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Coexpression cluster:C4059: Difference between revisions

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|full_id=C4059_Hodgkin_splenic_acute_xeroderma_Burkitt_plasma_thymus
|full_id=C4059_Hodgkin_splenic_acute_xeroderma_Burkitt_plasma_thymus
|id=C4059
|id=C4059
|ontology_enrichment_celltype=CL:0000945!4.10e-14!24;CL:0000826!4.10e-14!24;CL:0002322!1.65e-12!5;CL:0000838!4.42e-12!52;CL:0000039!5.29e-12!7;CL:0000586!5.29e-12!7;CL:0000542!9.19e-12!53;CL:0000051!9.19e-12!53;CL:0000817!5.67e-09!3
|ontology_enrichment_celltype=CL:0000945!3.64e-22!24;CL:0000826!3.64e-22!24;CL:0000838!7.16e-13!52;CL:0000542!1.42e-12!53;CL:0000051!1.42e-12!53;CL:0002242!5.15e-12!55;CL:0000785!8.55e-11!2;CL:0000955!8.55e-11!2;CL:0000818!8.55e-11!2;CL:0000954!8.55e-11!2;CL:0000816!8.55e-11!2;CL:0000817!1.84e-07!3
|ontology_enrichment_disease=DOID:0060058!1.22e-20!10
|ontology_enrichment_disease=DOID:0060058!4.11e-23!10
|ontology_enrichment_uberon=UBERON:0002619!2.46e-17!22;UBERON:0001869!1.41e-16!32;UBERON:0001950!2.49e-16!20;UBERON:0001893!2.21e-15!34;UBERON:0000956!6.18e-15!25;UBERON:0000203!6.18e-15!25;UBERON:0002791!4.85e-14!33;UBERON:0007023!7.97e-14!115;UBERON:0002020!1.59e-13!34;UBERON:0003528!1.59e-13!34;UBERON:0000200!3.75e-13!6;UBERON:0002780!4.12e-12!41;UBERON:0001890!4.12e-12!41;UBERON:0006240!4.12e-12!41;UBERON:0003080!9.85e-12!42;UBERON:0001871!2.92e-10!7;UBERON:0004177!1.46e-09!7;UBERON:0001049!1.08e-08!57;UBERON:0005068!1.08e-08!57;UBERON:0006241!1.08e-08!57;UBERON:0007135!1.08e-08!57;UBERON:0000349!1.42e-08!5;UBERON:0002106!1.76e-08!3;UBERON:0004854!1.76e-08!3;UBERON:0009034!1.76e-08!3;UBERON:0002095!1.76e-08!3;UBERON:0004782!1.76e-08!3;UBERON:0003281!1.76e-08!3;UBERON:0009664!1.76e-08!3;UBERON:0002296!1.76e-08!3;UBERON:0005602!1.76e-08!3;UBERON:0001179!1.76e-08!3;UBERON:0006293!1.76e-08!3;UBERON:0002616!2.88e-08!59;UBERON:0000955!3.47e-08!69;UBERON:0006238!3.47e-08!69;UBERON:0003056!7.15e-08!61;UBERON:0002771!3.61e-07!3
|ontology_enrichment_uberon=UBERON:0004177!1.16e-16!7;UBERON:0005057!1.16e-16!7;UBERON:0000349!1.11e-14!5;UBERON:0002106!2.54e-14!3;UBERON:0004854!2.54e-14!3;UBERON:0009034!2.54e-14!3;UBERON:0002095!2.54e-14!3;UBERON:0004782!2.54e-14!3;UBERON:0003281!2.54e-14!3;UBERON:0009664!2.54e-14!3;UBERON:0002296!2.54e-14!3;UBERON:0005602!2.54e-14!3;UBERON:0001179!2.54e-14!3;UBERON:0006293!2.54e-14!3;UBERON:0002619!4.20e-14!22;UBERON:0001869!5.39e-14!32;UBERON:0001893!4.49e-13!34;UBERON:0001950!2.59e-12!20;UBERON:0000956!2.67e-12!25;UBERON:0000203!2.67e-12!25;UBERON:0002791!1.52e-11!32;UBERON:0003528!8.82e-11!34;UBERON:0002020!8.82e-11!34;UBERON:0002780!1.51e-10!41;UBERON:0001890!1.51e-10!41;UBERON:0003080!1.51e-10!41;UBERON:0006240!1.51e-10!41;UBERON:0001876!2.66e-10!2;UBERON:0007023!9.99e-10!114;UBERON:0000073!9.47e-08!53;UBERON:0002616!9.47e-08!53;UBERON:0001049!3.08e-07!56;UBERON:0005068!3.08e-07!56;UBERON:0006241!3.08e-07!56;UBERON:0007135!3.08e-07!56
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279905541320839!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916055172719258!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463053851057197!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167698803309544!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186845298469936!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195131522593287!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269950174092137!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.0047166926518389!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173146648489987!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00665014857906306!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00485252710482402!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165374733290509!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309524198544536!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.006300842757712!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329847783015232!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140449599589557!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243033723689623!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00389637545941654
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}}
}}

Revision as of 15:38, 19 October 2012


Full id: C4059_Hodgkin_splenic_acute_xeroderma_Burkitt_plasma_thymus



Phase1 CAGE Peaks

Hg19::chr20:61640680..61640707,+p3@LOC63930
Hg19::chr20:61640711..61640756,+p1@LOC63930
Hg19::chr20:61640760..61640777,+p2@LOC63930


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>


Uber Anatomy
Ontology termp-valuen
hemopoietic organ1.16e-167
immune organ1.16e-167
limbic system1.11e-145
spleen2.54e-143
gastrointestinal system mesentery2.54e-143
stomach region2.54e-143
mesentery2.54e-143
gastrointestinal system serosa2.54e-143
mesentery of stomach2.54e-143
gut mesentery2.54e-143
dorsal mesentery2.54e-143
dorsal mesogastrium2.54e-143
peritoneal cavity2.54e-143
spleen primordium2.54e-143
regional part of cerebral cortex4.20e-1422
cerebral hemisphere5.39e-1432
telencephalon4.49e-1334
neocortex2.59e-1220
cerebral cortex2.67e-1225
pallium2.67e-1225
regional part of telencephalon1.52e-1132
brain grey matter8.82e-1134
gray matter8.82e-1134
regional part of forebrain1.51e-1041
forebrain1.51e-1041
anterior neural tube1.51e-1041
future forebrain1.51e-1041
amygdala2.66e-102
adult organism9.99e-10114
regional part of nervous system9.47e-0853
regional part of brain9.47e-0853
neural tube3.08e-0756
neural rod3.08e-0756
future spinal cord3.08e-0756
neural keel3.08e-0756
Disease
Ontology termp-valuen
lymphoma4.11e-2310


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
CTCF#1066435.360256373075030.0064925092527670.0279905541320839
EBF1#187938.9064668465690.00141523283560980.00916055172719258
ELF1#199734.258097958807540.01295179875054610.0463053851057197
EP300#203336.77394172622320.003216880500103790.0167698803309544
MAX#414936.452555509007120.003721913834265510.0186845298469936
MEF2A#4205318.74323090964410.0001518243905622470.00195131522593287
NFKB1#479035.488063424193840.006049381815655430.0269950174092137
NRF1#4899312.21027944771090.0005492172401020010.0047166926518389
PAX5#507936.669565531177830.003370290999677260.0173146648489987
RAD21#5885310.35503389545630.0009004912073565420.00665014857906306
RFX5#5993312.04791082719510.0005717246050312580.00485252710482402
RXRA#6256320.07461713913330.0001235730348432220.00165374733290509
SMC3#9126315.04493284493280.0002935825420371870.00309524198544536
TCF12#6938310.63446490218640.0008313523990202070.006300842757712
YY1#752834.911170749853860.008441455341808260.0329847783015232
ZBTB7A#5134137.35190930787590.002516255860282270.0140449599589557
ZEB1#6935316.88843201754390.0002075486917327580.00243033723689623
ZNF143#7702313.50087655222790.0004062804962997170.00389637545941654



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.