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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:50, 17 September 2013


Full id: C179_CD19_Peripheral_lymphoma_blood_lymph_spleen_tonsil



Phase1 CAGE Peaks

Hg19::chr10:3527599..3527602,-p@chr10:3527599..3527602
-
Hg19::chr10:5882480..5882508,+p@chr10:5882480..5882508
+
Hg19::chr10:63778623..63778634,+p@chr10:63778623..63778634
+
Hg19::chr11:118754537..118754552,+p3@CXCR5
Hg19::chr11:65769302..65769311,+p9@BANF1
Hg19::chr12:104322982..104322991,+p@chr12:104322982..104322991
+
Hg19::chr12:12510353..12510360,+p8@LOH12CR1
Hg19::chr12:14515635..14515638,+p@chr12:14515635..14515638
+
Hg19::chr12:14518377..14518403,-p1@ENST00000509114
Hg19::chr12:9917894..9917913,+p@chr12:9917894..9917913
+
Hg19::chr13:48878761..48878787,-p@chr13:48878761..48878787
-
Hg19::chr14:106179161..106179199,-p1@DQ083946
Hg19::chr14:106242022..106242047,-p@chr14:106242022..106242047
-
Hg19::chr14:106284502..106284505,-p@chr14:106284502..106284505
-
Hg19::chr14:106311825..106311837,-p@chr14:106311825..106311837
-
Hg19::chr14:107170052..107170092,-p1@AF460718
p1@AF460720
p1@AF460732
p1@AF460746
p1@AF460772
p1@AY179836
p1@AY179837
p1@AY179838
p1@AY179839
p1@AY179840
p1@AY179841
p1@AY179842
p1@AY179843
p1@AY179844
p1@AY179845
p1@AY179846
p1@AY179847
p1@AY179848
p1@AY179849
p1@AY179850
p1@AY179851
p1@AY179852
p1@AY179853
p1@AY179854
p1@AY179855
p1@AY179856
p1@AY179857
p1@AY179858
p1@AY179859
p1@AY179860
p1@AY179861
Hg19::chr14:32902600..32902611,+p13@AKAP6
Hg19::chr14:51135220..51135270,-p3@SAV1
Hg19::chr14:51296927..51296947,+p@chr14:51296927..51296947
+
Hg19::chr14:69262916..69262929,-p11@ZFP36L1
Hg19::chr14:89770523..89770533,+p@chr14:89770523..89770533
+
Hg19::chr15:50717036..50717040,+p@chr15:50717036..50717040
+
Hg19::chr15:75639655..75639667,+p7@NEIL1
Hg19::chr15:75639688..75639732,+p4@NEIL1
Hg19::chr15:75639737..75639769,+p5@NEIL1
Hg19::chr15:81585123..81585150,+p@chr15:81585123..81585150
+
Hg19::chr17:1084487..1084497,-p@chr17:1084487..1084497
-
Hg19::chr18:13612332..13612346,-p@chr18:13612332..13612346
-
Hg19::chr19:41803774..41803784,+p@chr19:41803774..41803784
+
Hg19::chr19:5130791..5130800,+p3@KDM4B
Hg19::chr1:157789081..157789088,-p@chr1:157789081..157789088
-
Hg19::chr1:160765884..160765903,+p3@LY9
Hg19::chr1:160765919..160765926,+p4@LY9
Hg19::chr1:160766011..160766032,+p2@LY9
Hg19::chr1:185125341..185125373,+p@chr1:185125341..185125373
+
Hg19::chr1:42089031..42089065,-p@chr1:42089031..42089065
-
Hg19::chr1:565509..565541,+p1@MTND2P28
Hg19::chr20:57483131..57483142,+p3@TUBB1
Hg19::chr20:62185378..62185413,-p@chr20:62185378..62185413
-
Hg19::chr21:43944597..43944614,-p@chr21:43944597..43944614
-
Hg19::chr21:44772878..44772893,+p@chr21:44772878..44772893
+
Hg19::chr21:44847626..44847649,-p@chr21:44847626..44847649
-
Hg19::chr21:45661307..45661319,-p4@ICOSLG
Hg19::chr21:45661330..45661349,-p3@ICOSLG
Hg19::chr22:18483455..18483483,+p@chr22:18483455..18483483
+
Hg19::chr22:18484430..18484462,-p4@MICAL3
Hg19::chr22:42322795..42322821,-p1@TNFRSF13C
Hg19::chr2:129075215..129075226,+p@chr2:129075215..129075226
+
Hg19::chr2:135011682..135011693,+p13@MGAT5
Hg19::chr2:135011731..135011735,+p10@MGAT5
Hg19::chr2:157189567..157189580,-p19@NR4A2
Hg19::chr2:209176298..209176309,+p@chr2:209176298..209176309
+
Hg19::chr3:13114770..13114779,-p28@IQSEC1
Hg19::chr3:150983738..150983749,-p@chr3:150983738..150983749
-
Hg19::chr3:193822398..193822431,+p@chr3:193822398..193822431
+
Hg19::chr3:193854589..193854595,+p@chr3:193854589..193854595
+
Hg19::chr3:193855472..193855483,-p@chr3:193855472..193855483
-
Hg19::chr3:193855488..193855506,-p@chr3:193855488..193855506
-
Hg19::chr3:42054559..42054603,+p@chr3:42054559..42054603
+
Hg19::chr3:71441479..71441522,-p@chr3:71441479..71441522
-
Hg19::chr4:185249225..185249228,-p@chr4:185249225..185249228
-
Hg19::chr4:26994323..26994338,-p@chr4:26994323..26994338
-
Hg19::chr4:86396521..86396541,+p6@ARHGAP24
Hg19::chr4:86396549..86396593,+p3@ARHGAP24
Hg19::chr5:158526693..158526706,-p8@EBF1
Hg19::chr5:176882204..176882216,+p17@PRR7
Hg19::chr5:55885073..55885104,+p@chr5:55885073..55885104
+
Hg19::chr6:109761502..109761506,+p7@SMPD2
Hg19::chr6:109776788..109776819,-p5@MICAL1
Hg19::chr6:14127002..14127011,+p@chr6:14127002..14127011
+
Hg19::chr6:159207686..159207690,-p@chr6:159207686..159207690
-
Hg19::chr6:32653438..32653462,-p@chr6:32653438..32653462
-
Hg19::chr6:64283334..64283352,-p@chr6:64283334..64283352
-
Hg19::chr6:90774843..90774847,-p@chr6:90774843..90774847
-
Hg19::chr6:90999484..90999495,-p@chr6:90999484..90999495
-
Hg19::chr6:91006575..91006602,-p2@BACH2
Hg19::chr7:151078944..151078972,+p@chr7:151078944..151078972
+
Hg19::chr8:11362416..11362421,+p@chr8:11362416..11362421
+
Hg19::chr8:11416651..11416663,+p@chr8:11416651..11416663
+
Hg19::chr8:11416709..11416726,+p@chr8:11416709..11416726
+
Hg19::chr8:11416744..11416760,+p@chr8:11416744..11416760
+
Hg19::chr8:11416763..11416790,+p@chr8:11416763..11416790
+
Hg19::chr8:28263906..28263913,-p@chr8:28263906..28263913
-
Hg19::chr8:42698292..42698321,-p8@THAP1
Hg19::chr8:86089827..86089843,-p@chr8:86089827..86089843
-
Hg19::chr9:36870181..36870202,-p@chr9:36870181..36870202
-
Hg19::chr9:37034147..37034157,-p7@PAX5
Hg19::chr9:37034186..37034216,-p2@PAX5
Hg19::chr9:37034258..37034270,-p3@PAX5
Hg19::chr9:37034280..37034297,-p6@PAX5
Hg19::chr9:37037005..37037011,+p@chr9:37037005..37037011
+
Hg19::chr9:84270861..84270865,-p@chr9:84270861..84270865
-
Hg19::chrX:106960180..106960197,-p2@TSC22D3
Hg19::chrX:106960221..106960236,-p3@TSC22D3
Hg19::chrX:106960249..106960260,-p5@TSC22D3


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:0003677DNA binding0.0356831774576607
GO:0006725aromatic compound metabolic process0.0356831774576607
GO:0043229intracellular organelle0.0455629228012851
GO:0043226organelle0.0455629228012851



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 lineage8.89e-6924
pro-B cell8.89e-6924
lymphocyte1.98e-6753
common lymphoid progenitor1.98e-6753
nucleate cell1.01e-6455
lymphoid lineage restricted progenitor cell3.18e-6452
B cell1.13e-5214
nongranular leukocyte5.01e-41115
leukocyte4.96e-38136
hematopoietic lineage restricted progenitor cell1.13e-29120
hematopoietic stem cell2.92e-29168
angioblastic mesenchymal cell2.92e-29168
hematopoietic cell2.31e-27177
hematopoietic oligopotent progenitor cell3.17e-25161
hematopoietic multipotent progenitor cell3.17e-25161
single nucleate cell3.77e-143
mononuclear cell3.77e-143
natural killer cell4.31e-143
pro-NK cell4.31e-143
mesenchymal cell1.41e-09354
mature B cell2.39e-092
pre-B-II cell2.39e-092
transitional stage B cell2.39e-092
small pre-B-II cell2.39e-092
immature B cell2.39e-092
connective tissue cell3.12e-09361
motile cell5.10e-08386
mature alpha-beta T cell5.19e-0818
alpha-beta T cell5.19e-0818
immature T cell5.19e-0818
mature T cell5.19e-0818
immature alpha-beta T cell5.19e-0818
circulating cell2.77e-076
CD4-positive, alpha-beta T cell4.23e-076
basophil9.02e-073
Uber Anatomy
Ontology termp-valuen
connective tissue9.22e-09371
Disease
Ontology termp-valuen
lymphoma6.91e-0710


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)
MA0003.10.592516
MA0004.10.392712
MA0006.10.235107
MA0007.10.343284
MA0009.10.346015
MA0014.10.182172
MA0017.10.0691471
MA0019.10.178639
MA0024.10.855735
MA0025.10.520706
MA0027.11.46439
MA0028.10.0500122
MA0029.10.533481
MA0030.10.8776
MA0031.11.08562
MA0038.10.0471975
MA0040.10.544583
MA0041.10.0202287
MA0042.11.04188
MA0043.10.106619
MA0046.10.101588
MA0048.10.780593
MA0050.11.04688
MA0051.10.998988
MA0052.10.937434
MA0055.10.916369
MA0056.10
MA0057.10.0529861
MA0058.10.175255
MA0059.11.07459
MA0060.10.338485
MA0061.13.71719
MA0063.10
MA0066.11.37047
MA0067.10.294478
MA0068.10.211065
MA0069.10.328461
MA0070.13.53642
MA0071.10.847356
MA0072.10.641324
MA0073.10.164276
MA0074.10.995587
MA0076.10.0532939
MA0077.10.301393
MA0078.10.0223541
MA0081.10.613646
MA0083.10.109916
MA0084.10.43698
MA0087.10.307396
MA0088.10.147148
MA0089.10
MA0090.10.234796
MA0091.10.127182
MA0092.10.469275
MA0093.10.243197
MA0095.10
MA0098.10
MA0100.10.14482
MA0101.12.74565
MA0103.10.81948
MA0105.13.29919
MA0106.10.174226
MA0107.12.64836
MA0108.20.39259
MA0109.10
MA0111.10.150971
MA0113.10.193252
MA0114.10.221064
MA0115.10.242118
MA0116.10.162861
MA0117.10.392457
MA0119.10.145462
MA0122.10.425774
MA0124.10.21537
MA0125.10.495758
MA0130.10
MA0131.10.264994
MA0132.10
MA0133.10
MA0135.10.120721
MA0136.11.05046
MA0139.10.174812
MA0140.10.364277
MA0141.10.169829
MA0142.10.149707
MA0143.10.377153
MA0144.10.113733
MA0145.10.21197
MA0146.10.062822
MA0147.10.668958
MA0148.10.463375
MA0149.10.54473
MA0062.20.135897
MA0035.20.202848
MA0039.20.00489643
MA0138.20.241898
MA0002.21.64956
MA0137.20.298531
MA0104.20.742208
MA0047.20.821787
MA0112.21.68357
MA0065.20.0648625
MA0150.10.222496
MA0151.10
MA0152.10.597142
MA0153.10.155952
MA0154.11.98694
MA0155.11.04712
MA0156.10.193793
MA0157.10.881871
MA0158.10
MA0159.10.261977
MA0160.10.0785767
MA0161.10
MA0162.10.226628
MA0163.10.0693788
MA0164.10.402022
MA0080.21.40246
MA0018.20.580863
MA0099.20.03431
MA0079.29.52907e-05
MA0102.20.467262
MA0258.10.93849
MA0259.10.555136
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
BCL11A#53335164.778013491133822.18512797816577e-071.16316300158845e-05
BCL3#602103.636537137235610.0004410942608554340.0041091288475141
CTBP2#148863.961073705641780.004255583223166070.020247317035408
EBF1#1879413.843843586413992.89200167945973e-155.2255668408494e-13
EGR1#1958301.575214450992670.005290886332464940.024501169586144
IRF4#3662153.460186213696442.64343752007663e-050.000569467762292251
MEF2A#4205254.932429186748432.08454704384398e-112.49951789566041e-09
MEF2C#4208187.827414535444561.4833447124312e-111.81404026254804e-09
NFKB1#4790543.119530788489134.82721888327918e-179.92421088485815e-15
PAX5#5079382.667826212471132.97301758062764e-092.49798055593862e-07
POLR2A#5430671.514519608730431.96019693606571e-067.2059488843987e-05
POU2F2#5452393.738303560546934.80278955173428e-147.81306133946381e-12
SP1#6667342.039420703755691.67437863287289e-050.000385857083050776
SPI1#6688332.849922902960531.08139906010628e-088.13690464253889e-07
TCF12#6938353.91796075343714.40484522190736e-136.4702901565511e-11
WRNIP1#5689755.779998123651370.001832868829667320.0108497980899861
YY1#7528291.499199492060650.01242146225930270.0449649959065305
ZEB1#6935213.733232340720221.38705564702414e-077.87725419899697e-06



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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