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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:12, 17 September 2013


Full id: C277_mesothelioma_epithelioid_thyroid_extraskeletal_alveolar_glioblastoma_adenocarcinoma



Phase1 CAGE Peaks

Hg19::chr11:28792916..28792929,+p@chr11:28792916..28792929
+
Hg19::chr14:36642956..36642966,+p@chr14:36642956..36642966
+
Hg19::chr14:36642986..36642989,+p@chr14:36642986..36642989
+
Hg19::chr14:36643089..36643094,+p@chr14:36643089..36643094
+
Hg19::chr19:21452679..21452684,-p@chr19:21452679..21452684
-
Hg19::chr19:21452690..21452695,-p@chr19:21452690..21452695
-
Hg19::chr19:21452713..21452724,-p@chr19:21452713..21452724
-
Hg19::chr19:23015117..23015128,+p@chr19:23015117..23015128
+
Hg19::chr19:36909811..36909826,-p3@ZFP82
Hg19::chr19:36909838..36909849,-p5@ZFP82
Hg19::chr19:36914887..36914892,-p@chr19:36914887..36914892
-
Hg19::chr19:37264112..37264129,+p2@uc002oes.1
Hg19::chr19:37264138..37264154,+p4@uc002oes.1
Hg19::chr19:37464799..37464817,+p@chr19:37464799..37464817
+
Hg19::chr19:38104849..38104860,+p@chr19:38104849..38104860
+
Hg19::chr19:38145832..38145833,-p@chr19:38145832..38145833
-
Hg19::chr19:38182936..38182940,-p@chr19:38182936..38182940
-
Hg19::chr19:38182963..38182975,-p@chr19:38182963..38182975
-
Hg19::chr19:38183029..38183044,-p@chr19:38183029..38183044
-
Hg19::chr19:38210552..38210570,-p2@ZNF607
Hg19::chr19:38281159..38281170,+p@chr19:38281159..38281170
+
Hg19::chr19:38281171..38281178,+p@chr19:38281171..38281178
+
Hg19::chr19:41727698..41727705,+p@chr19:41727698..41727705
+
Hg19::chr19:44331295..44331299,-p4@ENST00000499389
p4@uc002oxo.1
Hg19::chr19:44331304..44331307,-p5@ENST00000499389
p5@uc002oxo.1
Hg19::chr19:44331332..44331339,-p3@ENST00000499389
p3@uc002oxo.1
Hg19::chr19:44331593..44331618,+p5@ZNF283
Hg19::chr19:44331766..44331774,+p@chr19:44331766..44331774
+
Hg19::chr19:44331769..44331809,-p2@ENST00000499389
p2@uc002oxo.1
Hg19::chr19:44331884..44331893,+p8@ZNF283
Hg19::chr19:44331916..44331929,+p6@ZNF283
Hg19::chr19:44405623..44405636,-p1@uc002oxt.2
Hg19::chr19:44405761..44405769,-p2@uc002oxt.2
Hg19::chr19:44405872..44405879,+p@chr19:44405872..44405879
+
Hg19::chr19:52932395..52932413,+p1@ZNF534
Hg19::chr19:52932444..52932455,+p2@ZNF534
Hg19::chr19:56879625..56879636,+p5@ZNF542
Hg19::chr19:56879817..56879825,+p4@ZNF542
Hg19::chr19:9406118..9406133,-p@chr19:9406118..9406133
-
Hg19::chr19:9420326..9420349,-p2@ZNF699
Hg19::chr1:240926680..240926686,+p@chr1:240926680..240926686
+
Hg19::chr21:47460896..47460904,+p@chr21:47460896..47460904
+
Hg19::chr21:47461437..47461440,+p@chr21:47461437..47461440
+
Hg19::chr5:1380178..1380183,-p1@ENST00000504989
p1@uc003jcj.1
Hg19::chr5:178696464..178696469,-p@chr5:178696464..178696469
-
Hg19::chr6:2938437..2938442,-p@chr6:2938437..2938442
-
Hg19::chr8:90710257..90710295,+p@chr8:90710257..90710295
+


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
1.69712115516446e-070.000107427769121914390{ASH2L,391} (Static Module):NA



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:0006355regulation of transcription, DNA-dependent0.000694105102075861
GO:0006351transcription, DNA-dependent0.000694105102075861
GO:0032774RNA biosynthetic process0.000694105102075861
GO:0045449regulation of transcription0.000694105102075861
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000694105102075861
GO:0006350transcription0.000694105102075861
GO:0010468regulation of gene expression0.000694105102075861
GO:0031323regulation of cellular metabolic process0.000694105102075861
GO:0019222regulation of metabolic process0.000694105102075861
GO:0016070RNA metabolic process0.000694105102075861
GO:0008270zinc ion binding0.000694105102075861
GO:0046914transition metal ion binding0.00122601820250566
GO:0010467gene expression0.00173584310847537
GO:0050794regulation of cellular process0.00192843172763104
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00198867441603267
GO:0050789regulation of biological process0.00226568844957581
GO:0003676nucleic acid binding0.00248129964629139
GO:0043169cation binding0.0025249278869468
GO:0065007biological regulation0.00275580653910112
GO:0046872metal ion binding0.00279506898691079
GO:0043167ion binding0.00284718050993229
GO:0043283biopolymer metabolic process0.00460895279211949
GO:0043170macromolecule metabolic process0.0171109407578659
GO:0044237cellular metabolic process0.0260519854613869
GO:0005634nucleus0.0260519854613869
GO:0044238primary metabolic process0.0260519854613869
GO:0005622intracellular0.0466634707599534



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 cell6.95e-1219


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)
MA0003.11.1986e-08
MA0004.10.143101
MA0006.10.234536
MA0007.12.74941
MA0009.10.275766
MA0014.10.0290855
MA0017.10.80242
MA0019.10.0887288
MA0024.11.11554
MA0025.10.376628
MA0027.11.7662
MA0028.11.35252
MA0029.10.216921
MA0030.11.13534
MA0031.12.21548
MA0038.10.898443
MA0040.10.22078
MA0041.10.159732
MA0042.10.131646
MA0043.10.275993
MA0046.10.738915
MA0048.10.213592
MA0050.10.132387
MA0051.10.240959
MA0052.10.223346
MA0055.10.00051892
MA0056.10
MA0057.12.47724e-05
MA0058.10.0721792
MA0059.10.185595
MA0060.13.68588
MA0061.10.0159627
MA0063.10
MA0066.10.0700626
MA0067.10.529198
MA0068.10.000173701
MA0069.10.732638
MA0070.10.714492
MA0071.11.19388
MA0072.11.30584
MA0073.10.0314763
MA0074.10.240126
MA0076.12.25149
MA0077.10.694833
MA0078.10.112125
MA0081.10.0714936
MA0083.10.769051
MA0084.10.695499
MA0087.10.703294
MA0088.12.275
MA0089.10
MA0090.11.04726
MA0091.10.145393
MA0092.10.511154
MA0093.10.0401794
MA0095.10
MA0098.10
MA0100.10.075437
MA0101.10.117887
MA0103.10.217682
MA0105.10.0245095
MA0106.10.0870163
MA0107.10.0538844
MA0108.20.501004
MA0109.10
MA0111.10.249833
MA0113.10.647283
MA0114.11.09148
MA0115.12.0421
MA0116.10.00282809
MA0117.10.303182
MA0119.10.0620298
MA0122.10.322548
MA0124.10.429905
MA0125.10.362554
MA0130.10
MA0131.10.384838
MA0132.10
MA0133.10
MA0135.10.297838
MA0136.10.540287
MA0139.10.0124273
MA0140.10.775021
MA0141.10.183298
MA0142.10.150759
MA0143.10.09444
MA0144.10.1009
MA0145.10.826647
MA0146.10.452181
MA0147.10.0587539
MA0148.10.165635
MA0149.10.0514353
MA0062.21.3192
MA0035.20.772964
MA0039.20.876238
MA0138.21.20325
MA0002.20.346191
MA0137.21.79359
MA0104.20.0665968
MA0047.20.988232
MA0112.20.165912
MA0065.20.533795
MA0150.11.02043
MA0151.10
MA0152.10.456823
MA0153.10.349438
MA0154.10.0228192
MA0155.10.0139187
MA0156.11.40933
MA0157.11.95087
MA0158.10
MA0159.10.136485
MA0160.10.404496
MA0161.10
MA0162.10.0230992
MA0163.10.0348315
MA0164.10.329079
MA0080.20.0402168
MA0018.20.0876241
MA0099.20.208436
MA0079.23.63232e-06
MA0102.20.729507
MA0258.10.178137
MA0259.10.14777
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
ELF1#1997201.811956578215970.002962197311299230.0157905739584922
SETDB1#986986.862983179235831.88787728036671e-050.000428253725639051
SIX5#147912134.726112757892921.99961092276306e-067.3199216671031e-05
ZNF143#7702144.021537696408314.85528166720061e-060.000150335239264976



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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