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

Latest revision as of 10:50, 17 September 2013


Full id: C181_liposarcoma_somatostatinoma_neuroblastoma_mesothelioma_nonsmall_small_Alveolar



Phase1 CAGE Peaks

Hg19::chr10:108432714..108432740,-p@chr10:108432714..108432740
-
Hg19::chr10:14216356..14216380,-p@chr10:14216356..14216380
-
Hg19::chr12:124950936..124950962,-p@chr12:124950936..124950962
-
Hg19::chr12:58122334..58122339,-p@chr12:58122334..58122339
-
Hg19::chr12:58123263..58123274,-p@chr12:58123263..58123274
-
Hg19::chr12:58123312..58123320,-p@chr12:58123312..58123320
-
Hg19::chr12:58123333..58123340,-p@chr12:58123333..58123340
-
Hg19::chr12:58123351..58123361,-p@chr12:58123351..58123361
-
Hg19::chr12:58123400..58123407,-p@chr12:58123400..58123407
-
Hg19::chr12:58128984..58128991,-p@chr12:58128984..58128991
-
Hg19::chr12:58131486..58131509,+p7@TSPAN31
Hg19::chr12:58131517..58131527,+p11@TSPAN31
Hg19::chr12:58131797..58131814,+p8@TSPAN31
Hg19::chr12:58131817..58131842,+p5@TSPAN31
Hg19::chr12:58131866..58131892,+p6@TSPAN31
Hg19::chr12:58131931..58131942,-p7@AGAP2
Hg19::chr12:58138778..58138789,+p2@TSPAN31
Hg19::chr12:58138800..58138860,+p1@TSPAN31
Hg19::chr12:58142093..58142107,-p@chr12:58142093..58142107
-
Hg19::chr12:58142121..58142144,-p@chr12:58142121..58142144
-
Hg19::chr12:58142150..58142249,-p@chr12:58142150..58142249
-
Hg19::chr12:58142997..58143015,-p@chr12:58142997..58143015
-
Hg19::chr12:58143018..58143051,-p@chr12:58143018..58143051
-
Hg19::chr12:58145555..58145603,-p3@CDK4
Hg19::chr12:58145604..58145631,-p4@CDK4
Hg19::chr12:58145889..58145914,-p5@CDK4
Hg19::chr12:58146048..58146118,-p1@CDK4
Hg19::chr12:58146128..58146169,-p2@CDK4
Hg19::chr12:58165870..58165911,-p1@METTL1
Hg19::chr12:58166370..58166423,+p1@METTL21B
Hg19::chr12:58166431..58166451,+p3@METTL21B
Hg19::chr12:58166726..58166754,+p1@ENST00000471530
Hg19::chr12:58176525..58176586,+p1@TSFM
Hg19::chr12:58287614..58287637,-p1@ENST00000548955
Hg19::chr12:58903110..58903112,-p@chr12:58903110..58903112
-
Hg19::chr12:58934549..58934562,+p@chr12:58934549..58934562
+
Hg19::chr12:59313930..59313955,-p7@LRIG3
Hg19::chr12:59313958..59314020,-p2@LRIG3
Hg19::chr12:59314028..59314071,-p3@LRIG3
Hg19::chr12:59314073..59314096,-p5@LRIG3
Hg19::chr12:59314097..59314106,-p9@LRIG3
Hg19::chr12:70637101..70637172,-p1@ENST00000549419
p1@ENST00000549651
p1@ENST00000550216
p1@ENST00000553135
Hg19::chr12:70637205..70637233,+p1@CNOT2
Hg19::chr12:72233530..72233563,+p1@TBC1D15
Hg19::chr12:72290195..72290204,+p11@TBC1D15
Hg19::chr12:78333879..78333896,+p21@NAV3
Hg19::chr12:78333898..78333912,+p27@NAV3
Hg19::chr12:78333998..78334003,+p20@NAV3
Hg19::chr12:78334005..78334016,+p7@NAV3
Hg19::chr12:78940817..78940821,-p@chr12:78940817..78940821
-
Hg19::chr12:78950321..78950324,-p@chr12:78950321..78950324
-
Hg19::chr12:82085811..82085817,+p@chr12:82085811..82085817
+
Hg19::chr12:82115146..82115152,+p@chr12:82115146..82115152
+
Hg19::chr12:82145204..82145208,+p@chr12:82145204..82145208
+
Hg19::chr12:90177655..90177684,-p@chr12:90177655..90177684
-
Hg19::chr18:14970228..14970238,-p@chr18:14970228..14970238
-
Hg19::chr18:14970256..14970271,-p@chr18:14970256..14970271
-
Hg19::chr18:14970301..14970343,-p@chr18:14970301..14970343
-
Hg19::chr18:65984050..65984068,-p@chr18:65984050..65984068
-
Hg19::chr18:66162229..66162240,-p@chr18:66162229..66162240
-
Hg19::chr18:66162271..66162278,-p@chr18:66162271..66162278
-
Hg19::chr1:78475606..78475614,+p@chr1:78475606..78475614
+
Hg19::chr1:78475616..78475640,+p@chr1:78475616..78475640
+
Hg19::chr1:78475650..78475661,+p@chr1:78475650..78475661
+
Hg19::chr1:78475671..78475674,+p@chr1:78475671..78475674
+
Hg19::chr2:28351645..28351666,+p@chr2:28351645..28351666
+
Hg19::chr2:40184868..40184873,-p@chr2:40184868..40184873
-
Hg19::chr2:40184895..40184905,-p@chr2:40184895..40184905
-
Hg19::chr2:40270530..40270541,+p@chr2:40270530..40270541
+
Hg19::chr2:40270606..40270613,+p@chr2:40270606..40270613
+
Hg19::chr3:174737010..174737023,+p@chr3:174737010..174737023
+
Hg19::chr4:157695641..157695666,-p14@PDGFC
Hg19::chr4:183072141..183072151,+p@chr4:183072141..183072151
+
Hg19::chr5:14144904..14144927,+p@chr5:14144904..14144927
+
Hg19::chr5:14144959..14144988,+p@chr5:14144959..14144988
+
Hg19::chr5:14145522..14145558,+p@chr5:14145522..14145558
+
Hg19::chr5:14145564..14145573,+p@chr5:14145564..14145573
+
Hg19::chr5:14146234..14146258,-p@chr5:14146234..14146258
-
Hg19::chr5:14165784..14165791,+p@chr5:14165784..14165791
+
Hg19::chr5:14165816..14165851,+p@chr5:14165816..14165851
+
Hg19::chr6:113702561..113702568,-p@chr6:113702561..113702568
-
Hg19::chr6:114168794..114168808,-p@chr6:114168794..114168808
-
Hg19::chr6:139904316..139904323,+p@chr6:139904316..139904323
+
Hg19::chr6:139904348..139904359,+p@chr6:139904348..139904359
+
Hg19::chr6:140325195..140325200,+p@chr6:140325195..140325200
+
Hg19::chr6:140577789..140577799,+p@chr6:140577789..140577799
+
Hg19::chr6:140756139..140756147,+p@chr6:140756139..140756147
+
Hg19::chr6:140981495..140981504,-p@chr6:140981495..140981504
-
Hg19::chr6:140981524..140981529,-p@chr6:140981524..140981529
-
Hg19::chr6:142622621..142622634,+p13@GPR126
Hg19::chr6:142622950..142622959,+p9@GPR126
Hg19::chr6:142622991..142623004,+p3@GPR126
Hg19::chr6:142623032..142623043,+p4@GPR126
Hg19::chr8:24530708..24530710,+p@chr8:24530708..24530710
+


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><br><br>disease_data<br>

Disease
Ontology termp-valuen
sarcoma2.29e-1120


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)
MA0003.10.176312
MA0004.12.22128
MA0006.10.0842645
MA0007.10.765917
MA0009.10.108434
MA0014.10.00333669
MA0017.10.521891
MA0019.10.070306
MA0024.10.0659499
MA0025.10.178003
MA0027.11.46891
MA0028.10.0221231
MA0029.10.0729219
MA0030.10.0687386
MA0031.10.0477711
MA0038.10.134853
MA0040.10.260464
MA0041.10.279916
MA0042.10.113625
MA0043.11.17566
MA0046.10.103496
MA0048.10.812374
MA0050.10.22044
MA0051.10.130742
MA0052.10.0765778
MA0055.10.383684
MA0056.10
MA0057.10.00603111
MA0058.13.22841
MA0059.11.09862
MA0060.10.0184443
MA0061.12.5027
MA0063.10
MA0066.10.476673
MA0067.10.806445
MA0068.10.0682333
MA0069.10.101776
MA0070.10.0968661
MA0071.10.379432
MA0072.10.315125
MA0073.11.97095e-07
MA0074.11.01328
MA0076.10.212338
MA0077.10.0916547
MA0078.10.463447
MA0081.10.179592
MA0083.10.728907
MA0084.11.1219
MA0087.11.58794
MA0088.10.00905621
MA0089.10
MA0090.10.783622
MA0091.10.410234
MA0092.10.311257
MA0093.12.74632
MA0095.10
MA0098.10
MA0100.10.0111846
MA0101.10.389151
MA0103.10.134059
MA0105.11.68869
MA0106.10.0145583
MA0107.11.5014
MA0108.20.0468855
MA0109.10
MA0111.10.272548
MA0113.10.384824
MA0114.10.150128
MA0115.10.685963
MA0116.10.0122756
MA0117.10.126376
MA0119.10.253209
MA0122.10.139514
MA0124.10.62302
MA0125.10.5018
MA0130.10
MA0131.10.806781
MA0132.10
MA0133.10
MA0135.10.777885
MA0136.10.0518698
MA0139.10.260158
MA0140.10.588203
MA0141.10.176118
MA0142.10.988617
MA0143.10.0772256
MA0144.10.0176279
MA0145.10.127372
MA0146.10.000648921
MA0147.10.179037
MA0148.10.022703
MA0149.10.00545172
MA0062.20.00284633
MA0035.20.371545
MA0039.21.82665e-07
MA0138.22.46541
MA0002.20.529087
MA0137.20.452283
MA0104.21.14702
MA0047.20.012985
MA0112.20.185536
MA0065.20.312906
MA0150.11.28084
MA0151.10
MA0152.10.10309
MA0153.10.15834
MA0154.10.280437
MA0155.11.24362
MA0156.10.315748
MA0157.10.131465
MA0158.10
MA0159.10.00473603
MA0160.10.0813271
MA0161.10
MA0162.10.0748725
MA0163.10.462816
MA0164.10.672731
MA0080.20.0177095
MA0018.20.0689878
MA0099.21.56072
MA0079.20.000211097
MA0102.20.47097
MA0258.10.343351
MA0259.10.300072
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
BHLHE40#8553125.728316623018391.30108808259288e-065.16867015054843e-05
JUN#3725182.396073675128230.0004265772376529160.00398562355727616
SMARCB1#6598112.135956102050340.01385744972100760.0487390783125314
SMARCC2#660166.009917516610480.0005234996866979160.00453348124204342
SUZ12#2351263.198879632621040.01154154027793980.0421921287090116
TCF7L2#6934161.833221542661680.01264583692655520.0457154227335582
ZNF263#10127211.836794408268340.00401472389237180.0192239580301416



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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