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Coexpression cluster:C2115: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.04e-28!102;UBERON:0003061!1.04e-28!102;UBERON:0002193!1.46e-27!112;UBERON:0002371!3.69e-21!80;UBERON:0007023!1.64e-19!115;UBERON:0001474!1.56e-18!86;UBERON:0002405!2.29e-17!115;UBERON:0004765!4.07e-14!101;UBERON:0001434!4.07e-14!101;UBERON:0003081!9.74e-10!216
|ontology_enrichment_uberon=UBERON:0002390!1.04e-28!102;UBERON:0003061!1.04e-28!102;UBERON:0002193!1.46e-27!112;UBERON:0002371!3.69e-21!80;UBERON:0007023!1.64e-19!115;UBERON:0001474!1.56e-18!86;UBERON:0002405!2.29e-17!115;UBERON:0004765!4.07e-14!101;UBERON:0001434!4.07e-14!101;UBERON:0003081!9.74e-10!216
|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286575155818506!BCL11A#53335;3:21.2770913277053:0.000170483911460614:0.00208052923919549!BCL3#602;3:25.9103271028037:9.48553136097325e-05:0.00137343603189891!BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.0436370779496063!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.024031001438859!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365644256769705!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.00488513661659495!MEF2C#4208;3:30.983515869468:5.56692972943475e-05:0.00094063189453557!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434690163634053!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428081512967641!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188002697476841!RXRA#6256;2:10.0373085695666:0.0139170380592011:0.0488680206389706!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162707981471375!WRNIP1#56897;2:54.909982174688:0.000491193103231144:0.00439134707313452
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}}
}}

Revision as of 13:41, 5 September 2012


Full id: C2115_b_myeloma_CD19_acute_non_xeroderma_Burkitt



Phase1 CAGE Peaks

Hg19::chr11:1543284..1543298,+p@chr11:1543284..1543298
+
Hg19::chr14:106328021..106328027,-p15@IGHM
Hg19::chr14:106328158..106328168,-p6@IGHM
Hg19::chr5:59817936..59817963,-p19@PDE4D


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:0042571immunoglobulin complex, circulating0.00794748769705615
GO:0045022early endosome to late endosome transport0.00794748769705615
GO:0019814immunoglobulin complex0.00794748769705615
GO:0019815B cell receptor complex0.00794748769705615
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0116168295419799
GO:0030890positive regulation of B cell proliferation0.0116168295419799
GO:0030888regulation of B cell proliferation0.0116168295419799
GO:0050853B cell receptor signaling pathway0.0116168295419799
GO:0000267cell fraction0.0116168295419799
GO:0001772immunological synapse0.0116168295419799
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.0116168295419799
GO:0045807positive regulation of endocytosis0.0116168295419799
GO:0050871positive regulation of B cell activation0.0116168295419799
GO:0042100B cell proliferation0.0116168295419799
GO:0005626insoluble fraction0.0116168295419799
GO:0042327positive regulation of phosphorylation0.0116168295419799
GO:0045937positive regulation of phosphate metabolic process0.0116168295419799
GO:0050864regulation of B cell activation0.0116168295419799
GO:0001934positive regulation of protein amino acid phosphorylation0.0116168295419799
GO:0033240positive regulation of amine metabolic process0.0116168295419799
GO:0045764positive regulation of amino acid metabolic process0.0116168295419799
GO:0050851antigen receptor-mediated signaling pathway0.0116168295419799
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0116168295419799
GO:0032946positive regulation of mononuclear cell proliferation0.0116168295419799
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0116168295419799
GO:0002429immune response-activating cell surface receptor signaling pathway0.0116168295419799
GO:0050671positive regulation of lymphocyte proliferation0.0116168295419799
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0116168295419799
GO:0002757immune response-activating signal transduction0.0116168295419799
GO:0002764immune response-regulating signal transduction0.0116168295419799
GO:0030100regulation of endocytosis0.0116168295419799
GO:0051050positive regulation of transport0.0116918571153127
GO:0016197endosome transport0.0116918571153127
GO:0018108peptidyl-tyrosine phosphorylation0.0116918571153127
GO:0050670regulation of lymphocyte proliferation0.0116918571153127
GO:0032944regulation of mononuclear cell proliferation0.0116918571153127
GO:0018212peptidyl-tyrosine modification0.0116918571153127
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0116918571153127
GO:0001932regulation of protein amino acid phosphorylation0.0116918571153127
GO:0033238regulation of amine metabolic process0.0116918571153127
GO:0006521regulation of amino acid metabolic process0.0116918571153127
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0116918571153127
GO:0009897external side of plasma membrane0.0116918571153127
GO:0051251positive regulation of lymphocyte activation0.0116918571153127
GO:0016064immunoglobulin mediated immune response0.0116918571153127
GO:0019724B cell mediated immunity0.0116918571153127
GO:0032943mononuclear cell proliferation0.0116918571153127
GO:0046651lymphocyte proliferation0.0116918571153127
GO:0000187activation of MAPK activity0.0123169181045036
GO:0042113B cell activation0.0129168768328704
GO:0042325regulation of phosphorylation0.013030321291359
GO:0048471perinuclear region of cytoplasm0.013030321291359
GO:0043406positive regulation of MAP kinase activity0.0131835922851881
GO:0051174regulation of phosphorus metabolic process0.0131881982696865
GO:0019220regulation of phosphate metabolic process0.0131881982696865
GO:0002253activation of immune response0.0131881982696865
GO:0002449lymphocyte mediated immunity0.0131881982696865
GO:0006959humoral immune response0.0131881982696865
GO:0002250adaptive immune response0.0131881982696865
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0131881982696865
GO:0051249regulation of lymphocyte activation0.0131881982696865
GO:0002443leukocyte mediated immunity0.0133165530938861
GO:0050865regulation of cell activation0.013440813355957
GO:0050778positive regulation of immune response0.0137908879340018
GO:0051247positive regulation of protein metabolic process0.0137908879340018
GO:0002684positive regulation of immune system process0.0137908879340018
GO:0043405regulation of MAP kinase activity0.0146892985009627
GO:0050776regulation of immune response0.0152502888001131
GO:0002682regulation of immune system process0.0153355378312316
GO:0051240positive regulation of multicellular organismal process0.0158711118749748
GO:0043235receptor complex0.0159424075836415
GO:0002252immune effector process0.0159424075836415
GO:0051049regulation of transport0.0159424075836415
GO:0018193peptidyl-amino acid modification0.0172968612425269
GO:0005813centrosome0.0181924364789254
GO:0008081phosphoric diester hydrolase activity0.0192030526561742
GO:0045860positive regulation of protein kinase activity0.0193204581157774
GO:0033674positive regulation of kinase activity0.0193204581157774
GO:0005815microtubule organizing center0.0193204581157774
GO:0051347positive regulation of transferase activity0.0193204581157774
GO:0009986cell surface0.0193204581157774
GO:0000165MAPKKK cascade0.019342175429056
GO:0046649lymphocyte activation0.0197446520568577
GO:0003823antigen binding0.0222714703628157
GO:0045321leukocyte activation0.0223815037690259
GO:0010324membrane invagination0.0239261978510177
GO:0006897endocytosis0.0239261978510177
GO:0001775cell activation0.0250907357025209
GO:0008284positive regulation of cell proliferation0.0274576146727099
GO:0005625soluble fraction0.0274576146727099
GO:0045859regulation of protein kinase activity0.0275028163566002
GO:0043549regulation of kinase activity0.0277757427115939
GO:0051338regulation of transferase activity0.0280427158273869
GO:0043085positive regulation of catalytic activity0.028751495277678
GO:0051239regulation of multicellular organismal process0.0307729921850535
GO:0016044membrane organization and biogenesis0.0312187665397194
GO:0044444cytoplasmic part0.0338985011741535
GO:0031325positive regulation of cellular metabolic process0.0392568258729603
GO:0007243protein kinase cascade0.0400249082645411
GO:0009893positive regulation of metabolic process0.0408226657216295
GO:0007165signal transduction0.0408226657216295
GO:0019882antigen processing and presentation0.0428523724164199
GO:0051246regulation of protein metabolic process0.0431476503037833
GO:0007154cell communication0.0463533562117629
GO:0042127regulation of cell proliferation0.0470070566661671
GO:0006520amino acid metabolic process0.0470565201783836



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>


Cell Type
Ontology termp-valuen
leukocyte5.56e-37140
nongranular leukocyte1.04e-36119
hematopoietic lineage restricted progenitor cell1.88e-33124
hematopoietic stem cell2.74e-32172
angioblastic mesenchymal cell2.74e-32172
hematopoietic cell1.96e-30182
hematopoietic oligopotent progenitor cell2.04e-30165
hematopoietic multipotent progenitor cell2.04e-30165
lymphocyte of B lineage3.71e-2924
pro-B cell3.71e-2924
granulocyte monocyte progenitor cell4.95e-2371
macrophage dendritic cell progenitor5.68e-2365
monopoietic cell3.63e-2163
monocyte3.63e-2163
monoblast3.63e-2163
promonocyte3.63e-2163
myeloid lineage restricted progenitor cell2.12e-1970
myeloid leukocyte1.53e-1876
B cell4.48e-1814
myeloid cell5.38e-17112
common myeloid progenitor5.38e-17112
CD14-positive, CD16-negative classical monocyte9.72e-1542
classical monocyte4.05e-1345
lymphocyte6.48e-1353
common lymphoid progenitor6.48e-1353
lymphoid lineage restricted progenitor cell4.40e-1252
conventional dendritic cell5.04e-108
dendritic cell9.80e-0810
immature conventional dendritic cell1.83e-075
common dendritic progenitor1.83e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.04e-28102
blood island1.04e-28102
hemolymphoid system1.46e-27112
bone marrow3.69e-2180
adult organism1.64e-19115
bone element1.56e-1886
immune system2.29e-17115
skeletal element4.07e-14101
skeletal system4.07e-14101
lateral plate mesoderm9.74e-10216


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)

{{{tfbs_overrepresentation_jaspar}}}



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
BATF#10538318.26835134422770.0002681660105721290.00286575155818506
BCL11A#53335321.27709132770530.0001704839114606140.00208052923919549
BCL3#602325.91032710280379.48553136097325e-050.00137343603189891
BCLAF1#9774210.82632380506090.01202203816432580.0436370779496063
EBF1#187936.679850134926750.005184294118278910.024031001438859
IRF4#3662316.43588451505810.0003669431395554610.00365644256769705
MEF2A#4205314.0574231822330.0005830038854186610.00488513661659495
MEF2C#4208330.9835158694685.56692972943475e-050.00094063189453557
PAX5#507935.002174148383370.01196533174786410.0434690163634053
PBX3#5090210.95725634337210.01174530180688030.0428081512967641
POU2F2#545249.106124057742520.000145395665174930.00188002697476841
RXRA#6256210.03730856956660.01391703805920110.0488680206389706
TCF12#693837.975848676639820.003090920396013070.0162707981471375
WRNIP1#56897254.9099821746880.0004911931032311440.00439134707313452



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.