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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:42, 17 September 2013


Full id: C1337_Burkitt_CD19_lymphoma_diffuse_acute_tonsil_appendix



Phase1 CAGE Peaks

Hg19::chr11:2406614..2406631,+p17@CD81
Hg19::chr11:2415061..2415109,+p20@CD81
Hg19::chr11:64900193..64900215,+p@chr11:64900193..64900215
+
Hg19::chr15:89182587..89182600,+p11@ISG20
Hg19::chr3:32001842..32001868,-p5@OSBPL10
Hg19::chr9:95824637..95824655,+p@chr9:95824637..95824655
+


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:0043128positive regulation of 1-phosphatidylinositol 4-kinase activity0.00307311903920876
GO:0008310single-stranded DNA specific 3'-5' exodeoxyribonuclease activity0.00307311903920876
GO:0043126regulation of 1-phosphatidylinositol 4-kinase activity0.00307311903920876
GO:0046813virion attachment, binding of host cell surface receptor0.00307311903920876
GO:0008859exoribonuclease II activity0.00307311903920876
GO:0008297single-stranded DNA specific exodeoxyribonuclease activity0.00512171429365841
GO:00082963'-5'-exodeoxyribonuclease activity0.00552014538017045
GO:0019062virion attachment to host cell surface receptor0.00552014538017045
GO:0051704multi-organism process0.00552014538017045
GO:0000738DNA catabolic process, exonucleolytic0.0061456953109873
GO:0006661phosphatidylinositol biosynthetic process0.00768053622240581
GO:0043550regulation of lipid kinase activity0.00768053622240581
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.00768053622240581
GO:0004529exodeoxyribonuclease activity0.00768053622240581
GO:0044409entry into host0.00768053622240581
GO:0030260entry into host cell0.00768053622240581
GO:0019059initiation of viral infection0.00768053622240581
GO:0052192movement in environment of other organism during symbiotic interaction0.00768053622240581
GO:0046718entry of virus into host cell0.00768053622240581
GO:0052126movement in host environment0.00768053622240581
GO:0051828entry into other organism during symbiotic interaction0.00768053622240581
GO:0051806entry into cell of other organism during symbiotic interaction0.00768053622240581
GO:00001753'-5'-exoribonuclease activity0.00801423663574463
GO:0016896exoribonuclease activity, producing 5'-phosphomonoesters0.00904943320919911
GO:0004532exoribonuclease activity0.00904943320919911
GO:0016605PML body0.00904943320919911
GO:0008283cell proliferation0.00904943320919911
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.00904943320919911
GO:0044255cellular lipid metabolic process0.00904943320919911
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0106295800771421
GO:0051701interaction with host0.0106295800771421
GO:0042327positive regulation of phosphorylation0.0106295800771421
GO:0045937positive regulation of phosphate metabolic process0.0106295800771421
GO:0046488phosphatidylinositol metabolic process0.0106295800771421
GO:0006629lipid metabolic process0.0106295800771421
GO:0001934positive regulation of protein amino acid phosphorylation0.0106295800771421
GO:0033240positive regulation of amine metabolic process0.0106295800771421
GO:00084083'-5' exonuclease activity0.0106295800771421
GO:0045764positive regulation of amino acid metabolic process0.0106295800771421
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0107473700634525
GO:0044403symbiosis, encompassing mutualism through parasitism0.0116964400431298
GO:0044419interspecies interaction between organisms0.0116964400431298
GO:0046489phosphoinositide biosynthetic process0.0122104034369311
GO:0006308DNA catabolic process0.0122104034369311
GO:0018108peptidyl-tyrosine phosphorylation0.0138408135504591
GO:0018212peptidyl-tyrosine modification0.0138408135504591
GO:0001932regulation of protein amino acid phosphorylation0.0138408135504591
GO:0046474glycerophospholipid biosynthetic process0.0138408135504591
GO:0033238regulation of amine metabolic process0.0138408135504591
GO:0006401RNA catabolic process0.0138408135504591
GO:0006521regulation of amino acid metabolic process0.0138408135504591
GO:0019058viral infectious cycle0.0144749454686281
GO:0004536deoxyribonuclease activity0.0144749454686281
GO:0000187activation of MAPK activity0.0158981075577646
GO:0022415viral reproductive process0.0158981075577646
GO:0042325regulation of phosphorylation0.0175281333520275
GO:0043406positive regulation of MAP kinase activity0.0177577205244823
GO:0051174regulation of phosphorus metabolic process0.017933986465953
GO:0019220regulation of phosphate metabolic process0.017933986465953
GO:0004527exonuclease activity0.0184002034618907
GO:0030384phosphoinositide metabolic process0.0201047733179097
GO:0051247positive regulation of protein metabolic process0.0210136885862123
GO:0008654phospholipid biosynthetic process0.0222677156438762
GO:0043405regulation of MAP kinase activity0.0222677156438762
GO:0009615response to virus0.0230949428438987
GO:0004540ribonuclease activity0.0230949428438987
GO:0006650glycerophospholipid metabolic process0.0230949428438987
GO:0016604nuclear body0.024327393602476
GO:0046467membrane lipid biosynthetic process0.0250810723586737
GO:0018193peptidyl-amino acid modification0.026466815327271
GO:0006869lipid transport0.0291011781757484
GO:0045860positive regulation of protein kinase activity0.0299671166871473
GO:0033674positive regulation of kinase activity0.0299873162667024
GO:0030145manganese ion binding0.0299873162667024
GO:0051347positive regulation of transferase activity0.0299873162667024
GO:0000165MAPKKK cascade0.0301940094590606
GO:0051707response to other organism0.0408603841728031
GO:0006644phospholipid metabolic process0.0420876339425699
GO:0008202steroid metabolic process0.0430909364360579
GO:0008284positive regulation of cell proliferation0.0444473594883361
GO:0045859regulation of protein kinase activity0.0446469816440654
GO:0043549regulation of kinase activity0.0448557680711419
GO:0004518nuclease activity0.0448557680711419
GO:0051338regulation of transferase activity0.0448557680711419
GO:0043085positive regulation of catalytic activity0.0459310451268304
GO:0006643membrane lipid metabolic process0.0482115020772507



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>

Disease
Ontology termp-valuen
lymphoma9.06e-1110
lymphatic system cancer6.80e-081
lymphosarcoma6.80e-081
acute leukemia1.22e-071


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.11.33289
MA0009.11.03681
MA0014.10.108006
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.93637
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.13.04208
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.11.76074
MA0105.10.419295
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.718193
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.332548
MA0065.21.7308
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.813808
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.20.476723
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
MEF2C#4208213.77045149754130.008235596942270060.0324646149714555



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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