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

Latest revision as of 11:26, 17 September 2013


Full id: C577_lymphoma_Burkitt_diffuse_b_myeloma_plasma_appendix



Phase1 CAGE Peaks

Hg19::chr10:11715600..11715620,+p1@uc001ikv.1
Hg19::chr12:25157568..25157581,+p@chr12:25157568..25157581
+
Hg19::chr12:25205026..25205040,+p9@LRMP
Hg19::chr14:106320502..106320513,-p12@IGHM
Hg19::chr15:59691821..59691828,+p@chr15:59691821..59691828
+
Hg19::chr15:59705215..59705224,-p@chr15:59705215..59705224
-
Hg19::chr15:75639773..75639782,+p15@NEIL1
Hg19::chr18:56563687..56563711,+p@chr18:56563687..56563711
+
Hg19::chr19:19281060..19281078,-p2@MEF2BNB-MEF2B
p2@MEF2B
Hg19::chr2:175462951..175462965,-p7@WIPF1
Hg19::chr2:220142900..220142916,-p22@TUBA4A
Hg19::chr2:42795391..42795403,+p17@MTA3
Hg19::chr2:64370395..64370418,+p1@ENST00000438115
Hg19::chr5:96293965..96293986,+p10@LNPEP
Hg19::chr7:101923076..101923085,+p@chr7:101923076..101923085
+


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:0051649establishment of cellular localization0.00552662192040757
GO:0051641cellular localization0.00552662192040757
GO:0042571immunoglobulin complex, circulating0.0192416604751251
GO:0007010cytoskeleton organization and biogenesis0.0192416604751251
GO:0019814immunoglobulin complex0.0216076366368423
GO:0045022early endosome to late endosome transport0.0216076366368423
GO:0019815B cell receptor complex0.0216076366368423
GO:0046907intracellular transport0.0216076366368423
GO:0030705cytoskeleton-dependent intracellular transport0.0216076366368423
GO:0006906vesicle fusion0.0234837102650863
GO:0005522profilin binding0.026683677801369
GO:0000702oxidized base lesion DNA N-glycosylase activity0.0270918033101799
GO:0008534oxidized purine base lesion DNA N-glycosylase activity0.0270918033101799
GO:0016044membrane organization and biogenesis0.0273904043885752
GO:0007516hemocyte development0.0273904043885752
GO:0042386hemocyte differentiation0.0277973802242663
GO:0007017microtubule-based process0.0277973802242663
GO:0003906DNA-(apurinic or apyrimidinic site) lyase activity0.0277973802242663
GO:0030890positive regulation of B cell proliferation0.0277973802242663
GO:0006903vesicle targeting0.0279419887118174
GO:0030888regulation of B cell proliferation0.0279419887118174
GO:0050853B cell receptor signaling pathway0.0280609975354872
GO:0051650establishment of vesicle localization0.0280609975354872
GO:0016043cellular component organization and biogenesis0.0281605506756081
GO:0051648vesicle localization0.0281605506756081
GO:0006996organelle organization and biogenesis0.0302840317239506
GO:0005622intracellular0.0310429794423133
GO:0030048actin filament-based movement0.0310429794423133
GO:0001772immunological synapse0.0310429794423133
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.0310429794423133
GO:0050871positive regulation of B cell activation0.0310429794423133
GO:0045807positive regulation of endocytosis0.0310429794423133
GO:0042100B cell proliferation0.0310429794423133
GO:0019104DNA N-glycosylase activity0.0310429794423133
GO:0051656establishment of organelle localization0.0331805783503322
GO:0042327positive regulation of phosphorylation0.0331805783503322
GO:0016799hydrolase activity, hydrolyzing N-glycosyl compounds0.0331805783503322
GO:0045937positive regulation of phosphate metabolic process0.0331805783503322
GO:0050864regulation of B cell activation0.0331805783503322
GO:0006810transport0.0331805783503322
GO:0001934positive regulation of protein amino acid phosphorylation0.0331805783503322
GO:0033240positive regulation of amine metabolic process0.0331805783503322
GO:0045764positive regulation of amino acid metabolic process0.0331805783503322
GO:0050851antigen receptor-mediated signaling pathway0.0331805783503322
GO:0051234establishment of localization0.0331805783503322
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0331805783503322
GO:0032946positive regulation of mononuclear cell proliferation0.0331805783503322
GO:0002429immune response-activating cell surface receptor signaling pathway0.0331805783503322
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0331805783503322
GO:0050671positive regulation of lymphocyte proliferation0.0331805783503322
GO:0043170macromolecule metabolic process0.0331805783503322
GO:0016192vesicle-mediated transport0.0331805783503322
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0331805783503322
GO:0002757immune response-activating signal transduction0.0331805783503322
GO:0004520endodeoxyribonuclease activity0.0331805783503322
GO:0051640organelle localization0.0331805783503322
GO:0002764immune response-regulating signal transduction0.0331805783503322
GO:0004179membrane alanyl aminopeptidase activity0.0331805783503322
GO:0030100regulation of endocytosis0.0331805783503322
GO:0016284alanine aminopeptidase activity0.0331805783503322
GO:0006284base-excision repair0.0335935694889657
GO:0051179localization0.0343797278606345
GO:0006944membrane fusion0.0343797278606345
GO:0051050positive regulation of transport0.0347541396382348
GO:0016197endosome transport0.0357691233612271
GO:0032944regulation of mononuclear cell proliferation0.0357691233612271
GO:0018108peptidyl-tyrosine phosphorylation0.0357691233612271
GO:0050670regulation of lymphocyte proliferation0.0357691233612271
GO:0044459plasma membrane part0.0357691233612271
GO:0006289nucleotide-excision repair0.035940294858417
GO:0018212peptidyl-tyrosine modification0.036254941554881
GO:0001932regulation of protein amino acid phosphorylation0.0363598696327606
GO:0033238regulation of amine metabolic process0.0363598696327606
GO:0006521regulation of amino acid metabolic process0.0363598696327606
GO:0003684damaged DNA binding0.03774397245156
GO:0009897external side of plasma membrane0.03774397245156
GO:0004536deoxyribonuclease activity0.03774397245156
GO:0016064immunoglobulin mediated immune response0.03774397245156
GO:0051251positive regulation of lymphocyte activation0.03774397245156
GO:0019724B cell mediated immunity0.037782428412284
GO:0032943mononuclear cell proliferation0.037782428412284
GO:0046651lymphocyte proliferation0.037782428412284
GO:0000187activation of MAPK activity0.0401301956548925
GO:0008154actin polymerization and/or depolymerization0.0419210442296136
GO:0042113B cell activation0.0419210442296136
GO:0044237cellular metabolic process0.0424084858387849
GO:0042325regulation of phosphorylation0.0424720760935587
GO:0048471perinuclear region of cytoplasm0.0424720760935587
GO:0044238primary metabolic process0.042725642634001
GO:0043406positive regulation of MAP kinase activity0.0428184511525644
GO:0051174regulation of phosphorus metabolic process0.043780004563187
GO:0019220regulation of phosphate metabolic process0.043780004563187
GO:0044424intracellular part0.044082719341471
GO:0002253activation of immune response0.044082719341471
GO:0002449lymphocyte mediated immunity0.0442291349268762
GO:0006959humoral immune response0.0447841817368642
GO:0002250adaptive immune response0.0447841817368642
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0447841817368642
GO:0051249regulation of lymphocyte activation0.0447841817368642
GO:0002443leukocyte mediated immunity0.0454950552453424
GO:0050865regulation of cell activation0.0461914459110638
GO:0007565female pregnancy0.0463062344559114
GO:0004177aminopeptidase activity0.0468465567744402
GO:0050778positive regulation of immune response0.0468465567744402
GO:0051247positive regulation of protein metabolic process0.0468465567744402
GO:0044260cellular macromolecule metabolic process0.0468465567744402
GO:0002684positive regulation of immune system process0.0468465567744402



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 lineage9.30e-10924
pro-B cell9.30e-10924
B cell7.86e-6314
lymphocyte9.83e-5353
common lymphoid progenitor9.83e-5353
nucleate cell1.09e-5055
lymphoid lineage restricted progenitor cell2.12e-4852
nongranular leukocyte3.91e-22115
hematopoietic lineage restricted progenitor cell8.25e-19120
leukocyte3.55e-18136
mature B cell1.33e-152
pre-B-II cell1.33e-152
transitional stage B cell1.33e-152
small pre-B-II cell1.33e-152
immature B cell1.33e-152
hematopoietic oligopotent progenitor cell8.48e-15161
hematopoietic multipotent progenitor cell8.48e-15161
hematopoietic stem cell4.96e-14168
angioblastic mesenchymal cell4.96e-14168
hematopoietic cell3.93e-13177
precursor B cell1.03e-103
B-1 B cell1.13e-081
antibody secreting cell1.22e-081
plasma cell1.22e-081
plasmablast1.22e-081
Disease
Ontology termp-valuen
lymphoma1.52e-1210
acute leukemia9.74e-091
lymphatic system cancer1.13e-081
lymphosarcoma1.13e-081
genetic disease1.32e-081
monogenic disease1.32e-081
xeroderma pigmentosum1.32e-081


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)
MA0003.10.0972587
MA0004.10.711841
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.00275422
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.11.97132
MA0043.10.669676
MA0046.10.659066
MA0048.11.0552
MA0050.10.688784
MA0051.10.337676
MA0052.10.598036
MA0055.10.229721
MA0056.10
MA0057.10.0196406
MA0058.11.03067
MA0059.10.536577
MA0060.10.877206
MA0061.11.17249
MA0063.10
MA0066.10.905108
MA0067.10.975379
MA0068.10.341559
MA0069.10.655419
MA0070.10.644843
MA0071.10.831024
MA0072.10.640598
MA0073.10.000193423
MA0074.10.894848
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.426561
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.647316
MA0093.10.851459
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.437519
MA0103.10.815939
MA0105.11.29048
MA0106.10.37688
MA0107.11.08326
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.30732
MA0115.10.900969
MA0116.10.660297
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.11.12143
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.917713
MA0139.10.181369
MA0140.10.826015
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.284854
MA0145.10.478485
MA0146.10.197185
MA0147.10.0991954
MA0148.10.276339
MA0149.15.05306
MA0062.20.0512998
MA0035.20.824687
MA0039.20.0386601
MA0138.21.08869
MA0002.20.82964
MA0137.20.153033
MA0104.20.236755
MA0047.20.366327
MA0112.21.33111
MA0065.20.140846
MA0150.10.201098
MA0151.10
MA0152.10.838393
MA0153.10.763487
MA0154.10.912675
MA0155.10.6552
MA0156.10.469333
MA0157.10.46471
MA0158.10
MA0159.10.327637
MA0160.10.288813
MA0161.10
MA0162.10.000900738
MA0163.10.0365728
MA0164.10.402162
MA0080.20.851709
MA0018.20.378086
MA0099.20.312108
MA0079.29.91681e-05
MA0102.21.1957
MA0258.10.964206
MA0259.11.1468
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#187974.156351195065540.0006359408919913270.00521531455191851
TCF12#693853.544821634062140.009855059238932190.0370314647713477
ZEB1#693544.503581871345030.009893096304177240.0371169696774784



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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