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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C1118_Burkitt_lymphoma_diffuse_b_acute_CD19_plasma
|full_id=C1118_Burkitt_lymphoma_diffuse_b_acute_CD19_plasma
|gostat_on_coexpression_clusters=GO:0007498!mesoderm development!0.00113915997785516!10320;22806$GO:0050858!negative regulation of antigen receptor-mediated signaling pathway!0.0110510789473724!1997$GO:0050860!negative regulation of T cell receptor signaling pathway!0.0110510789473724!1997$GO:0003835!beta-galactoside alpha-2,6-sialyltransferase activity!0.0110510789473724!6480$GO:0009888!tissue development!0.0110510789473724!10320;22806$GO:0050856!regulation of T cell receptor signaling pathway!0.0136552916438453!1997$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0151262752753576!1997;22806$GO:0050854!regulation of antigen receptor-mediated signaling pathway!0.0170660998902863!1997$GO:0050852!T cell receptor signaling pathway!0.0203224915910323!1997$GO:0006366!transcription from RNA polymerase II promoter!0.0203224915910323!1997;22806$GO:0009311!oligosaccharide metabolic process!0.0203224915910323!6480$GO:0043283!biopolymer metabolic process!0.0203224915910323!1997;6480;10320;22806$GO:0050851!antigen receptor-mediated signaling pathway!0.0203224915910323!1997$GO:0002429!immune response-activating cell surface receptor signaling pathway!0.0203224915910323!1997$GO:0006355!regulation of transcription, DNA-dependent!0.0203224915910323!1997;10320;22806$GO:0002768!immune response-regulating cell surface receptor signaling pathway!0.0203224915910323!1997$GO:0002757!immune response-activating signal transduction!0.0203224915910323!1997$GO:0006351!transcription, DNA-dependent!0.0203224915910323!1997;10320;22806$GO:0032774!RNA biosynthetic process!0.0203224915910323!1997;10320;22806$GO:0002764!immune response-regulating signal transduction!0.0203224915910323!1997$GO:0003677!DNA binding!0.0203224915910323!1997;10320;22806$GO:0008373!sialyltransferase activity!0.0203224915910323!6480$GO:0043231!intracellular membrane-bound organelle!0.0203224915910323!1997;6480;10320;22806$GO:0043227!membrane-bound organelle!0.0203224915910323!1997;6480;10320;22806$GO:0045449!regulation of transcription!0.0203224915910323!1997;10320;22806$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0203224915910323!1997;10320;22806$GO:0001817!regulation of cytokine production!0.0203224915910323!1997$GO:0006350!transcription!0.0203224915910323!1997;10320;22806$GO:0032501!multicellular organismal process!0.0203224915910323!1997;10320;22806$GO:0010468!regulation of gene expression!0.0203224915910323!1997;10320;22806$GO:0031323!regulation of cellular metabolic process!0.0211958981572183!1997;10320;22806$GO:0048513!organ development!0.0226650306162141!10320;22806$GO:0019222!regulation of metabolic process!0.0226650306162141!1997;10320;22806$GO:0016070!RNA metabolic process!0.0226650306162141!1997;10320;22806$GO:0006955!immune response!0.023081999290727!1997;6480$GO:0030173!integral to Golgi membrane!0.023081999290727!6480$GO:0031228!intrinsic to Golgi membrane!0.0254406974024787!6480$GO:0002253!activation of immune response!0.0254406974024787!1997$GO:0006959!humoral immune response!0.0261802736985663!6480$GO:0002376!immune system process!0.0266008630112318!1997;6480$GO:0050778!positive regulation of immune response!0.0266008630112318!1997$GO:0043229!intracellular organelle!0.0266008630112318!1997;6480;10320;22806$GO:0002684!positive regulation of immune system process!0.0266008630112318!1997$GO:0043226!organelle!0.0266008630112318!1997;6480;10320;22806$GO:0003700!transcription factor activity!0.0283306583325041!1997;22806$GO:0050776!regulation of immune response!0.0283306583325041!1997$GO:0043170!macromolecule metabolic process!0.0283306583325041!1997;6480;10320;22806$GO:0002682!regulation of immune system process!0.0283306583325041!1997$GO:0051240!positive regulation of multicellular organismal process!0.0291327884348958!1997$GO:0048731!system development!0.0291327884348958!10320;22806$GO:0001816!cytokine production!0.0301131886371956!1997$GO:0010467!gene expression!0.0324642110987445!1997;10320;22806$GO:0031301!integral to organelle membrane!0.0348911570496159!6480$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0348911570496159!1997$GO:0050794!regulation of cellular process!0.0348911570496159!1997;10320;22806$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0361800227319635!1997;10320;22806$GO:0031300!intrinsic to organelle membrane!0.0361800227319635!6480$GO:0048856!anatomical structure development!0.0373638643779623!10320;22806$GO:0044237!cellular metabolic process!0.0373638643779623!1997;6480;10320;22806$GO:0005634!nucleus!0.0373638643779623!1997;10320;22806$GO:0044238!primary metabolic process!0.0373638643779623!1997;6480;10320;22806$GO:0006486!protein amino acid glycosylation!0.0373638643779623!6480$GO:0050789!regulation of biological process!0.0373638643779623!1997;10320;22806$GO:0043413!biopolymer glycosylation!0.0373638643779623!6480$GO:0044424!intracellular part!0.0373638643779623!1997;6480;10320;22806$GO:0009101!glycoprotein biosynthetic process!0.0373638643779623!6480$GO:0003676!nucleic acid binding!0.0393452323018888!1997;10320;22806$GO:0009100!glycoprotein metabolic process!0.0413980314412772!6480$GO:0016564!transcription repressor activity!0.0415170191575038!1997$GO:0007275!multicellular organismal development!0.0415170191575038!10320;22806$GO:0045893!positive regulation of transcription, DNA-dependent!0.0424799337304436!1997$GO:0065007!biological regulation!0.0426644596032794!1997;10320;22806
|id=C1118
|id=C1118
}}
}}

Revision as of 17:33, 18 May 2012


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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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

No analysis results for this cluster

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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