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Coexpression cluster:C282: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C282_acute_B_tonsil_CD19_submaxillary_lymph_throat
 

Latest revision as of 11:13, 17 September 2013


Full id: C282_acute_B_tonsil_CD19_submaxillary_lymph_throat



Phase1 CAGE Peaks

Hg19::chr11:69440459..69440517,-p@chr11:69440459..69440517
-
Hg19::chr11:69452606..69452638,-p@chr11:69452606..69452638
-
Hg19::chr13:80975502..80975505,+p@chr13:80975502..80975505
+
Hg19::chr13:80975508..80975547,+p@chr13:80975508..80975547
+
Hg19::chr14:106240433..106240439,-p@chr14:106240433..106240439
-
Hg19::chr14:106240442..106240463,-p@chr14:106240442..106240463
-
Hg19::chr14:106241955..106241965,-p@chr14:106241955..106241965
-
Hg19::chr14:106241968..106241975,-p@chr14:106241968..106241975
-
Hg19::chr14:106318085..106318118,-p@chr14:106318085..106318118
-
Hg19::chr14:106320365..106320378,-p7@IGHM
Hg19::chr14:106330248..106330263,-p@chr14:106330248..106330263
-
Hg19::chr14:106330406..106330426,-p1@uc001yrs.2
p1@uc001yrx.1
p1@uc001yrz.1
p1@uc001yse.2
p1@uc001ysm.1
Hg19::chr14:106330458..106330479,-p1@IGHJ4
Hg19::chr14:106573756..106573760,-p1@IGHV3-11
Hg19::chr14:96178718..96178752,-p3@TCL1A
Hg19::chr16:33647774..33647776,-p1@IGHV3OR16-8
Hg19::chr17:22021942..22021966,+p@chr17:22021942..22021966
+
Hg19::chr1:105475811..105475815,+p@chr1:105475811..105475815
+
Hg19::chr1:206290083..206290090,-p@chr1:206290083..206290090
-
Hg19::chr1:206290105..206290116,-p@chr1:206290105..206290116
-
Hg19::chr1:206290131..206290135,-p@chr1:206290131..206290135
-
Hg19::chr1:206290138..206290146,-p@chr1:206290138..206290146
-
Hg19::chr21:43896378..43896387,-p@chr21:43896378..43896387
-
Hg19::chr21:43896807..43896814,-p@chr21:43896807..43896814
-
Hg19::chr21:43896815..43896826,-p@chr21:43896815..43896826
-
Hg19::chr21:43896828..43896833,-p@chr21:43896828..43896833
-
Hg19::chr21:43896856..43896865,-p@chr21:43896856..43896865
-
Hg19::chr21:43896927..43896934,-p@chr21:43896927..43896934
-
Hg19::chr21:43896964..43896973,-p@chr21:43896964..43896973
-
Hg19::chr22:22380255..22380263,-p@chr22:22380255..22380263
-
Hg19::chr22:22380413..22380443,+p1@uc002zvv.2
Hg19::chr22:22550153..22550172,+p1@IGLV6-57
Hg19::chr22:22550534..22550548,-p@chr22:22550534..22550548
-
Hg19::chr22:23246848..23246854,+p@chr22:23246848..23246854
+
Hg19::chr22:23247044..23247061,+p1@IGLJ3
Hg19::chr22:23247146..23247167,+p1@AL713800
Hg19::chr2:111806761..111806769,+p@chr2:111806761..111806769
+
Hg19::chr2:111806795..111806824,+p@chr2:111806795..111806824
+
Hg19::chr2:212793161..212793168,-p@chr2:212793161..212793168
-
Hg19::chr2:239016429..239016447,+p4@ESPNL
Hg19::chr3:169650168..169650205,+p1@ENST00000493762
Hg19::chr3:3150439..3150454,-p1@X61177
Hg19::chr4:144312629..144312638,+p30@GAB1
Hg19::chr5:114607144..114607156,-p9@CCDC112
Hg19::chr7:115799916..115799932,-p6@TFEC
Hg19::chr7:115799942..115799955,-p5@TFEC


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:0000187activation of MAPK activity0.0023026497156705
GO:0043406positive regulation of MAP kinase activity0.0023026497156705
GO:0043405regulation of MAP kinase activity0.00304662663369834
GO:0045860positive regulation of protein kinase activity0.00304662663369834
GO:0033674positive regulation of kinase activity0.00304662663369834
GO:0051347positive regulation of transferase activity0.00304662663369834
GO:0000165MAPKKK cascade0.00304662663369834
GO:0042571immunoglobulin complex, circulating0.00304662663369834
GO:0045859regulation of protein kinase activity0.00487417214319682
GO:0043549regulation of kinase activity0.00487417214319682
GO:0051338regulation of transferase activity0.00487417214319682
GO:0043085positive regulation of catalytic activity0.00487417214319682
GO:0045022early endosome to late endosome transport0.00487417214319682
GO:0019814immunoglobulin complex0.00487417214319682
GO:0019815B cell receptor complex0.00487417214319682
GO:0045120pronucleus0.00761522141604439
GO:0007243protein kinase cascade0.00879561980076875
GO:0030890positive regulation of B cell proliferation0.0121822023344553
GO:0030888regulation of B cell proliferation0.0128228046362587
GO:0050853B cell receptor signaling pathway0.0133992391451083
GO:0050790regulation of catalytic activity0.0163912991334839
GO:0001772immunological synapse0.0163912991334839
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.0163912991334839
GO:0045807positive regulation of endocytosis0.0163912991334839
GO:0050871positive regulation of B cell activation0.0163912991334839
GO:0042100B cell proliferation0.0163912991334839
GO:0065009regulation of a molecular function0.0163912991334839
GO:0005624membrane fraction0.0163912991334839
GO:0007257activation of JNK activity0.0163912991334839
GO:0042327positive regulation of phosphorylation0.0163912991334839
GO:0043507positive regulation of JNK activity0.0163912991334839
GO:0008283cell proliferation0.0163912991334839
GO:0043506regulation of JNK activity0.0163912991334839
GO:0045937positive regulation of phosphate metabolic process0.0163912991334839
GO:0050864regulation of B cell activation0.0163912991334839
GO:0001934positive regulation of protein amino acid phosphorylation0.0163912991334839
GO:0033240positive regulation of amine metabolic process0.0163912991334839
GO:0045764positive regulation of amino acid metabolic process0.0163912991334839
GO:0050851antigen receptor-mediated signaling pathway0.0163912991334839
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0163912991334839
GO:0032946positive regulation of mononuclear cell proliferation0.0163912991334839
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0163912991334839
GO:0002429immune response-activating cell surface receptor signaling pathway0.0163912991334839
GO:0050671positive regulation of lymphocyte proliferation0.0163912991334839
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0163912991334839
GO:0002757immune response-activating signal transduction0.0163912991334839
GO:0008286insulin receptor signaling pathway0.0163912991334839
GO:0007173epidermal growth factor receptor signaling pathway0.0163912991334839
GO:0002764immune response-regulating signal transduction0.0163912991334839
GO:0030100regulation of endocytosis0.0165495141687404
GO:0000267cell fraction0.0165497714336796
GO:0051050positive regulation of transport0.0177819698294001
GO:0016197endosome transport0.0179265752713593
GO:0005515protein binding0.0179265752713593
GO:0018108peptidyl-tyrosine phosphorylation0.0179265752713593
GO:0050670regulation of lymphocyte proliferation0.0179265752713593
GO:0032944regulation of mononuclear cell proliferation0.0179265752713593
GO:0018212peptidyl-tyrosine modification0.0183431605664613
GO:0001932regulation of protein amino acid phosphorylation0.0183431605664613
GO:0033238regulation of amine metabolic process0.0183431605664613
GO:0006521regulation of amino acid metabolic process0.0183431605664613
GO:0005070SH3/SH2 adaptor activity0.0189530390991739
GO:0009897external side of plasma membrane0.0189530390991739
GO:0051251positive regulation of lymphocyte activation0.0189530390991739
GO:0016064immunoglobulin mediated immune response0.0189530390991739
GO:0019724B cell mediated immunity0.0189530390991739
GO:0032943mononuclear cell proliferation0.0189530390991739
GO:0046651lymphocyte proliferation0.0189530390991739
GO:0060090molecular adaptor activity0.02083679111693
GO:0030334regulation of cell migration0.02083679111693
GO:0042113B cell activation0.0208847812912211
GO:0042325regulation of phosphorylation0.0210207957278815
GO:0048471perinuclear region of cytoplasm0.0210207957278815
GO:0005938cell cortex0.0210207957278815
GO:0007254JNK cascade0.021063658652235
GO:0031098stress-activated protein kinase signaling pathway0.0212209605631963
GO:0051174regulation of phosphorus metabolic process0.0212209605631963
GO:0019220regulation of phosphate metabolic process0.0212209605631963
GO:0051270regulation of cell motility0.0212209605631963
GO:0002253activation of immune response0.0212209605631963
GO:0002449lymphocyte mediated immunity0.0212209605631963
GO:0040012regulation of locomotion0.0212209605631963
GO:0040011locomotion0.0212209605631963
GO:0006959humoral immune response0.0212209605631963
GO:0002250adaptive immune response0.0212209605631963
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0212209605631963
GO:0051249regulation of lymphocyte activation0.0212209605631963
GO:0002443leukocyte mediated immunity0.0215300114771818
GO:0050865regulation of cell activation0.0218320211279736
GO:0050778positive regulation of immune response0.0226816985347564
GO:0051247positive regulation of protein metabolic process0.0226816985347564
GO:0002684positive regulation of immune system process0.0226980986752123
GO:0030674protein binding, bridging0.0237542528318918
GO:0050776regulation of immune response0.0253015340852191
GO:0002682regulation of immune system process0.0255438676217569
GO:0051240positive regulation of multicellular organismal process0.0265358127991985
GO:0003714transcription corepressor activity0.0266815515246408
GO:0043235receptor complex0.0266815515246408
GO:0002252immune effector process0.0266815515246408
GO:0051049regulation of transport0.0266815515246408
GO:0006979response to oxidative stress0.0287602416636037
GO:0018193peptidyl-amino acid modification0.0287602416636037
GO:0050794regulation of cellular process0.0332470558260694
GO:0009986cell surface0.0344601844956273
GO:0046649lymphocyte activation0.0357352879018642
GO:0007242intracellular signaling cascade0.0362287889255353
GO:0005792microsome0.0366396893322418
GO:0042598vesicular fraction0.037857257568268
GO:0050789regulation of biological process0.0387558675942245
GO:0003823antigen binding0.0389146599002675
GO:0045321leukocyte activation0.0391106792141685
GO:0044424intracellular part0.0391106792141685
GO:0003713transcription coactivator activity0.0400040428996724
GO:0010324membrane invagination0.041392071455171
GO:0006897endocytosis0.041392071455171
GO:0001775cell activation0.0433443669758211
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0433443669758211
GO:0016564transcription repressor activity0.0437879095111814
GO:0065007biological regulation0.0460642644108429
GO:0016477cell migration0.0464545485533415
GO:0008284positive regulation of cell proliferation0.0464545485533415
GO:0007166cell surface receptor linked signal transduction0.0473492756125023



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>disease_data<br>

Disease
Ontology termp-valuen
acute leukemia6.62e-411


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)
MA0003.10.0058989
MA0004.11.39148
MA0006.10.0418213
MA0007.10.314162
MA0009.10.282049
MA0014.10.012421
MA0017.11.16703
MA0019.10.0923449
MA0024.10.209896
MA0025.10.383675
MA0027.11.77546
MA0028.10.049363
MA0029.11.18622
MA0030.11.15704
MA0031.12.25373
MA0038.10.542133
MA0040.10.226506
MA0041.10.166866
MA0042.10.0344066
MA0043.10.282278
MA0046.10.274202
MA0048.10.477418
MA0050.10.324596
MA0051.10.249836
MA0052.10.2291
MA0055.10.484343
MA0056.10
MA0057.10.312951
MA0058.11.72139
MA0059.10.628755
MA0060.10.00788673
MA0061.111.9752
MA0063.10
MA0066.12.50831
MA0067.10.537012
MA0068.10.302463
MA0069.10.271442
MA0070.10.263481
MA0071.10.805793
MA0072.10.721253
MA0073.10.0552396
MA0074.10.531919
MA0076.10.0195703
MA0077.10.254892
MA0078.10.748495
MA0081.11.71368
MA0083.10.287504
MA0084.10.703837
MA0087.10.258584
MA0088.10.105486
MA0089.10
MA0090.10.0971665
MA0091.10.15216
MA0092.10.0289567
MA0093.11.31245
MA0095.10
MA0098.10
MA0100.10.570953
MA0101.10.125201
MA0103.12.93385
MA0105.17.48109
MA0106.12.13275
MA0107.11.17151
MA0108.20.172469
MA0109.10
MA0111.10.26112
MA0113.12.87652
MA0114.11.13532
MA0115.10.471806
MA0116.11.19632
MA0117.10.309701
MA0119.10.0139875
MA0122.10.329219
MA0124.10.437263
MA0125.10.36951
MA0130.10
MA0131.10.12559
MA0132.10
MA0133.10
MA0135.10.304312
MA0136.10.262713
MA0139.10.585192
MA0140.10.797927
MA0141.10.376049
MA0142.10.155551
MA0143.10.665408
MA0144.10.0134674
MA0145.10.210673
MA0146.10.0511259
MA0147.10.919595
MA0148.10.692946
MA0149.10.0540502
MA0062.20.0443033
MA0035.20.457865
MA0039.20.170143
MA0138.20.751292
MA0002.22.30707
MA0137.20.14359
MA0104.20.597809
MA0047.20.603156
MA0112.25.8839
MA0065.25.83688
MA0150.11.89015
MA0151.10
MA0152.10.059761
MA0153.10.356306
MA0154.11.48306
MA0155.10.23489
MA0156.10.296535
MA0157.11.3775
MA0158.10
MA0159.11.22606
MA0160.10.0502284
MA0161.10
MA0162.10.0017378
MA0163.11.31498
MA0164.10.692518
MA0080.20.253231
MA0018.20.0912146
MA0099.20.0598901
MA0079.24.99145e-08
MA0102.20.737926
MA0258.12.76074
MA0259.10.471374
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
EBF1#1879163.097901511850092.26378724662489e-050.000494515114516329
SPI1#6688122.140258306571150.007697937987721090.0316883428126445



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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