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Coexpression cluster:C2440: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!9.57e-26!102;UBERON:0003061!9.57e-26!102;UBERON:0002193!9.34e-25!112;UBERON:0002371!5.73e-18!80;UBERON:0001474!1.19e-13!86;UBERON:0002405!1.28e-11!115;UBERON:0004765!2.68e-10!101;UBERON:0001434!2.68e-10!101;UBERON:0003081!4.10e-09!216;UBERON:0007023!4.42e-07!115
|ontology_enrichment_uberon=UBERON:0002390!9.57e-26!102;UBERON:0003061!9.57e-26!102;UBERON:0002193!9.34e-25!112;UBERON:0002371!5.73e-18!80;UBERON:0001474!1.19e-13!86;UBERON:0002405!1.28e-11!115;UBERON:0004765!2.68e-10!101;UBERON:0001434!2.68e-10!101;UBERON:0003081!4.10e-09!216;UBERON:0007023!4.42e-07!115
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817229697076356!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106491111296728!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199557085805082!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160869993195901!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00887585844815333!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767826977754884!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.00031122520321009!REST#5978;4:9.65002871612802:0.000115282561421917:0.00156995637401794!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.00082641526788655!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241435991559387!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684040540722072!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322123453673718!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115434373512297!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106833251366933!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304138803132482!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279727923450163
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}}
}}

Revision as of 11:39, 5 September 2012


Full id: C2440_CD14_lymphoma_migratory_CD19_b_splenic_immature



Phase1 CAGE Peaks

Hg19::chr17:76732851..76732873,-p4@CYTH1
Hg19::chr17:76732876..76732900,-p5@CYTH1
Hg19::chr17:76732909..76732922,-p7@CYTH1
Hg19::chr17:76732928..76732991,-p2@CYTH1


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><br>


Cell Type
Ontology termp-valuen
leukocyte3.29e-44140
nongranular leukocyte6.56e-35119
hematopoietic stem cell6.59e-35172
angioblastic mesenchymal cell6.59e-35172
hematopoietic lineage restricted progenitor cell1.45e-34124
hematopoietic cell3.99e-33182
hematopoietic oligopotent progenitor cell5.36e-33165
hematopoietic multipotent progenitor cell5.36e-33165
myeloid leukocyte6.01e-2476
CD14-positive, CD16-negative classical monocyte4.44e-2242
granulocyte monocyte progenitor cell1.99e-2171
classical monocyte1.07e-2045
macrophage dendritic cell progenitor4.03e-2065
monopoietic cell5.41e-1963
monocyte5.41e-1963
monoblast5.41e-1963
promonocyte5.41e-1963
myeloid lineage restricted progenitor cell7.89e-1970
myeloid cell4.30e-18112
common myeloid progenitor4.30e-18112
lymphocyte2.91e-1453
common lymphoid progenitor2.91e-1453
lymphoid lineage restricted progenitor cell3.89e-1452
lymphocyte of B lineage1.27e-1024
pro-B cell1.27e-1024
B cell1.31e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.57e-26102
blood island9.57e-26102
hemolymphoid system9.34e-25112
bone marrow5.73e-1880
bone element1.19e-1386
immune system1.28e-11115
skeletal element2.68e-10101
skeletal system2.68e-10101
lateral plate mesoderm4.10e-09216
adult organism4.42e-07115


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#1066445.360256373075030.001211145381643620.00817229697076356
E2F1#186944.907389214879320.001724022357361790.0106491111296728
EBF1#187948.9064668465690.00015887907472010.00199557085805082
ELF1#199744.258097958807540.003041525565781240.0160869993195901
MYC#460945.22228187160940.001344309395272740.00887585844815333
NFKB1#479045.488063424193840.001102199566301980.00767826977754884
NFYB#4801416.75979325353651.26678572070404e-050.00031122520321009
REST#597849.650028716128020.0001152825614219170.00156995637401794
RFX5#5993412.04791082719514.74457429336527e-050.00082641526788655
SMARCB1#6598418.25271578115749.00423392720929e-060.000241435991559387
SP1#666745.69838137814090.0009482606065333980.00684040540722072
TAF1#687243.343046285745290.008005664898701650.0322123453673718
TCF7L2#6934410.77017656313737.42969445082454e-050.00115434373512297
YY1#752844.911170749853860.00171871838055440.0106833251366933
ZEB1#6935416.88843201754391.22862303393937e-050.000304138803132482
ZNF263#1012736.166381227758010.006539814347975980.0279727923450163



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.