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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:38, 17 September 2013


Full id: C1118_Burkitt_lymphoma_diffuse_b_acute_CD19_plasma



Phase1 CAGE Peaks

Hg19::chr10:45869433..45869467,-p@chr10:45869433..45869467
-
Hg19::chr13:30951306..30951346,-p3@LINC00426
Hg19::chr13:31019875..31019895,+p@chr13:31019875..31019895
+
Hg19::chr13:41593493..41593506,-p8@ELF1
Hg19::chr17:37934138..37934150,-p12@IKZF3
Hg19::chr3:186739636..186739649,+p2@ST6GAL1
Hg19::chr7:50348268..50348366,+p4@IKZF1


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:0007498mesoderm development0.00113915997785516
GO:0050858negative regulation of antigen receptor-mediated signaling pathway0.0110510789473724
GO:0050860negative regulation of T cell receptor signaling pathway0.0110510789473724
GO:0003835beta-galactoside alpha-2,6-sialyltransferase activity0.0110510789473724
GO:0009888tissue development0.0110510789473724
GO:0050856regulation of T cell receptor signaling pathway0.0136552916438453
GO:0006357regulation of transcription from RNA polymerase II promoter0.0151262752753576
GO:0050854regulation of antigen receptor-mediated signaling pathway0.0170660998902863
GO:0050852T cell receptor signaling pathway0.0203224915910323
GO:0006366transcription from RNA polymerase II promoter0.0203224915910323
GO:0009311oligosaccharide metabolic process0.0203224915910323
GO:0043283biopolymer metabolic process0.0203224915910323
GO:0050851antigen receptor-mediated signaling pathway0.0203224915910323
GO:0002429immune response-activating cell surface receptor signaling pathway0.0203224915910323
GO:0006355regulation of transcription, DNA-dependent0.0203224915910323
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0203224915910323
GO:0002757immune response-activating signal transduction0.0203224915910323
GO:0006351transcription, DNA-dependent0.0203224915910323
GO:0032774RNA biosynthetic process0.0203224915910323
GO:0002764immune response-regulating signal transduction0.0203224915910323
GO:0003677DNA binding0.0203224915910323
GO:0008373sialyltransferase activity0.0203224915910323
GO:0043231intracellular membrane-bound organelle0.0203224915910323
GO:0043227membrane-bound organelle0.0203224915910323
GO:0045449regulation of transcription0.0203224915910323
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0203224915910323
GO:0001817regulation of cytokine production0.0203224915910323
GO:0006350transcription0.0203224915910323
GO:0032501multicellular organismal process0.0203224915910323
GO:0010468regulation of gene expression0.0203224915910323
GO:0031323regulation of cellular metabolic process0.0211958981572183
GO:0048513organ development0.0226650306162141
GO:0019222regulation of metabolic process0.0226650306162141
GO:0016070RNA metabolic process0.0226650306162141
GO:0006955immune response0.023081999290727
GO:0030173integral to Golgi membrane0.023081999290727
GO:0031228intrinsic to Golgi membrane0.0254406974024787
GO:0002253activation of immune response0.0254406974024787
GO:0006959humoral immune response0.0261802736985663
GO:0002376immune system process0.0266008630112318
GO:0050778positive regulation of immune response0.0266008630112318
GO:0043229intracellular organelle0.0266008630112318
GO:0002684positive regulation of immune system process0.0266008630112318
GO:0043226organelle0.0266008630112318
GO:0003700transcription factor activity0.0283306583325041
GO:0050776regulation of immune response0.0283306583325041
GO:0043170macromolecule metabolic process0.0283306583325041
GO:0002682regulation of immune system process0.0283306583325041
GO:0051240positive regulation of multicellular organismal process0.0291327884348958
GO:0048731system development0.0291327884348958
GO:0001816cytokine production0.0301131886371956
GO:0010467gene expression0.0324642110987445
GO:0031301integral to organelle membrane0.0348911570496159
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0348911570496159
GO:0050794regulation of cellular process0.0348911570496159
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0361800227319635
GO:0031300intrinsic to organelle membrane0.0361800227319635
GO:0048856anatomical structure development0.0373638643779623
GO:0044237cellular metabolic process0.0373638643779623
GO:0005634nucleus0.0373638643779623
GO:0044238primary metabolic process0.0373638643779623
GO:0006486protein amino acid glycosylation0.0373638643779623
GO:0050789regulation of biological process0.0373638643779623
GO:0043413biopolymer glycosylation0.0373638643779623
GO:0044424intracellular part0.0373638643779623
GO:0009101glycoprotein biosynthetic process0.0373638643779623
GO:0003676nucleic acid binding0.0393452323018888
GO:0009100glycoprotein metabolic process0.0413980314412772
GO:0016564transcription repressor activity0.0415170191575038
GO:0007275multicellular organismal development0.0415170191575038
GO:0045893positive regulation of transcription, DNA-dependent0.0424799337304436
GO:0065007biological regulation0.0426644596032794



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><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.65e-13114
blood3.18e-1015
haemolymphatic fluid3.18e-1015
organism substance3.18e-1015


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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.12.07492
MA0055.10.362619
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.11.70839
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.21.4671
MA0138.21.6801
MA0002.20.213296
MA0137.20.36398
MA0104.20.636673
MA0047.20.636643
MA0112.20.0758925
MA0065.21.48254
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.10.0167306
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.945415
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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#53335312.15833790154590.001376980163459870.00897021153265877
MEF2C#4208211.80324414074970.01134538181234960.0415958832795051
PAX5#507943.811180303530190.01208261681555190.0438219342130651
POLR2A#543072.147453176558070.004747636447610280.0223229967113258
SRF#672235.913076398071920.01066868130167450.0393886597308253



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

This analysis result is provided for C0 - C305 clusters.

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