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Coexpression cluster:C4710: Difference between revisions

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|full_id=C4710_Monocytederived_Mesenchymal_Macrophage_papillotubular_Dendritic_Alveolar_CD14CD16
|full_id=C4710_Monocytederived_Mesenchymal_Macrophage_papillotubular_Dendritic_Alveolar_CD14CD16
|id=C4710
|id=C4710
|ontology_enrichment_celltype=CL:0002371!3.65e-45!591;CL:0000144!1.33e-42!625;CL:0000003!1.91e-39!722;CL:0000548!1.42e-33!679;CL:0000004!1.42e-33!679;CL:0000255!1.42e-33!679;CL:0000012!2.47e-33!682;CL:0000048!3.35e-28!430;CL:0000723!5.08e-28!436;CL:0000034!1.03e-25!444;CL:0000063!1.56e-25!578;CL:0002194!2.44e-21!63;CL:0000576!2.44e-21!63;CL:0000040!2.44e-21!63;CL:0000559!2.44e-21!63;CL:0000766!7.38e-21!76;CL:0002320!1.48e-20!365;CL:0002009!1.69e-20!65;CL:0000134!2.34e-20!358;CL:0002087!1.01e-19!119;CL:0000738!2.05e-19!140;CL:0000037!1.51e-18!172;CL:0000566!1.51e-18!172;CL:0002032!3.54e-18!165;CL:0000837!3.54e-18!165;CL:0000988!4.43e-18!182;CL:0000557!5.28e-18!71;CL:0000839!1.63e-17!70;CL:0002057!2.79e-17!42;CL:0000763!3.11e-17!112;CL:0000049!3.11e-17!112;CL:0002031!1.97e-16!124;CL:0000222!1.46e-15!119;CL:0000219!1.67e-15!390;CL:0000860!1.15e-14!45;CL:0000183!1.21e-08!59;CL:0002078!1.56e-08!44;CL:0000192!1.68e-08!42;CL:0000514!1.68e-08!42;CL:0000115!3.59e-08!35;CL:0000680!3.90e-08!57;CL:0000056!3.90e-08!57;CL:0000355!3.90e-08!57;CL:0000359!4.65e-08!32;CL:0000187!5.50e-08!54;CL:0000213!8.98e-08!57;CL:0000215!8.98e-08!57
|ontology_enrichment_celltype=CL:0002371!2.01e-45!588;CL:0000003!5.47e-39!722;CL:0000548!1.76e-33!679;CL:0000255!1.76e-33!679;CL:0000048!3.78e-28!427;CL:0000723!4.34e-28!433;CL:0000034!8.09e-26!441;CL:0002194!9.13e-22!59;CL:0000576!9.13e-22!59;CL:0000040!9.13e-22!59;CL:0000559!9.13e-22!59;CL:0002320!2.23e-21!361;CL:0002087!3.26e-21!115;CL:0000134!4.17e-21!354;CL:0000766!8.86e-21!72;CL:0002009!1.16e-20!61;CL:0000037!1.58e-20!168;CL:0000566!1.58e-20!168;CL:0000738!2.75e-20!136;CL:0002032!4.97e-20!161;CL:0000837!4.97e-20!161;CL:0000988!1.20e-19!177;CL:0000473!7.95e-19!48;CL:0000234!7.95e-19!48;CL:0000763!3.06e-18!108;CL:0000049!3.06e-18!108;CL:0000557!4.86e-18!67;CL:0000839!1.30e-17!66;CL:0002031!2.84e-17!120;CL:0000219!1.66e-16!386;CL:0000860!5.29e-15!42;CL:0002057!5.29e-15!42;CL:0000222!1.31e-14!121;CL:0000325!4.63e-10!87;CL:0002078!1.63e-08!45;CL:0000115!5.13e-08!36;CL:0000213!9.05e-08!58;CL:0000215!9.05e-08!58;CL:0000183!2.00e-07!59;CL:0000192!2.26e-07!43;CL:0000514!2.26e-07!43;CL:0000680!3.70e-07!58;CL:0000056!3.70e-07!58;CL:0000355!3.70e-07!58;CL:0000359!3.89e-07!32;CL:0000187!5.58e-07!55
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!2.52e-33!216;UBERON:0002193!2.14e-23!112;UBERON:0002390!6.92e-23!102;UBERON:0003061!6.92e-23!102;UBERON:0002204!1.94e-21!167;UBERON:0002371!1.88e-19!80;UBERON:0002384!1.10e-18!375;UBERON:0001474!2.15e-16!86;UBERON:0004765!6.15e-16!101;UBERON:0001434!6.15e-16!101;UBERON:0002405!1.11e-14!115;UBERON:0004535!2.82e-12!110;UBERON:0000926!1.74e-11!448;UBERON:0004120!1.74e-11!448;UBERON:0006603!1.74e-11!448;UBERON:0001009!3.04e-11!113;UBERON:0000055!2.22e-10!69;UBERON:0001981!7.97e-10!60;UBERON:0007500!7.97e-10!60;UBERON:0004537!7.97e-10!60;UBERON:0006965!7.97e-10!60;UBERON:0002049!1.74e-09!79;UBERON:0007798!1.74e-09!79;UBERON:0001637!3.10e-09!42;UBERON:0003509!3.10e-09!42;UBERON:0004572!3.10e-09!42;UBERON:0004872!5.40e-09!84;UBERON:0000486!1.69e-08!82;UBERON:0003914!4.19e-08!118;UBERON:0004290!2.89e-07!70;UBERON:0000914!2.98e-07!83;UBERON:0002329!2.98e-07!83;UBERON:0003077!2.98e-07!83;UBERON:0003059!2.98e-07!83;UBERON:0007282!2.98e-07!83;UBERON:0009618!2.98e-07!83;UBERON:0007285!2.98e-07!83;UBERON:0004573!5.79e-07!33;UBERON:0004571!5.79e-07!33
|ontology_enrichment_uberon=UBERON:0003081!3.21e-29!203;UBERON:0002193!1.19e-23!108;UBERON:0002390!3.83e-23!98;UBERON:0003061!3.83e-23!98;UBERON:0000926!7.95e-21!315;UBERON:0004120!7.95e-21!315;UBERON:0006603!7.95e-21!315;UBERON:0002204!3.15e-20!167;UBERON:0002405!3.91e-20!93;UBERON:0002371!1.22e-19!76;UBERON:0002384!1.52e-19!371;UBERON:0004765!4.29e-17!90;UBERON:0001474!1.47e-16!82;UBERON:0001434!6.65e-16!100;UBERON:0004535!2.14e-11!109;UBERON:0001009!2.11e-10!112;UBERON:0000055!1.20e-09!68;UBERON:0007500!3.37e-09!59;UBERON:0001981!3.37e-09!59;UBERON:0004537!3.37e-09!59;UBERON:0006965!3.37e-09!59;UBERON:0002049!9.95e-09!78;UBERON:0007798!9.95e-09!78;UBERON:0007503!1.18e-08!78;UBERON:0001637!1.83e-08!42;UBERON:0003509!1.83e-08!42;UBERON:0004572!1.83e-08!42;UBERON:0004872!5.01e-08!83;UBERON:0000486!7.27e-08!83;UBERON:0003914!1.61e-07!117
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191181298833535!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662922083663422!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327790210208597!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324370010831998!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322540562188136!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465027815493772!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00765364469389672!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109236138296245!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296107055286413!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173684901665496!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.008857649942902!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278317337221431!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00204107676267796!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109430869275952!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545829166481088!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331298017527756!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140939207225153
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1683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 16:11, 19 October 2012


Full id: C4710_Monocytederived_Mesenchymal_Macrophage_papillotubular_Dendritic_Alveolar_CD14CD16



Phase1 CAGE Peaks

Hg19::chr7:98972311..98972326,+p2@ARPC1B
Hg19::chr7:98972327..98972338,+p3@ARPC1B
Hg19::chr7:98972345..98972360,+p1@ARPC1B


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
somatic cell2.01e-45588
native cell5.47e-39722
animal cell1.76e-33679
eukaryotic cell1.76e-33679
multi fate stem cell3.78e-28427
somatic stem cell4.34e-28433
stem cell8.09e-26441
monopoietic cell9.13e-2259
monocyte9.13e-2259
monoblast9.13e-2259
promonocyte9.13e-2259
connective tissue cell2.23e-21361
nongranular leukocyte3.26e-21115
mesenchymal cell4.17e-21354
myeloid leukocyte8.86e-2172
macrophage dendritic cell progenitor1.16e-2061
hematopoietic stem cell1.58e-20168
angioblastic mesenchymal cell1.58e-20168
leukocyte2.75e-20136
hematopoietic oligopotent progenitor cell4.97e-20161
hematopoietic multipotent progenitor cell4.97e-20161
hematopoietic cell1.20e-19177
defensive cell7.95e-1948
phagocyte7.95e-1948
myeloid cell3.06e-18108
common myeloid progenitor3.06e-18108
granulocyte monocyte progenitor cell4.86e-1867
myeloid lineage restricted progenitor cell1.30e-1766
hematopoietic lineage restricted progenitor cell2.84e-17120
motile cell1.66e-16386
classical monocyte5.29e-1542
CD14-positive, CD16-negative classical monocyte5.29e-1542
mesodermal cell1.31e-14121
stuff accumulating cell4.63e-1087
meso-epithelial cell1.63e-0845
endothelial cell5.13e-0836
lining cell9.05e-0858
barrier cell9.05e-0858
contractile cell2.00e-0759
smooth muscle cell2.26e-0743
smooth muscle myoblast2.26e-0743
muscle precursor cell3.70e-0758
myoblast3.70e-0758
multi-potent skeletal muscle stem cell3.70e-0758
vascular associated smooth muscle cell3.89e-0732
muscle cell5.58e-0755
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm3.21e-29203
hemolymphoid system1.19e-23108
hematopoietic system3.83e-2398
blood island3.83e-2398
mesoderm7.95e-21315
mesoderm-derived structure7.95e-21315
presumptive mesoderm7.95e-21315
musculoskeletal system3.15e-20167
immune system3.91e-2093
bone marrow1.22e-1976
connective tissue1.52e-19371
skeletal element4.29e-1790
bone element1.47e-1682
skeletal system6.65e-16100
cardiovascular system2.14e-11109
circulatory system2.11e-10112
vessel1.20e-0968
epithelial tube open at both ends3.37e-0959
blood vessel3.37e-0959
blood vasculature3.37e-0959
vascular cord3.37e-0959
vasculature9.95e-0978
vascular system9.95e-0978
epithelial vesicle1.18e-0878
artery1.83e-0842
arterial blood vessel1.83e-0842
arterial system1.83e-0842
splanchnic layer of lateral plate mesoderm5.01e-0883
multilaminar epithelium7.27e-0883
epithelial tube1.61e-07117


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
CCNT2#90536.336201576962630.003930750035764890.0191181298833535
CHD2#1106310.34402283411690.0009033701102746880.00662922083663422
E2F1#186934.907389214879320.008460985347239390.0327790210208597
E2F6#187635.017155731697390.00791769806886330.0324370010831998
EGR1#195834.988179094810140.008056488137383440.0322540562188136
ELF1#199734.258097958807540.01295179875054610.0465027815493772
ETS1#211339.728760922202340.001085840092584840.00765364469389672
HMGN3#932438.178547723350590.001827766942164210.0109236138296245
MYC#460935.22228187160940.007020843755740150.0296107055286413
PAX5#507936.669565531177830.003370290999677260.0173684901665496
POU2F2#545239.106124057742520.001324165192682130.008857649942902
SIN3A#2594235.408884726815140.006318961977991520.0278317337221431
SMARCB1#6598318.25271578115740.000164397760679890.00204107676267796
SPI1#668838.204323508522730.001810593189410520.0109430869275952
TAF7#6879311.43306940492390.0006690181981945830.00545829166481088
YY1#752834.911170749853860.008441455341808260.0331298017527756
ZBTB7A#5134137.35190930787590.002516255860282270.0140939207225153



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.