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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:42, 17 September 2013


Full id: C146_lymphangiectasia_lymphoma_gall_lymph_tonsil_gastric_transitionalcell



Phase1 CAGE Peaks

Hg19::chr10:125804180..125804187,-p@chr10:125804180..125804187
-
Hg19::chr10:125804206..125804217,-p@chr10:125804206..125804217
-
Hg19::chr11:71963829..71963837,+p@chr11:71963829..71963837
+
Hg19::chr11:724548..724568,+p11@EPS8L2
Hg19::chr11:724584..724593,+p33@EPS8L2
Hg19::chr12:106670279..106670293,-p@chr12:106670279..106670293
-
Hg19::chr12:13105091..13105109,-p1@GPRC5D
Hg19::chr12:13105142..13105150,-p2@GPRC5D
Hg19::chr12:2649754..2649779,+p@chr12:2649754..2649779
+
Hg19::chr12:275886..275889,+p@chr12:275886..275889
+
Hg19::chr12:3085848..3085864,+p@chr12:3085848..3085864
+
Hg19::chr12:3086859..3086867,+p@chr12:3086859..3086867
+
Hg19::chr12:772661..772710,-p4@NINJ2
Hg19::chr13:101158539..101158553,-p@chr13:101158539..101158553
-
Hg19::chr13:101158558..101158564,-p@chr13:101158558..101158564
-
Hg19::chr13:101158570..101158577,-p@chr13:101158570..101158577
-
Hg19::chr13:112025198..112025208,+p@chr13:112025198..112025208
+
Hg19::chr13:112025250..112025251,+p@chr13:112025250..112025251
+
Hg19::chr13:31038224..31038249,-p16@HMGB1
Hg19::chr14:100409975..100409977,-p@chr14:100409975..100409977
-
Hg19::chr14:106090812..106090849,-p@chr14:106090812..106090849
-
Hg19::chr14:106090925..106090928,-p@chr14:106090925..106090928
-
Hg19::chr14:106091078..106091112,+p@chr14:106091078..106091112
+
Hg19::chr14:106091231..106091258,+p@chr14:106091231..106091258
+
Hg19::chr14:106091272..106091292,-p@chr14:106091272..106091292
-
Hg19::chr14:106091457..106091461,-p@chr14:106091457..106091461
-
Hg19::chr14:106091525..106091542,+p@chr14:106091525..106091542
+
Hg19::chr14:106091539..106091550,-p@chr14:106091539..106091550
-
Hg19::chr14:106091671..106091696,+p@chr14:106091671..106091696
+
Hg19::chr14:106091710..106091721,-p@chr14:106091710..106091721
-
Hg19::chr14:106092126..106092139,+p@chr14:106092126..106092139
+
Hg19::chr14:106092169..106092199,-p1@IGHG4
Hg19::chr14:106758085..106758088,-p1@AJ010447
Hg19::chr14:106758101..106758120,-p1@IGHV2-26
Hg19::chr14:81393459..81393461,-p@chr14:81393459..81393461
-
Hg19::chr14:81408012..81408023,-p6@CEP128
Hg19::chr16:3140060..3140067,-p@chr16:3140060..3140067
-
Hg19::chr16:3140126..3140134,-p@chr16:3140126..3140134
-
Hg19::chr16:3140147..3140160,-p@chr16:3140147..3140160
-
Hg19::chr17:266747..266756,-p@chr17:266747..266756
-
Hg19::chr17:36859613..36859621,-p@chr17:36859613..36859621
-
Hg19::chr17:40833858..40833861,-p1@CCR10
Hg19::chr17:76620398..76620400,-p@chr17:76620398..76620400
-
Hg19::chr17:78866954..78866969,+p@chr17:78866954..78866969
+
Hg19::chr17:80588297..80588315,-p@chr17:80588297..80588315
-
Hg19::chr17:80594899..80594906,+p@chr17:80594899..80594906
+
Hg19::chr17:80825728..80825741,+p@chr17:80825728..80825741
+
Hg19::chr18:20776409..20776412,+p@chr18:20776409..20776412
+
Hg19::chr18:44811094..44811096,-p@chr18:44811094..44811096
-
Hg19::chr18:44814866..44814869,+p@chr18:44814866..44814869
+
Hg19::chr18:44826080..44826084,+p@chr18:44826080..44826084
+
Hg19::chr18:44833203..44833207,+p@chr18:44833203..44833207
+
Hg19::chr18:44938716..44938721,+p@chr18:44938716..44938721
+
Hg19::chr18:49921251..49921263,+p@chr18:49921251..49921263
+
Hg19::chr18:49921266..49921277,+p@chr18:49921266..49921277
+
Hg19::chr18:49921287..49921290,+p@chr18:49921287..49921290
+
Hg19::chr18:72201634..72201656,+p6@CNDP1
Hg19::chr19:42041922..42041936,+p2@CEACAM21
Hg19::chr19:45205949..45205998,-p@chr19:45205949..45205998
-
Hg19::chr19:55450365..55450381,-p@chr19:55450365..55450381
-
Hg19::chr19:55450392..55450405,-p@chr19:55450392..55450405
-
Hg19::chr19:55450450..55450476,-p@chr19:55450450..55450476
-
Hg19::chr1:154644064..154644074,+p@chr1:154644064..154644074
+
Hg19::chr1:154926344..154926365,-p4@PBXIP1
Hg19::chr1:154971578..154971599,+p@chr1:154971578..154971599
+
Hg19::chr1:155291162..155291166,+p40@RUSC1
Hg19::chr1:155291376..155291428,+p6@RUSC1
Hg19::chr1:155291432..155291437,+p38@RUSC1
Hg19::chr1:155292811..155292840,+p9@RUSC1
Hg19::chr1:155293702..155293729,+p5@RUSC1
Hg19::chr1:155293747..155293758,+p28@RUSC1
Hg19::chr1:155294058..155294061,+p22@RUSC1
Hg19::chr1:155294079..155294093,+p14@RUSC1
Hg19::chr1:155294096..155294110,+p13@RUSC1
Hg19::chr1:155294116..155294127,+p20@RUSC1
Hg19::chr1:155294335..155294340,+p16@RUSC1
Hg19::chr1:155296085..155296101,+p@chr1:155296085..155296101
+
Hg19::chr1:155484570..155484579,+p@chr1:155484570..155484579
+
Hg19::chr1:156119466..156119480,+p9@SEMA4A
Hg19::chr1:156763299..156763338,+p@chr1:156763299..156763338
+
Hg19::chr1:209306591..209306595,-p@chr1:209306591..209306595
-
Hg19::chr20:23188058..23188060,+p@chr20:23188058..23188060
+
Hg19::chr20:33898933..33898940,+p@chr20:33898933..33898940
+
Hg19::chr21:47592889..47592890,+p@chr21:47592889..47592890
+
Hg19::chr22:23232400..23232413,+p@chr22:23232400..23232413
+
Hg19::chr22:37608458..37608470,-p6@SSTR3
Hg19::chr22:37608473..37608487,-p4@SSTR3
Hg19::chr22:42148515..42148527,+p6@MEI1
Hg19::chr22:42148573..42148591,+p5@MEI1
Hg19::chr22:42148599..42148609,+p10@MEI1
Hg19::chr2:242493013..242493022,-p@chr2:242493013..242493022
-
Hg19::chr2:58850778..58850780,-p@chr2:58850778..58850780
-
Hg19::chr2:89156772..89156780,+p11@CU688247
p11@CU689025
p11@CU689831
p11@CU689833
p11@CU689835
p11@CU691143
Hg19::chr2:89156797..89156840,+p2@CU688247
p2@CU689025
p2@CU689831
p2@CU689833
p2@CU689835
p2@CU691143
Hg19::chr2:89156845..89156884,+p3@CU688247
p3@CU689025
p3@CU689831
p3@CU689833
p3@CU689835
p3@CU691143
Hg19::chr2:89156977..89156984,-p8@AJ294735
Hg19::chr2:89157562..89157566,-p@chr2:89157562..89157566
-
Hg19::chr2:89157749..89157766,-p2@X96754
Hg19::chr2:89247083..89247117,-p1@AB006847
p1@AB022651
p1@AB027436
p1@AB027438
p1@AB063935
p1@AB063948
p1@AB063959
p1@AB064046
p1@AB064047
p1@AB064049
p1@AB064077
p1@AB064078
p1@AB064100
p1@AB084082
p1@AB363262
p1@AB363306
p1@AB363308
p1@AF039298
p1@AF103421
p1@AF103459
p1@AF103461
p1@AF103465
p1@AF103466
p1@AF103483
p1@AF103494
p1@AF103521
p1@AF103561
p1@AF234257
p1@AF338918
p1@AF455555
p1@AJ241396
p1@AJ241398
p1@AJ388640
p1@AJ388645
p1@AJ576038
p1@AJ697904
p1@AM181151
p1@AM184029
p1@AY043112
p1@AY043144
p1@AY247655
p1@AY423217
p1@AY423218
p1@AY423219
p1@AY423220
p1@AY423221
p1@AY685274
p1@AY685276
p1@AY685336
p1@AY685337
p1@AY686910
p1@AY686919
p1@AY867118
p1@AY867141
p1@AY867162
p1@AY867181
p1@AY867190
p1@AY867249
p1@AY867258
p1@AY867281
p1@AY867339
p1@AY867374
p1@AY867387
p1@AY867404
p1@AY942011
p1@AY942052
p1@AY998712
p1@DQ021406
p1@DQ100651
p1@DQ101022
p1@DQ101029
p1@DQ101031
p1@DQ101034
p1@DQ101055
p1@DQ101056
p1@DQ101064
p1@DQ101094
p1@DQ101098
p1@DQ101105
p1@DQ101110
p1@DQ101118
p1@DQ101151
p1@DQ101181
p1@DQ187522
p1@DQ187687
p1@DQ187692
p1@DQ187693
p1@DQ205176
p1@DQ322855
p1@DQ322856
p1@DQ322857
p1@DQ322858
p1@DQ322859
p1@DQ322982
p1@DQ490731
p1@DQ840690
p1@DQ840946
p1@DQ840954
p1@DQ840956
p1@DQ840958
p1@DQ840961
p1@DQ840973
p1@DQ840975
p1@DQ840985
p1@DQ840989
p1@DQ840997
p1@DQ841022
p1@DQ841027
p1@DQ841058
p1@DQ841077
p1@EF589421
p1@EF589548
p1@EF710807
p1@EF710808
p1@EF710809
p1@EU599324
p1@EU599327
p1@EU599336
p1@GQ856064
p1@GQ856068
p1@HM996211
p1@HM996229
p1@HM996239
p1@HQ378416
p1@HQ378444
p1@HQ378454
p1@HQ689707
p1@HQ689710
p1@HQ689726
p1@HQ689751
p1@JF740066
p1@L01413
p1@L28047
p1@L39957
p1@L43086
p1@M97806
p1@M99603
p1@S56182
p1@U07989
p1@U96294
p1@X84341
p1@X97481
p1@X97551
p1@Y14866
Hg19::chr3:182821083..182821085,-p@chr3:182821083..182821085
-
Hg19::chr3:99257372..99257376,-p@chr3:99257372..99257376
-
Hg19::chr5:28809366..28809397,-p1@ENST00000504398
Hg19::chr5:28982718..28982721,+p@chr5:28982718..28982721
+
Hg19::chr5:32207221..32207232,+p@chr5:32207221..32207232
+
Hg19::chr5:32207239..32207246,+p@chr5:32207239..32207246
+
Hg19::chr5:32207273..32207278,+p@chr5:32207273..32207278
+
Hg19::chr5:32207376..32207386,+p@chr5:32207376..32207386
+
Hg19::chr6:7901024..7901028,-p@chr6:7901024..7901028
-
Hg19::chr6:7911675..7911678,-p@chr6:7911675..7911678
-
Hg19::chr9:90728611..90728622,+p@chr9:90728611..90728622
+
Hg19::chr9:97369321..97369332,-p@chr9:97369321..97369332
-
Hg19::chr9:97369347..97369365,-p@chr9:97369347..97369365
-
Hg19::chr9:97369372..97369433,-p@chr9:97369372..97369433
-
Hg19::chrX:152162653..152162667,-p1@PNMA5
Hg19::chrX:152162673..152162689,-p2@PNMA5
Hg19::chrX:43138795..43138813,+p@chrX:43138795..43138813
+
Hg19::chrX:48770919..48770934,-p@chrX:48770919..48770934
-
Hg19::chrX:48781694..48781709,-p@chrX:48781694..48781709
-


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:0017055negative regulation of transcriptional preinitiation complex assembly0.0375479531005184
GO:0035081induction of programmed cell death by hormones0.0375479531005184
GO:0008628induction of apoptosis by hormones0.0375479531005184
GO:0005118sevenless binding0.0375479531005184
GO:0006288base-excision repair, DNA ligation0.0375479531005184
GO:0001653peptide receptor activity0.0375479531005184
GO:0008528peptide receptor activity, G-protein coupled0.0375479531005184
GO:0005887integral to plasma membrane0.0375479531005184
GO:0031226intrinsic to plasma membrane0.0375479531005184
GO:0004994somatostatin receptor activity0.0375479531005184
GO:0051103DNA ligation during DNA repair0.0375479531005184
GO:0004871signal transducer activity0.0375479531005184
GO:0060089molecular transducer activity0.0375479531005184
GO:0051123transcriptional preinitiation complex assembly0.0375479531005184
GO:0045898regulation of transcriptional preinitiation complex assembly0.0375479531005184
GO:0007158neuron adhesion0.0410602174877673
GO:0042277peptide binding0.0422462021578661
GO:0006266DNA ligation0.0422462021578661
GO:0007601visual perception0.0422462021578661
GO:0050953sensory perception of light stimulus0.0422462021578661
GO:0008301DNA bending activity0.0491229303210624



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>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
tonsil2.55e-981
mucosa-associated lymphoid tissue2.55e-981
lymphoid tissue2.55e-981
tonsillar ring2.55e-981
lymphoid system3.02e-1110
chordate pharynx3.02e-1110
pharyngeal region of foregut3.02e-1110
pharynx2.37e-1011


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)
MA0003.11.55126e-09
MA0004.11.53133
MA0006.10.0530487
MA0007.10.0450115
MA0009.10.248015
MA0014.11.74758e-07
MA0017.11.35884
MA0019.10.213362
MA0024.10.0387786
MA0025.10.127601
MA0027.11.37206
MA0028.10.292502
MA0029.10.168049
MA0030.10.650119
MA0031.10.499198
MA0038.10.95096
MA0040.10.0454121
MA0041.10.00738401
MA0042.10.0480928
MA0043.10.248338
MA0046.10.0668699
MA0048.11.52049
MA0050.11.4332
MA0051.10.667751
MA0052.11.08459
MA0055.10.357231
MA0056.10
MA0057.10.474541
MA0058.11.32276
MA0059.11.06097
MA0060.10.249533
MA0061.10.471947
MA0063.10
MA0066.11.99456
MA0067.10.232687
MA0068.11.35664
MA0069.10.503043
MA0070.10.0617509
MA0071.11.0413
MA0072.10.821554
MA0073.10.000402148
MA0074.10.44632
MA0076.10.091736
MA0077.10.461195
MA0078.10.292986
MA0081.10.640557
MA0083.13.85355
MA0084.10.364722
MA0087.10.0594678
MA0088.10.831731
MA0089.10
MA0090.10.441401
MA0091.10.122393
MA0092.10.0127546
MA0093.12.07822
MA0095.10
MA0098.10
MA0100.10.0249586
MA0101.10.85655
MA0103.13.21135
MA0105.10.168477
MA0106.10.207699
MA0107.10.28862
MA0108.20.492448
MA0109.10
MA0111.11.41765
MA0113.10.232155
MA0114.11.15019
MA0115.10.54544
MA0116.11.04007
MA0117.10.601801
MA0119.10.181281
MA0122.10.0955865
MA0124.10.162077
MA0125.10.11896
MA0130.10
MA0131.10.0611022
MA0132.10
MA0133.10
MA0135.10.0820988
MA0136.10.480547
MA0139.10.00775822
MA0140.10.207627
MA0141.10.630583
MA0142.10.702738
MA0143.10.110139
MA0144.10.147193
MA0145.11.35264
MA0146.10.0521656
MA0147.11.07549
MA0148.10.265585
MA0149.10.0400845
MA0062.20.185721
MA0035.20.532441
MA0039.20.00152439
MA0138.20.503457
MA0002.20.366804
MA0137.20.0391036
MA0104.21.39932
MA0047.20.190536
MA0112.20.51015
MA0065.20.866882
MA0150.10.051181
MA0151.10
MA0152.10.113579
MA0153.10.358216
MA0154.10.403273
MA0155.10.237289
MA0156.10.322381
MA0157.10.622995
MA0158.10
MA0159.10.0155417
MA0160.11.196
MA0161.10
MA0162.10.00123815
MA0163.10.00037894
MA0164.10.120813
MA0080.20.164943
MA0018.20.209706
MA0099.20.0479845
MA0079.21.74609e-10
MA0102.20.393325
MA0258.12.24245
MA0259.12.15919
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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