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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:57, 17 September 2013


Full id: C210_Burkitt_lymphoma_appendix_acute_diffuse_CD19_tonsil



Phase1 CAGE Peaks

Hg19::chr10:135303603..135303618,+p@chr10:135303603..135303618
+
Hg19::chr10:22897333..22897359,-p@chr10:22897333..22897359
-
Hg19::chr11:11283171..11283182,-p@chr11:11283171..11283182
-
Hg19::chr11:128132520..128132527,-p@chr11:128132520..128132527
-
Hg19::chr11:128132940..128132950,+p@chr11:128132940..128132950
+
Hg19::chr11:27719240..27719248,+p3@BDNF-AS1
Hg19::chr12:120972848..120972851,-p@chr12:120972848..120972851
-
Hg19::chr12:2296630..2296642,+p@chr12:2296630..2296642
+
Hg19::chr12:24514988..24515011,-p@chr12:24514988..24515011
-
Hg19::chr12:45746341..45746345,-p@chr12:45746341..45746345
-
Hg19::chr12:45820229..45820249,-p@chr12:45820229..45820249
-
Hg19::chr12:45820263..45820279,-p@chr12:45820263..45820279
-
Hg19::chr12:45820291..45820337,-p@chr12:45820291..45820337
-
Hg19::chr12:45820371..45820378,-p@chr12:45820371..45820378
-
Hg19::chr13:27239109..27239118,+p18@WASF3
Hg19::chr13:27239129..27239135,+p20@WASF3
Hg19::chr14:106367355..106367369,-p@chr14:106367355..106367369
-
Hg19::chr14:106692294..106692298,+p@chr14:106692294..106692298
+
Hg19::chr14:107283278..107283282,-p1@IGHV7-81
Hg19::chr14:94942577..94942588,-p3@SERPINA9
Hg19::chr15:101459149..101459160,+p7@LRRK1
Hg19::chr16:25122760..25122779,-p@chr16:25122760..25122779
-
Hg19::chr16:72863895..72863905,-p@chr16:72863895..72863905
-
Hg19::chr17:38029166..38029196,+p@chr17:38029166..38029196
+
Hg19::chr1:109240181..109240184,+p15@PRPF38B
Hg19::chr1:154687293..154687306,-p@chr1:154687293..154687306
-
Hg19::chr1:154838149..154838194,+p@chr1:154838149..154838194
+
Hg19::chr1:174242560..174242587,+p@chr1:174242560..174242587
+
Hg19::chr1:174244231..174244244,+p14@RABGAP1L
Hg19::chr22:17286728..17286732,-p@chr22:17286728..17286732
-
Hg19::chr22:22400891..22400899,-p@chr22:22400891..22400899
-
Hg19::chr2:159842651..159842671,+p@chr2:159842651..159842671
+
Hg19::chr2:61198713..61198728,-p@chr2:61198713..61198728
-
Hg19::chr3:114168260..114168264,+p@chr3:114168260..114168264
+
Hg19::chr3:114168924..114168928,+p@chr3:114168924..114168928
+
Hg19::chr3:182129942..182129947,-p@chr3:182129942..182129947
-
Hg19::chr3:187694166..187694181,-p1@ENST00000446091
p1@uc003frr.1
Hg19::chr3:187694197..187694208,-p3@ENST00000446091
p3@uc003frr.1
Hg19::chr3:187694215..187694226,-p2@ENST00000446091
p2@uc003frr.1
Hg19::chr3:36966509..36966515,-p@chr3:36966509..36966515
-
Hg19::chr3:96336749..96336764,-p@chr3:96336749..96336764
-
Hg19::chr4:172396445..172396474,+p@chr4:172396445..172396474
+
Hg19::chr5:53467645..53467648,-p@chr5:53467645..53467648
-
Hg19::chr5:5739493..5739498,-p@chr5:5739493..5739498
-
Hg19::chr6:157999774..157999779,+p@chr6:157999774..157999779
+
Hg19::chr6:161590361..161590366,+p@chr6:161590361..161590366
+
Hg19::chr6:6587418..6587427,-p8@LY86-AS1
Hg19::chr6:6587629..6587640,-p4@LY86-AS1
Hg19::chr6:71567823..71567834,+p@chr6:71567823..71567834
+
Hg19::chr6:88630940..88630960,-p@chr6:88630940..88630960
-
Hg19::chr6:91012903..91012921,+p@chr6:91012903..91012921
+
Hg19::chr6:91012993..91013003,+p@chr6:91012993..91013003
+
Hg19::chr6:91013009..91013026,+p@chr6:91013009..91013026
+
Hg19::chr6:91085662..91085676,+p@chr6:91085662..91085676
+
Hg19::chr6:91085680..91085705,+p@chr6:91085680..91085705
+
Hg19::chr6:91085725..91085738,+p@chr6:91085725..91085738
+
Hg19::chr6:91085838..91085849,+p@chr6:91085838..91085849
+
Hg19::chr6:91086164..91086168,+p@chr6:91086164..91086168
+
Hg19::chr7:28609735..28609737,-p@chr7:28609735..28609737
-
Hg19::chr7:50191009..50191027,+p@chr7:50191009..50191027
+
Hg19::chr7:50191034..50191048,+p@chr7:50191034..50191048
+
Hg19::chr7:50191051..50191060,+p@chr7:50191051..50191060
+
Hg19::chr7:55996143..55996147,+p@chr7:55996143..55996147
+
Hg19::chr8:119294370..119294381,+p4@ENST00000366457
Hg19::chr8:128685152..128685161,-p@chr8:128685152..128685161
-
Hg19::chr8:128723579..128723583,-p@chr8:128723579..128723583
-
Hg19::chr8:67039167..67039176,+p7@TRIM55
Hg19::chr8:93029879..93029904,-p30@RUNX1T1
Hg19::chrX:19902375..19902384,-p@chrX:19902375..19902384
-
Hg19::chrX:20033553..20033556,-p@chrX:20033553..20033556
-
Hg19::chrX:20033585..20033604,-p@chrX:20033585..20033604
-


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>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
lymphocyte of B lineage3.75e-1224
pro-B cell3.75e-1224
Uber Anatomy
Ontology termp-valuen
tonsil4.66e-661
mucosa-associated lymphoid tissue4.66e-661
lymphoid tissue4.66e-661
tonsillar ring4.66e-661
lymphoid system6.56e-0810
chordate pharynx6.56e-0810
pharyngeal region of foregut6.56e-0810
pharynx2.63e-0711
Disease
Ontology termp-valuen
lymphoma2.08e-2710


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)
MA0003.16.28018e-13
MA0004.10.0482897
MA0006.10.000909962
MA0007.10.11523
MA0009.10.167294
MA0014.11.792e-07
MA0017.10.333733
MA0019.10.140881
MA0024.10.112144
MA0025.10.251058
MA0027.11.58895
MA0028.10.00854842
MA0029.10.385412
MA0030.10.370833
MA0031.10.292982
MA0038.10.260217
MA0040.10.124436
MA0041.10.795639
MA0042.10.0426264
MA0043.10.167475
MA0046.10.485396
MA0048.10.00488071
MA0050.10.252201
MA0051.10.103799
MA0052.10.397946
MA0055.10.00367074
MA0056.10
MA0057.10.00387016
MA0058.10.0171149
MA0059.10.054811
MA0060.10.0478587
MA0061.10.248652
MA0063.10
MA0066.10.26083
MA0067.10.386062
MA0068.10.0794576
MA0069.10.932616
MA0070.10.464544
MA0071.10.400562
MA0072.10.89623
MA0073.18.15676e-13
MA0074.10.0241146
MA0076.10.0209018
MA0077.10.878498
MA0078.10.412262
MA0081.11.13756
MA0083.10.171631
MA0084.10.54013
MA0087.10.148885
MA0088.10.00167119
MA0089.10
MA0090.10.0248067
MA0091.10.479358
MA0092.10.214476
MA0093.10.0255993
MA0095.10
MA0098.10
MA0100.10.280487
MA0101.10.250452
MA0103.10.514167
MA0105.10.00541835
MA0106.10.137742
MA0107.10.436874
MA0108.20.60462
MA0109.10
MA0111.10.00516992
MA0113.10.9809
MA0114.10.280725
MA0115.10.873945
MA0116.10.45205
MA0117.10.189485
MA0119.10.0135541
MA0122.10.592894
MA0124.10.80563
MA0125.11.93705
MA0130.10
MA0131.10.0547804
MA0132.10
MA0133.10
MA0135.11.0394
MA0136.11.17189
MA0139.10.000690779
MA0140.10.394881
MA0141.10.59745
MA0142.11.92732
MA0143.10.349233
MA0144.10.0159858
MA0145.10.00126662
MA0146.13.82549e-08
MA0147.10.00875312
MA0148.11.95707
MA0149.10.620724
MA0062.20.00338786
MA0035.20.203158
MA0039.23.03475e-10
MA0138.20.41442
MA0002.20.308683
MA0137.20.452124
MA0104.20.000439463
MA0047.20.128175
MA0112.20.000305966
MA0065.20.0151498
MA0150.11.29974
MA0151.10
MA0152.10.408977
MA0153.10.64606
MA0154.10.0635627
MA0155.10.00752557
MA0156.10.906765
MA0157.10.494631
MA0158.10
MA0159.10.061385
MA0160.11.22809
MA0161.10
MA0162.11.83928e-08
MA0163.11.02717e-06
MA0164.11.02547
MA0080.21.03822
MA0018.20.0346569
MA0099.21.37247
MA0079.20
MA0102.20.572237
MA0258.10.0131237
MA0259.10.0102998
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
POLR2A#5430481.451799330630810.0002797849223209270.00297803276623271



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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