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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:58, 17 September 2013


Full id: C216_osteosarcoma_Smooth_Mesenchymal_large_neuroectodermal_acute_CD34



Phase1 CAGE Peaks

Hg19::chr10:24754616..24754639,+p@chr10:24754616..24754639
+
Hg19::chr11:124482705..124482719,+p@chr11:124482705..124482719
+
Hg19::chr12:124298058..124298065,+p@chr12:124298058..124298065
+
Hg19::chr12:53729525..53729541,-p5@SP7
Hg19::chr12:53729546..53729565,-p4@SP7
Hg19::chr12:53730126..53730146,-p1@SP7
Hg19::chr12:91395963..91395968,-p@chr12:91395963..91395968
-
Hg19::chr12:91398742..91398768,-p1@EPYC
Hg19::chr12:91398796..91398808,-p2@EPYC
Hg19::chr14:70656111..70656132,-p6@SLC8A3
Hg19::chr14:70656139..70656147,-p9@SLC8A3
Hg19::chr16:65210813..65210818,-p3@AL110259
Hg19::chr16:69963162..69963192,+p@chr16:69963162..69963192
+
Hg19::chr16:89687120..89687166,+p3@DPEP1
Hg19::chr17:16342343..16342358,+p1@C17orf76-AS1
Hg19::chr17:16342617..16342648,+p3@C17orf76-AS1
Hg19::chr17:16948336..16948342,-p@chr17:16948336..16948342
-
Hg19::chr17:17109452..17109461,-p4@PLD6
Hg19::chr17:17109579..17109683,-p2@PLD6
Hg19::chr17:17140420..17140429,-p3@FLCN
Hg19::chr17:40998129..40998141,+p@chr17:40998129..40998141
+
Hg19::chr17:40998185..40998200,+p@chr17:40998185..40998200
+
Hg19::chr17:40998201..40998206,+p@chr17:40998201..40998206
+
Hg19::chr19:14674382..14674403,+p@chr19:14674382..14674403
+
Hg19::chr19:18543312..18543351,+p@chr19:18543312..18543351
+
Hg19::chr19:18543503..18543510,+p@chr19:18543503..18543510
+
Hg19::chr1:170242760..170242801,-p1@LOC284688
Hg19::chr1:199050098..199050109,-p@chr1:199050098..199050109
-
Hg19::chr1:40916251..40916260,+p7@ZNF643
Hg19::chr1:47501378..47501387,+p12@CYP4X1
Hg19::chr1:47501412..47501425,+p9@CYP4X1
Hg19::chr1:47501441..47501449,+p11@CYP4X1
Hg19::chr1:47501501..47501514,+p8@CYP4X1
Hg19::chr21:17340298..17340318,+p@chr21:17340298..17340318
+
Hg19::chr21:26890785..26890790,-p2@ENST00000419694
Hg19::chr21:45874953..45874970,-p@chr21:45874953..45874970
-
Hg19::chr2:53859899..53859908,-p@chr2:53859899..53859908
-
Hg19::chr3:124485247..124485272,-p@chr3:124485247..124485272
-
Hg19::chr3:144069136..144069152,+p@chr3:144069136..144069152
+
Hg19::chr3:144069187..144069198,+p@chr3:144069187..144069198
+
Hg19::chr3:178525080..178525086,+p10@KCNMB2
Hg19::chr4:108815559..108815563,+p11@SGMS2
Hg19::chr6:160023967..160023971,+p@chr6:160023967..160023971
+
Hg19::chr6:168333044..168333049,+p36@MLLT4
Hg19::chr6:168333065..168333071,+p33@MLLT4
Hg19::chr6:169126213..169126247,+p@chr6:169126213..169126247
+
Hg19::chr6:33145331..33145378,-p@chr6:33145331..33145378
-
Hg19::chr6:36733547..36733556,-p@chr6:36733547..36733556
-
Hg19::chr6:36733562..36733582,-p@chr6:36733562..36733582
-
Hg19::chr6:36733583..36733590,-p@chr6:36733583..36733590
-
Hg19::chr6:36733594..36733607,-p@chr6:36733594..36733607
-
Hg19::chr6:36737372..36737379,+p@chr6:36737372..36737379
+
Hg19::chr6:36737414..36737422,+p@chr6:36737414..36737422
+
Hg19::chr6:44447751..44447754,+p@chr6:44447751..44447754
+
Hg19::chr6:45296191..45296203,+p13@RUNX2
Hg19::chr6:45296266..45296277,+p34@RUNX2
Hg19::chr6:45296391..45296400,+p52@RUNX2
Hg19::chr6:45297658..45297701,-p@chr6:45297658..45297701
-
Hg19::chr6:45352470..45352474,+p@chr6:45352470..45352474
+
Hg19::chr8:117778736..117778808,+p1@UTP23
Hg19::chr8:120651826..120651840,-p@chr8:120651826..120651840
-
Hg19::chr8:122398817..122398818,-p@chr8:122398817..122398818
-
Hg19::chr8:122442654..122442661,-p@chr8:122442654..122442661
-
Hg19::chr8:122442669..122442674,-p@chr8:122442669..122442674
-
Hg19::chr8:122442675..122442684,-p@chr8:122442675..122442684
-
Hg19::chr8:38470503..38470508,+p@chr8:38470503..38470508
+
Hg19::chr8:52721907..52721937,-p2@PXDNL
Hg19::chr9:116398779..116398800,+p@chr9:116398779..116398800
+
Hg19::chr9:95186583..95186648,-p1@OMD


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:0001649osteoblast differentiation0.0100475295887183
GO:0001503ossification0.0272192921654796
GO:0031214biomineral formation0.0272192921654796
GO:0046849bone remodeling0.0272192921654796
GO:0048771tissue remodeling0.0272192921654796
GO:0033188sphingomyelin synthase activity0.0272192921654796
GO:0047493ceramide cholinephosphotransferase activity0.0272192921654796
GO:0006686sphingomyelin biosynthetic process0.0357190113645948
GO:0004237membrane dipeptidase activity0.0380935499990268
GO:0019228generation of action potential0.0380935499990268
GO:0005792microsome0.0384084890398877
GO:0042598vesicular fraction0.0384084890398877



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
osteoblast2.16e-5411
osteoprogenitor cell2.16e-5411
mesenchyme condensation cell2.16e-5411
single fate stem cell1.56e-3020
Uber Anatomy
Ontology termp-valuen
bone element3.31e-0882
skeletal element1.43e-0790
skeletal system6.45e-07100


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)
MA0003.10.000756242
MA0004.10.292819
MA0006.10.256826
MA0007.10.044566
MA0009.10.517127
MA0014.12.95732e-05
MA0017.10.213922
MA0019.10.14975
MA0024.10.117627
MA0025.10.259105
MA0027.11.6012
MA0028.10.0347192
MA0029.10.127243
MA0030.10.385339
MA0031.10.0915635
MA0038.10.0272934
MA0040.10.407817
MA0041.10.328436
MA0042.10.130177
MA0043.10.174193
MA0046.11.54245
MA0048.10.272343
MA0050.10.131075
MA0051.10.269382
MA0052.11.92329
MA0055.10.292178
MA0056.10
MA0057.10.331463
MA0058.10.433486
MA0059.13.21349
MA0060.10.0255608
MA0061.10.39435
MA0063.10
MA0066.10.0273846
MA0067.10.395513
MA0068.11.5865
MA0069.10.496197
MA0070.10.159116
MA0071.10.221073
MA0072.10.474249
MA0073.12.81404
MA0074.10.5001
MA0076.10.0234504
MA0077.10.463589
MA0078.10.431633
MA0081.10.0190455
MA0083.11.01248
MA0084.10.550575
MA0087.10.155228
MA0088.10.125281
MA0089.10
MA0090.10.0835855
MA0091.10.297728
MA0092.10.230604
MA0093.10.264179
MA0095.10
MA0098.10
MA0100.10.545306
MA0101.10.15613
MA0103.10.0636
MA0105.10.0501905
MA0106.10.960752
MA0107.10.0267769
MA0108.20.302419
MA0109.10
MA0111.10.364669
MA0113.10.366819
MA0114.10.112981
MA0115.10.336593
MA0116.10.126731
MA0117.10.196603
MA0119.10.816592
MA0122.10.212824
MA0124.10.305891
MA0125.11.27855
MA0130.10
MA0131.10.0584108
MA0132.10
MA0133.10
MA0135.10.192163
MA0136.10.286137
MA0139.10.01008
MA0140.10.0862468
MA0141.10.137348
MA0142.10.269716
MA0143.10.367116
MA0144.10.0920551
MA0145.10.517096
MA0146.10.23179
MA0147.11.74988
MA0148.11.59445
MA0149.10.017743
MA0062.20.00111419
MA0035.20.0192298
MA0039.20.244795
MA0138.21.1617
MA0002.23.94928
MA0137.20.183399
MA0104.20.915725
MA0047.20.917939
MA0112.20.0409959
MA0065.20.0886989
MA0150.11.72899
MA0151.10
MA0152.11.86465
MA0153.10.66414
MA0154.10.429153
MA0155.10.614755
MA0156.10.0950739
MA0157.10.240059
MA0158.10
MA0159.10.227059
MA0160.11.2806
MA0161.10
MA0162.17.61812e-05
MA0163.10.0247177
MA0164.10.17148
MA0080.20.0741679
MA0018.20.147652
MA0099.20.226802
MA0079.22.40796e-07
MA0102.20.582837
MA0258.10.350658
MA0259.10.24749
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

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