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Coexpression cluster:C4267: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!9.74e-08!51;DOID:0060083!9.74e-08!51;DOID:0060058!4.89e-07!10
|ontology_enrichment_disease=DOID:2531!9.74e-08!51;DOID:0060083!9.74e-08!51;DOID:0060058!4.89e-07!10
|ontology_enrichment_uberon=UBERON:0002390!2.44e-11!102;UBERON:0003061!2.44e-11!102;UBERON:0000178!3.22e-11!15;UBERON:0000179!3.22e-11!15;UBERON:0000463!3.22e-11!15;UBERON:0002193!5.00e-10!112;UBERON:0007023!3.45e-07!115
|ontology_enrichment_uberon=UBERON:0002390!2.44e-11!102;UBERON:0003061!2.44e-11!102;UBERON:0000178!3.22e-11!15;UBERON:0000179!3.22e-11!15;UBERON:0000463!3.22e-11!15;UBERON:0002193!5.00e-10!112;UBERON:0007023!3.45e-07!115
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778894544818736!BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000527631901498158!BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00139413329066565!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661852479459686!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917419788456659!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463688780237311!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167891550922163!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00137057001772615!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195227622826034!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270250400994627!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472329540011635!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173334230420689!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00883896769516355!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666098174127841!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00485765912991047!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277614870443991!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309899606911479!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247200937586666!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109253837594664!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644105581368597!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630496065654429!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330292654894018!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243279212299411
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}}
}}

Revision as of 12:31, 5 September 2012


Full id: C4267_splenic_plasma_Burkitt_diffuse_xeroderma_b_migratory



Phase1 CAGE Peaks

Hg19::chr3:111852046..111852053,-p4@GCET2
Hg19::chr3:111852061..111852127,-p1@GCET2
Hg19::chr3:111852128..111852139,-p2@GCET2


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

No GOStat results

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
hematopoietic stem cell7.82e-37172
angioblastic mesenchymal cell7.82e-37172
lymphocyte2.76e-3653
common lymphoid progenitor2.76e-3653
lymphoid lineage restricted progenitor cell2.18e-3552
hematopoietic cell4.63e-35182
leukocyte2.70e-34140
hematopoietic oligopotent progenitor cell1.54e-32165
hematopoietic multipotent progenitor cell1.54e-32165
hematopoietic lineage restricted progenitor cell1.45e-28124
nongranular leukocyte1.18e-27119
lymphocyte of B lineage1.40e-2124
pro-B cell1.40e-2124
T cell2.09e-1325
pro-T cell2.09e-1325
B cell4.98e-1314
mature alpha-beta T cell6.41e-1318
alpha-beta T cell6.41e-1318
immature T cell6.41e-1318
mature T cell6.41e-1318
immature alpha-beta T cell6.41e-1318
CD8-positive, alpha-beta T cell6.17e-1011
dendritic cell4.04e-0810
myeloid cell4.21e-07112
common myeloid progenitor4.21e-07112
conventional dendritic cell5.13e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.44e-11102
blood island2.44e-11102
blood3.22e-1115
haemolymphatic fluid3.22e-1115
organism substance3.22e-1115
hemolymphoid system5.00e-10112
adult organism3.45e-07115
Disease
Ontology termp-valuen
hematologic cancer9.74e-0851
immune system cancer9.74e-0851
lymphoma4.89e-0710


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
BCL11A#53335328.36945510360714.37778126761649e-050.000778894544818736
BCL3#602334.54710280373832.42397750207122e-050.000527631901498158
BCLAF1#9774321.65264761012189.8473954032885e-050.00139413329066565
CHD2#1106310.34402283411690.0009033701102746880.00661852479459686
EBF1#187938.9064668465690.00141523283560980.00917419788456659
ELF1#199734.258097958807540.01295179875054610.0463688780237311
EP300#203336.77394172622320.003216880500103790.0167891550922163
IRF4#3662321.91451268674419.49854535978121e-050.00137057001772615
MEF2A#4205318.74323090964410.0001518243905622470.00195227622826034
NFKB1#479035.488063424193840.006049381815655430.0270250400994627
NRF1#4899312.21027944771090.0005492172401020010.00472329540011635
PAX5#507936.669565531177830.003370290999677260.0173334230420689
POU2F2#545239.106124057742520.001324165192682130.00883896769516355
RAD21#5885310.35503389545630.0009004912073565420.00666098174127841
RFX5#5993312.04791082719510.0005717246050312580.00485765912991047
SIN3A#2594235.408884726815140.006318961977991520.0277614870443991
SMC3#9126315.04493284493280.0002935825420371870.00309899606911479
SP1#666735.69838137814090.005403962701712170.0247200937586666
SPI1#668838.204323508522730.001810593189410520.0109253837594664
STAT3#6774310.51946499715420.0008589184530415310.00644105581368597
TCF12#6938310.63446490218640.0008313523990202070.00630496065654429
YY1#752834.911170749853860.008441455341808260.0330292654894018
ZEB1#6935316.88843201754390.0002075486917327580.00243279212299411



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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