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Coexpression cluster:C691: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:6.08945044807591:0.0115136703549497:0.042112356174287!BCL11A#53335;5:11.8206062931696:3.49540037901642e-05:0.00068145626317733!IRF4#3662;5:9.13104695281005:0.000119452296579471:0.00162145547211637!MEF2C#4208;3:10.327838623156:0.00264680895377695:0.0146205151702285!NANOG#79923;3:7.31119462025316:0.00697119958520868:0.02948109465013!NFKB1#4790;7:3.20137033077974:0.00222865791151487:0.0128023103031022!PAX5#5079;6:3.33478276558891:0.00462982151105892:0.0218615575003835!POLR2A#5430;11:1.96849874517823:0.0015351588645567:0.0097601787700394!POU2F2#5452;5:3.79421835739272:0.00649961629267657:0.0278350525276109!SP1#6667;9:4.27378603360567:2.0740195727163e-05:0.000458333749798811!SPI1#6688;8:5.46954900568182:1.52450635998341e-05:0.000360466198166871!TBP#6908;8:2.47118045806426:0.00467271370660667:0.0220551157772989!USF2#7392;6:6.4960986925348:0.000127663267259117:0.00169782554046542
|tf_chipseq_enrich=BATF#10538;3:6.08945044807591:0.0115136703549497:0.042112356174287!BCL11A#53335;5:11.8206062931696:3.49540037901642e-05:0.00068145626317733!IRF4#3662;5:9.13104695281005:0.000119452296579471:0.00162145547211637!MEF2C#4208;3:10.327838623156:0.00264680895377695:0.0146205151702285!NANOG#79923;3:7.31119462025316:0.00697119958520868:0.02948109465013!NFKB1#4790;7:3.20137033077974:0.00222865791151487:0.0128023103031022!PAX5#5079;6:3.33478276558891:0.00462982151105892:0.0218615575003835!POLR2A#5430;11:1.96849874517823:0.0015351588645567:0.0097601787700394!POU2F2#5452;5:3.79421835739272:0.00649961629267657:0.0278350525276109!SP1#6667;9:4.27378603360567:2.0740195727163e-05:0.000458333749798811!SPI1#6688;8:5.46954900568182:1.52450635998341e-05:0.000360466198166871!TBP#6908;8:2.47118045806426:0.00467271370660667:0.0220551157772989!USF2#7392;6:6.4960986925348:0.000127663267259117:0.00169782554046542
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}}
}}

Revision as of 14:24, 26 November 2012


Full id: C691_Monocytederived_CD14_Macrophage_CD19_Dendritic_immature_Whole



Phase1 CAGE Peaks

Hg19::chr11:67771024..67771043,-p2@UNC93B1
Hg19::chr11:67771513..67771604,-p1@UNC93B1
Hg19::chr14:21249200..21249248,+p1@RNASE6
Hg19::chr14:21249254..21249267,+p3@RNASE6
Hg19::chr14:21249300..21249314,+p2@RNASE6
Hg19::chr14:21249998..21250018,+p5@RNASE6
Hg19::chr5:66492562..66492635,-p1@CD180
Hg19::chr6:32908739..32908746,-p3@HLA-DMB
Hg19::chr6:32908765..32908786,-p2@HLA-DMB
Hg19::chr6:32908792..32908830,-p1@HLA-DMB
Hg19::chr6:6588941..6588960,+p1@LY86
Hg19::chr6:6588974..6589011,+p2@LY86


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


p.valueFDRnGenesnPathwayName
5.55202746254732e-050.01757216691896233511Signaling in Immune system (Reactome):REACT_6900
3.63134547651233e-050.0175721669189623255{TRAF6,55} (Static Module):NA



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:0006952defense response0.00398983501859937
GO:0006955immune response0.0145573104414221
GO:0002376immune system process0.0145573104414221
GO:0006954inflammatory response0.0145573104414221
GO:0009611response to wounding0.0244421873004799
GO:0009605response to external stimulus0.0357037352160071
GO:0004522pancreatic ribonuclease activity0.0357037352160071
GO:0016892endoribonuclease activity, producing 3'-phosphomonoesters0.0357037352160071
GO:0031902late endosome membrane0.0357037352160071
GO:0016894endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters0.0357037352160071
GO:0006401RNA catabolic process0.0466318094114567
GO:0005765lysosomal membrane0.0466318094114567
GO:0005770late endosome0.0466318094114567
GO:0005774vacuolar membrane0.0485780051467031
GO:0044437vacuolar part0.0485780051467031
GO:0004521endoribonuclease activity0.0485780051467031
GO:0006959humoral immune response0.0485780051467031
GO:0005886plasma membrane0.0485780051467031
GO:0006950response to stress0.0485780051467031
GO:0010008endosome membrane0.0485780051467031
GO:0044440endosomal part0.0485780051467031



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
leukocyte2.17e-56136
nongranular leukocyte1.19e-52115
hematopoietic stem cell1.14e-51168
angioblastic mesenchymal cell1.14e-51168
hematopoietic lineage restricted progenitor cell1.04e-48120
hematopoietic oligopotent progenitor cell9.91e-48161
hematopoietic multipotent progenitor cell9.91e-48161
hematopoietic cell1.92e-46177
macrophage dendritic cell progenitor4.70e-4361
monopoietic cell2.59e-4159
monocyte2.59e-4159
monoblast2.59e-4159
promonocyte2.59e-4159
granulocyte monocyte progenitor cell3.23e-4167
myeloid leukocyte4.01e-4072
myeloid lineage restricted progenitor cell3.86e-3766
defensive cell6.01e-3748
phagocyte6.01e-3748
myeloid cell2.31e-34108
common myeloid progenitor2.31e-34108
classical monocyte2.09e-3142
CD14-positive, CD16-negative classical monocyte2.09e-3142
lymphocyte of B lineage2.65e-1624
pro-B cell2.65e-1624
B cell1.22e-1214
stuff accumulating cell8.16e-1287
lymphocyte8.50e-1253
common lymphoid progenitor8.50e-1253
lymphoid lineage restricted progenitor cell2.65e-1152
nucleate cell6.77e-1155
dendritic cell5.16e-0810
intermediate monocyte1.38e-079
CD14-positive, CD16-positive monocyte1.38e-079
macrophage6.28e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.74e-4498
blood island5.74e-4498
adult organism3.89e-43114
hemolymphoid system1.55e-39108
bone marrow1.34e-3576
immune system1.33e-3293
bone element6.13e-3182
skeletal element9.06e-2690
skeletal system4.39e-22100
neural tube3.11e-1356
neural rod3.11e-1356
future spinal cord3.11e-1356
neural keel3.11e-1356
lateral plate mesoderm1.09e-12203
regional part of nervous system8.14e-1253
regional part of brain8.14e-1253
regional part of forebrain9.77e-1141
forebrain9.77e-1141
anterior neural tube9.77e-1141
future forebrain9.77e-1141
telencephalon3.49e-0934
brain grey matter3.54e-0934
gray matter3.54e-0934
regional part of telencephalon2.21e-0832
cerebral hemisphere3.45e-0832
blood1.52e-0715
haemolymphatic fluid1.52e-0715
organism substance1.52e-0715
central nervous system1.61e-0781
brain1.81e-0768
future brain1.81e-0768
neural plate2.59e-0782
presumptive neural plate2.59e-0782
tissue3.01e-07773
musculoskeletal system3.17e-07167
regional part of cerebral cortex3.44e-0722


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#1053836.089450448075910.01151367035494970.042112356174287
BCL11A#53335511.82060629316963.49540037901642e-050.00068145626317733
IRF4#366259.131046952810050.0001194522965794710.00162145547211637
MEF2C#4208310.3278386231560.002646808953776950.0146205151702285
NANOG#7992337.311194620253160.006971199585208680.02948109465013
NFKB1#479073.201370330779740.002228657911514870.0128023103031022
PAX5#507963.334782765588910.004629821511058920.0218615575003835
POLR2A#5430111.968498745178230.00153515886455670.0097601787700394
POU2F2#545253.794218357392720.006499616292676570.0278350525276109
SP1#666794.273786033605672.0740195727163e-050.000458333749798811
SPI1#668885.469549005681821.52450635998341e-050.000360466198166871
TBP#690882.471180458064260.004672713706606670.0220551157772989
USF2#739266.49609869253480.0001276632672591170.00169782554046542



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.