0547858,0.312345,0.823441,0.281646,0.535841,0.356444,0.309213,0.228095,0.492893,0.530844,0.45406,1.00701,0.547557,0.440324,0.711872,0.14483,0.0851122,0.390957,0.528368,0.365282,0.196252,0.817503,0.544005,0.0482922,0.173882,0.395564,0.451443,0.682065,0.925065,0.209033,0.795647,0.923346,0.413094,0.262802,0.502315,1.71531,0.478363,0.617901,0.176632,0.73532,0.789697,0.875585,0.169018,0.980958,0.204325,0.83506,1.67608,1.2779,0.799588,0.264127,0.532681,0.389296,0.23014,0.375295,1.51807,0.161595,0.763964,0.0369316,2.97808,0.618251,0.332338,0.743448,1.0011,0.339339,0.291183,0.145027,0.127152,0.798435,0.601304,0.470393,0.129103,1.04003,0.283401,0.4086,0.735846,0.0266587|tfbs_overrepresentation_jaspar=MA0003.1;0.000581566,MA0004.1;0.193314,MA0006.1;1.57519,MA0007.1;0.532323,MA0009.1;0.580032,MA0014.1;0.0234339,MA0017.1;0.114723,MA0019.1;0.305657,MA0024.1;0.485346,MA0025.1;0.70396,MA0027.1;2.15732,MA0028.1;0.332468,MA0029.1;0.50258,MA0030.1;1.23309,MA0031.1;0.435419,MA0038.1;0.269828,MA0040.1;0.507819,MA0041.1;0.206566,MA0042.1;0.541224,MA0043.1;0.580321,MA0046.1;0.570066,MA0048.1;0.0472517,MA0050.1;1.03704,MA0051.1;0.735579,MA0052.1;0.511289,MA0055.1;0.317307,MA0056.1;0,MA0057.1;0.122328,MA0058.1;0.12994,MA0059.1;0.129144,MA0060.1;0.350607,MA0061.1;0.290613,MA0063.1;0,MA0066.1;0.270161,MA0067.1;0.879057,MA0068.1;0.213016,MA0069.1;0.566544,MA0070.1;0.556335,MA0071.1;0.240074,MA0072.1;0.552241,MA0073.1;0.0464223,MA0074.1;0.265952,MA0076.1;0.139892,MA0077.1;0.545231,MA0078.1;0.915792,MA0081.1;0.129245,MA0083.1;0.586921,MA0084.1;1.06048,MA0087.1;0.550016,MA0088.1;0.600624,MA0089.1;0,MA0090.1;0.149167,MA0091.1;0.568335,MA0092.1;0.504823,MA0093.1;0.313082,MA0095.1;0,MA0098.1;0,MA0100.1;0.280715,MA0101.1;0.317957,MA0103.1;0.614572,MA0105.1;0.220534,MA0106.1;0.302526,MA0107.1;0.46886,MA0108.2;2.88516,MA0109.1;0,MA0111.1;0.15804,MA0113.1;0.315797,MA0114.1;0.0569149,MA0115.1;0.805883,MA0116.1;0.0607301,MA0117.1;0.614633,MA0119.1;0.119385,MA0122.1;0.638621,MA0124.1;0.766407,MA0125.1;0.687166,MA0130.1;0,MA0131.1;0.361613,MA0132.1;0,MA0133.1;0,MA0135.1;0.60795,MA0136.1;0.27535,MA0139.1;0.0257123,MA0140.1;0.238066,MA0141.1;0.128074,MA0142.1;0.407878,MA0143.1;0.315941,MA0144.1;0.422223,MA0145.1;0.0209869,MA0146.1;0.128454,MA0147.1;0.838322,MA0148.1;0.606512,MA0149.1;0.230803,MA0062.2;0.116085,MA0035.2;0.237534,MA0039.2;0.29451,MA0138.2;0.347473,MA0002.2;0.138689,MA0137.2;0.697429,MA0104.2;0.627988,MA0047.2;0.795472,MA0112.2;0.0591493,MA0065.2;0.0221473,MA0150.1;0.145358,MA0151.1;0,MA0152.1;0.681299,MA0153.1;0.67139,MA0154.1;0.214105,MA0155.1;0.0530942,MA0156.1;0.345664,MA0157.1;0.384449,MA0158.1;0,MA0159.1;0.224647,MA0160.1;0.222325,MA0161.1;0,MA0162.1;0.281783,MA0163.1;0.000591497,MA0164.1;0.870085,MA0080.2;0.31321,MA0018.2;0.30364,MA0099.2;0.681929,MA0079.2;0.00460199,MA0102.2;1.09681,MA0258.1;0.177641,MA0259.1;0.869556,MA0442.1;0}}
|full_id=C495_mesothelioma_Preadipocyte_Smooth_Multipotent_Placental_Sertoli_Adipocyte
|id=C495
}}

Latest revision as of 11:24, 17 September 2013


Full id: C495_mesothelioma_Preadipocyte_Smooth_Multipotent_Placental_Sertoli_Adipocyte



Phase1 CAGE Peaks

Hg19::chr11:29181712..29181720,+p@chr11:29181712..29181720
+
Hg19::chr11:7506866..7506875,+p8@OLFML1
Hg19::chr12:116440921..116440925,-p@chr12:116440921..116440925
-
Hg19::chr14:72053507..72053516,+p@chr14:72053507..72053516
+
Hg19::chr15:37242699..37242705,-p@chr15:37242699..37242705
-
Hg19::chr15:99191698..99191705,+p13@IGF1R
Hg19::chr17:39724493..39724502,-p@chr17:39724493..39724502
-
Hg19::chr19:39627507..39627526,+p@chr19:39627507..39627526
+
Hg19::chr1:64506368..64506373,-p@chr1:64506368..64506373
-
Hg19::chr3:123512832..123512846,-p46@MYLK
Hg19::chr3:49449521..49449532,-p2@RHOA
Hg19::chr5:167087144..167087148,-p1@ENST00000522956
Hg19::chr5:167088934..167088938,-p@chr5:167088934..167088938
-
Hg19::chr5:174774305..174774318,+p@chr5:174774305..174774318
+
Hg19::chr5:174905496..174905507,+p3@SFXN1
Hg19::chr6:125550179..125550191,+p20@TPD52L1
Hg19::chr8:117695642..117695657,-p@chr8:117695642..117695657
-
Hg19::chr8:74498117..74498133,-p@chr8:74498117..74498133
-
Hg19::chr9:97562440..97562463,+p18@C9orf3


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

p.valueFDRnGenesnPathwayName
0.0003392454293836480.04294847135996982116Vascular smooth muscle contraction (KEGG):04270
1.16148822114083e-050.002450740146607153200Focal adhesion (KEGG):04510
0.0001343373570822960.0212588867582733273Adherens junction (KEGG):04520
9.48585957389088e-070.000600454911027293387MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544
9.65003594215768e-060.002450740146607153188Focal Adhesion (Wikipathways):WP306



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:0004687myosin light chain kinase activity0.0435818046170126
GO:0005010insulin-like growth factor receptor activity0.0435818046170126
GO:0043548phosphoinositide 3-kinase binding0.0435818046170126
GO:0043560insulin receptor substrate binding0.0435818046170126
GO:0030238male sex determination0.0435818046170126
GO:0042346positive regulation of NF-kappaB import into nucleus0.0435818046170126
GO:0048009insulin-like growth factor receptor signaling pathway0.0435818046170126
GO:0042993positive regulation of transcription factor import into nucleus0.0435818046170126
GO:0042307positive regulation of protein import into nucleus0.0435818046170126
GO:0046824positive regulation of nucleocytoplasmic transport0.0435818046170126
GO:0051222positive regulation of protein transport0.0435818046170126
GO:0042802identical protein binding0.0435818046170126
GO:0042345regulation of NF-kappaB import into nucleus0.0435818046170126
GO:0042348NF-kappaB import into nucleus0.0435818046170126
GO:0000287magnesium ion binding0.0465671813510537
GO:0000086G2/M transition of mitotic cell cycle0.0465671813510537
GO:0051262protein tetramerization0.0465671813510537
GO:0007530sex determination0.0465671813510537
GO:0042990regulation of transcription factor import into nucleus0.0465671813510537
GO:0042991transcription factor import into nucleus0.0465671813510537
GO:0043450alkene biosynthetic process0.0465671813510537
GO:0019370leukotriene biosynthetic process0.0465671813510537
GO:0042306regulation of protein import into nucleus0.0465671813510537
GO:0033157regulation of intracellular protein transport0.0465671813510537



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><br><br>

Cell Type
Ontology termp-valuen
mesothelial cell5.37e-2219
lining cell4.33e-0858
barrier cell4.33e-0858
squamous epithelial cell1.52e-0763


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)
MA0003.10.000581566
MA0004.10.193314
MA0006.11.57519
MA0007.10.532323
MA0009.10.580032
MA0014.10.0234339
MA0017.10.114723
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.332468
MA0029.10.50258
MA0030.11.23309
MA0031.10.435419
MA0038.10.269828
MA0040.10.507819
MA0041.10.206566
MA0042.10.541224
MA0043.10.580321
MA0046.10.570066
MA0048.10.0472517
MA0050.11.03704
MA0051.10.735579
MA0052.10.511289
MA0055.10.317307
MA0056.10
MA0057.10.122328
MA0058.10.12994
MA0059.10.129144
MA0060.10.350607
MA0061.10.290613
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.213016
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.10.0464223
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.915792
MA0081.10.129245
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.600624
MA0089.10
MA0090.10.149167
MA0091.10.568335
MA0092.10.504823
MA0093.10.313082
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.317957
MA0103.10.614572
MA0105.10.220534
MA0106.10.302526
MA0107.10.46886
MA0108.22.88516
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.0569149
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.10.119385
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.0257123
MA0140.10.238066
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.10.422223
MA0145.10.0209869
MA0146.10.128454
MA0147.10.838322
MA0148.10.606512
MA0149.10.230803
MA0062.20.116085
MA0035.20.237534
MA0039.20.29451
MA0138.20.347473
MA0002.20.138689
MA0137.20.697429
MA0104.20.627988
MA0047.20.795472
MA0112.20.0591493
MA0065.20.0221473
MA0150.10.145358
MA0151.10
MA0152.10.681299
MA0153.10.67139
MA0154.10.214105
MA0155.10.0530942
MA0156.10.345664
MA0157.10.384449
MA0158.10
MA0159.10.224647
MA0160.10.222325
MA0161.10
MA0162.10.281783
MA0163.10.000591497
MA0164.10.870085
MA0080.20.31321
MA0018.20.30364
MA0099.20.681929
MA0079.20.00460199
MA0102.21.09681
MA0258.10.177641
MA0259.10.869556
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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