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Coexpression cluster:C183: Difference between revisions

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

Latest revision as of 10:51, 17 September 2013


Full id: C183_acute_non_CD34_diffuse_CD133_myeloma_Burkitt



Phase1 CAGE Peaks

Hg19::chr10:1609627..1609637,+p@chr10:1609627..1609637
+
Hg19::chr10:1610285..1610290,+p@chr10:1610285..1610290
+
Hg19::chr10:1610305..1610313,+p@chr10:1610305..1610313
+
Hg19::chr10:62677334..62677342,-p@chr10:62677334..62677342
-
Hg19::chr10:97802785..97802826,+p5@CCNJ
Hg19::chr11:130424330..130424335,+p@chr11:130424330..130424335
+
Hg19::chr11:61647647..61647669,-p8@FADS3
Hg19::chr11:61647670..61647707,-p6@FADS3
Hg19::chr11:61648015..61648020,-p27@FADS3
Hg19::chr13:108867101..108867111,-p4@LIG4
Hg19::chr13:108867697..108867736,-p@chr13:108867697..108867736
-
Hg19::chr13:114060116..114060133,+p@chr13:114060116..114060133
+
Hg19::chr13:114060144..114060162,+p@chr13:114060144..114060162
+
Hg19::chr13:114062339..114062349,-p@chr13:114062339..114062349
-
Hg19::chr14:106327749..106327771,-p3@DQ431661
Hg19::chr14:107170012..107170028,-p1@M18519
Hg19::chr15:53828219..53828224,-p@chr15:53828219..53828224
-
Hg19::chr16:19778948..19778952,-p@chr16:19778948..19778952
-
Hg19::chr16:27240496..27240530,-p@chr16:27240496..27240530
-
Hg19::chr16:460857..460875,+p@chr16:460857..460875
+
Hg19::chr16:56703571..56703581,+p5@MT1H
Hg19::chr16:67580076..67580092,+p@chr16:67580076..67580092
+
Hg19::chr16:8736179..8736193,+p@chr16:8736179..8736193
+
Hg19::chr16:8736232..8736233,+p@chr16:8736232..8736233
+
Hg19::chr17:1926445..1926449,+p@chr17:1926445..1926449
+
Hg19::chr17:39884392..39884402,-p@chr17:39884392..39884402
-
Hg19::chr17:704185..704233,+p@chr17:704185..704233
+
Hg19::chr18:46550026..46550037,+p1@uc002ldh.2
Hg19::chr18:7766328..7766335,+p@chr18:7766328..7766335
+
Hg19::chr19:1371065..1371074,-p@chr19:1371065..1371074
-
Hg19::chr1:156314455..156314464,+p@chr1:156314455..156314464
+
Hg19::chr1:173384829..173384841,+p@chr1:173384829..173384841
+
Hg19::chr1:205827116..205827123,+p@chr1:205827116..205827123
+
Hg19::chr1:69785119..69785128,+p@chr1:69785119..69785128
+
Hg19::chr20:15903956..15903959,-p1@uc002wpc.2
Hg19::chr20:36405635..36405644,+p7@CTNNBL1
Hg19::chr20:36405665..36405672,+p12@CTNNBL1
Hg19::chr20:47026586..47026596,+p@chr20:47026586..47026596
+
Hg19::chr20:58045621..58045634,+p@chr20:58045621..58045634
+
Hg19::chr20:58045652..58045658,+p@chr20:58045652..58045658
+
Hg19::chr20:61464221..61464233,+p8@COL9A3
Hg19::chr20:61464247..61464260,+p4@COL9A3
Hg19::chr20:61464274..61464281,+p21@COL9A3
Hg19::chr22:22599062..22599073,+p3@VPREB1
Hg19::chr22:22599075..22599079,+p6@VPREB1
Hg19::chr22:22599175..22599177,+p4@VPREB1
Hg19::chr22:22599180..22599185,+p2@VPREB1
Hg19::chr22:22599189..22599212,+p1@VPREB1
Hg19::chr22:23213535..23213539,+p4@IGLV4-3
Hg19::chr22:23213543..23213569,+p2@IGLV4-3
Hg19::chr22:23213658..23213683,+p1@IGLV4-3
Hg19::chr22:23214117..23214120,+p3@AM184012
p3@AM184013
p3@AM184014
p3@AM184015
Hg19::chr22:30416763..30416806,+p@chr22:30416763..30416806
+
Hg19::chr22:40810934..40810938,+p@chr22:40810934..40810938
+
Hg19::chr22:48976727..48976745,+p@chr22:48976727..48976745
+
Hg19::chr2:18730657..18730670,+p@chr2:18730657..18730670
+
Hg19::chr2:54855884..54855893,+p@chr2:54855884..54855893
+
Hg19::chr2:62408796..62408800,-p@chr2:62408796..62408800
-
Hg19::chr3:126941733..126941746,+p@chr3:126941733..126941746
+
Hg19::chr3:175229206..175229218,+p@chr3:175229206..175229218
+
Hg19::chr3:183305348..183305354,-p@chr3:183305348..183305354
-
Hg19::chr3:82128943..82128947,+p@chr3:82128943..82128947
+
Hg19::chr4:133184051..133184063,+p@chr4:133184051..133184063
+
Hg19::chr4:133184088..133184095,+p@chr4:133184088..133184095
+
Hg19::chr4:133184105..133184115,+p@chr4:133184105..133184115
+
Hg19::chr4:144312659..144312668,+p25@GAB1
Hg19::chr4:146402557..146402563,+p25@SMAD1
Hg19::chr4:146411403..146411429,+p@chr4:146411403..146411429
+
Hg19::chr5:112020452..112020462,+p@chr5:112020452..112020462
+
Hg19::chr5:118626064..118626077,-p@chr5:118626064..118626077
-
Hg19::chr5:126305543..126305566,+p@chr5:126305543..126305566
+
Hg19::chr5:157336889..157336907,+p@chr5:157336889..157336907
+
Hg19::chr5:157816902..157816905,-p@chr5:157816902..157816905
-
Hg19::chr5:173615558..173615565,-p@chr5:173615558..173615565
-
Hg19::chr5:59829780..59829788,+p@chr5:59829780..59829788
+
Hg19::chr6:107096763..107096780,+p@chr6:107096763..107096780
+
Hg19::chr7:2108982..2108997,-p@chr7:2108982..2108997
-
Hg19::chr7:2109002..2109005,-p@chr7:2109002..2109005
-
Hg19::chr8:100727488..100727513,+p@chr8:100727488..100727513
+
Hg19::chr8:100727528..100727539,+p@chr8:100727528..100727539
+
Hg19::chr8:21327108..21327114,-p@chr8:21327108..21327114
-
Hg19::chr8:95412143..95412159,-p17@RAD54B
Hg19::chr9:128908654..128908669,-p@chr9:128908654..128908669
-
Hg19::chr9:137658050..137658053,-p@chr9:137658050..137658053
-
Hg19::chr9:137658629..137658647,+p@chr9:137658629..137658647
+
Hg19::chr9:137658649..137658674,+p@chr9:137658649..137658674
+
Hg19::chr9:37326030..37326040,+p10@ZCCHC7
Hg19::chr9:37327677..37327701,+p9@ZCCHC7
Hg19::chr9:37327716..37327725,+p12@ZCCHC7
Hg19::chr9:97261442..97261444,+p@chr9:97261442..97261444
+
Hg19::chrX:154028053..154028060,-p21@MPP1
Hg19::chrX:42815602..42815616,-p@chrX:42815602..42815616
-
Hg19::chrY:14649728..14649734,+p5@SHROOM2P1


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:0006302double-strand break repair0.0097620500305064
GO:0035019somatic stem cell maintenance0.0097620500305064
GO:0033152immunoglobulin V(D)J recombination0.0097620500305064
GO:0006297nucleotide-excision repair, DNA gap filling0.0097620500305064
GO:0002328pro-B cell differentiation0.0097620500305064
GO:0033153T cell receptor V(D)J recombination0.0097620500305064
GO:0051102DNA ligation during DNA recombination0.0097620500305064
GO:0015616DNA translocase activity0.0097620500305064
GO:0002320lymphoid progenitor cell differentiation0.0097620500305064
GO:0002568somatic diversification of T cell receptor genes0.0097620500305064
GO:0002681somatic recombination of T cell receptor gene segments0.0097620500305064
GO:0002244hemopoietic progenitor cell differentiation0.0165177176615476
GO:0032807DNA ligase IV complex0.0165177176615476
GO:0005594collagen type IX0.0198727830856386
GO:0010332response to gamma radiation0.0198727830856386
GO:0033151V(D)J recombination0.0198727830856386
GO:0000165MAPKKK cascade0.0198727830856386
GO:0003910DNA ligase (ATP) activity0.0198727830856386
GO:0033559unsaturated fatty acid metabolic process0.0198727830856386
GO:0006636unsaturated fatty acid biosynthetic process0.0198727830856386
GO:0005624membrane fraction0.0198727830856386
GO:0003823antigen binding0.0198727830856386
GO:0000012single strand break repair0.0198727830856386
GO:0048864stem cell development0.0198727830856386
GO:0019827stem cell maintenance0.0198727830856386
GO:0003909DNA ligase activity0.0198727830856386
GO:0051103DNA ligation during DNA repair0.0198727830856386
GO:0008283cell proliferation0.0208416084245456
GO:0048863stem cell differentiation0.0208416084245456
GO:0005593FACIT collagen0.0208416084245456
GO:0006310DNA recombination0.0208416084245456
GO:0010165response to X-ray0.0234671255630068
GO:0030901midbrain development0.0253997908929044
GO:0007417central nervous system development0.0253997908929044
GO:0009790embryonic development0.0253997908929044
GO:0033077T cell differentiation in the thymus0.0253997908929044
GO:0030934anchoring collagen0.0253997908929044
GO:0006266DNA ligation0.0253997908929044
GO:0000267cell fraction0.0267388074334204
GO:0048146positive regulation of fibroblast proliferation0.0267978742474436
GO:0006303double-strand break repair via nonhomologous end joining0.0267978742474436
GO:0043524negative regulation of neuron apoptosis0.0267978742474436
GO:0004385guanylate kinase activity0.0267978742474436
GO:0000724double-strand break repair via homologous recombination0.0267978742474436
GO:0048145regulation of fibroblast proliferation0.0267978742474436
GO:0000725recombinational repair0.0267978742474436
GO:0016717oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water0.0267978742474436
GO:0048144fibroblast proliferation0.0267978742474436
GO:0000726non-recombinational repair0.0273189007123177
GO:0016447somatic recombination of immunoglobulin gene segments0.0273189007123177
GO:0010212response to ionizing radiation0.0273189007123177
GO:0007167enzyme linked receptor protein signaling pathway0.0282869466382443
GO:0016886ligase activity, forming phosphoric ester bonds0.0283055709501709
GO:0016444somatic cell DNA recombination0.0286980704673784
GO:0016445somatic diversification of immunoglobulins0.0286980704673784
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.0286980704673784
GO:0002200somatic diversification of immune receptors0.0295509311029511
GO:0050769positive regulation of neurogenesis0.0295509311029511
GO:0002377immunoglobulin production0.0321262379384611
GO:0030509BMP signaling pathway0.0321262379384611
GO:0007257activation of JNK activity0.0361579353040573
GO:0006955immune response0.0361579353040573
GO:0007243protein kinase cascade0.0361579353040573
GO:0006950response to stress0.0368426436459173
GO:0030902hindbrain development0.0368426436459173
GO:0043507positive regulation of JNK activity0.0368426436459173
GO:0006281DNA repair0.0368426436459173
GO:0043506regulation of JNK activity0.0387558832636219
GO:0043523regulation of neuron apoptosis0.0387558832636219
GO:0002440production of molecular mediator of immune response0.0412450586479103
GO:0009880embryonic pattern specification0.0421634003045384
GO:0006974response to DNA damage stimulus0.0439231859912359
GO:0051402neuron apoptosis0.0439231859912359
GO:0008286insulin receptor signaling pathway0.0457833866411841
GO:0002376immune system process0.0457833866411841
GO:0042127regulation of cell proliferation0.0457833866411841
GO:0007173epidermal growth factor receptor signaling pathway0.0457833866411841



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
precursor B cell2.39e-663
B cell1.43e-1514
lymphocyte of B lineage1.01e-0924
pro-B cell1.01e-0924


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)
MA0003.19.88472e-08
MA0004.11.49182
MA0006.10.0882867
MA0007.10.551956
MA0009.10.356463
MA0014.14.29139e-08
MA0017.10.733202
MA0019.10.610929
MA0024.10.0674529
MA0025.10.180577
MA0027.11.47347
MA0028.10.00771978
MA0029.10.549655
MA0030.10.0702794
MA0031.10.411856
MA0038.10.485912
MA0040.10.265033
MA0041.10.692546
MA0042.10.225617
MA0043.10.110579
MA0046.10.105445
MA0048.10.845202
MA0050.10.118636
MA0051.10.134581
MA0052.10.0782202
MA0055.12.69531
MA0056.10
MA0057.10.0233716
MA0058.12.08409
MA0059.10.645772
MA0060.10.00321193
MA0061.10.167763
MA0063.10
MA0066.10.487036
MA0067.10.300856
MA0068.10.0128081
MA0069.10.691233
MA0070.10.325403
MA0071.10.38864
MA0072.10.320137
MA0073.10.00274307
MA0074.10.274755
MA0076.10.0220041
MA0077.10.311192
MA0078.10.251196
MA0081.10.869018
MA0083.10.365674
MA0084.10.444296
MA0087.10.317288
MA0088.11.01481
MA0089.10
MA0090.10.396529
MA0091.11.87853
MA0092.10.18779
MA0093.12.42805
MA0095.10
MA0098.10
MA0100.10.308238
MA0101.10.0198727
MA0103.10.662637
MA0105.10.00735224
MA0106.12.1
MA0107.10.103774
MA0108.21.10454
MA0109.10
MA0111.10.280997
MA0113.10.202943
MA0114.10.808138
MA0115.10.248011
MA0116.10.269212
MA0117.10.128545
MA0119.10.400063
MA0122.10.437218
MA0124.10.62968
MA0125.10.979276
MA0130.10
MA0131.10.276516
MA0132.10
MA0133.10
MA0135.10.394272
MA0136.10.29591
MA0139.10.194085
MA0140.11.18352
MA0141.10.299495
MA0142.11.42798
MA0143.11.33268
MA0144.10.125834
MA0145.10.0691563
MA0146.10.00137589
MA0147.10.543233
MA0148.10.717841
MA0149.10.0314055
MA0062.20.0601835
MA0035.20.214415
MA0039.21.77879e-05
MA0138.21.11883
MA0002.20.14866
MA0137.20.060521
MA0104.20.363554
MA0047.20.336644
MA0112.20.405453
MA0065.20.611982
MA0150.10.237559
MA0151.10
MA0152.10.398019
MA0153.10.160772
MA0154.11.89169
MA0155.10.0163643
MA0156.10.656303
MA0157.10.909384
MA0158.10
MA0159.11.36615
MA0160.10.779867
MA0161.10
MA0162.19.03452e-08
MA0163.10.0188339
MA0164.10.218454
MA0080.20.547461
MA0018.20.603687
MA0099.20.398881
MA0079.20
MA0102.20.474727
MA0258.10.632079
MA0259.10.591783
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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