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Coexpression cluster:C2069: Difference between revisions

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|full_id=C2069_CD14_Neutrophils_Peripheral_Eosinophils_Basophils_immature_CD14CD16
|full_id=C2069_CD14_Neutrophils_Peripheral_Eosinophils_Basophils_immature_CD14CD16
|id=C2069
|id=C2069
|ontology_enrichment_celltype=CL:0000766!1.24e-74!76;CL:0000860!1.07e-72!45;CL:0002057!2.46e-72!42;CL:0000557!5.25e-65!71;CL:0000738!2.08e-61!140;CL:0000839!2.74e-58!70;CL:0002009!1.59e-56!65;CL:0000763!7.37e-54!112;CL:0000049!7.37e-54!112;CL:0002194!1.43e-53!63;CL:0000576!1.43e-53!63;CL:0000040!1.43e-53!63;CL:0000559!1.43e-53!63;CL:0000037!2.83e-50!172;CL:0000566!2.83e-50!172;CL:0000988!3.09e-46!182;CL:0002032!6.66e-45!165;CL:0000837!6.66e-45!165;CL:0002031!8.81e-45!124;CL:0002087!2.18e-41!119;CL:0000134!2.07e-20!358;CL:0002320!1.49e-19!365;CL:0000219!7.85e-18!390;CL:0002393!2.80e-17!9;CL:0002397!2.80e-17!9;CL:0000094!8.22e-16!8;CL:0000048!8.50e-15!430;CL:0000723!2.94e-14!436;CL:0000034!3.44e-14!444;CL:0000081!5.72e-11!11;CL:0002274!2.68e-08!5;CL:0000457!2.68e-08!5;CL:0002191!2.68e-08!5;CL:0000097!2.68e-08!5;CL:0000831!2.68e-08!5;CL:0002028!2.68e-08!5;CL:0000842!3.49e-07!3;CL:0000775!5.45e-07!3;CL:0000840!7.08e-07!5;CL:0001029!7.08e-07!5;CL:0000767!9.10e-07!3
|ontology_enrichment_celltype=CL:0000860!8.61e-126!42;CL:0002057!8.61e-126!42;CL:0000473!7.56e-109!48;CL:0000234!7.56e-109!48;CL:0000766!2.11e-102!72;CL:0002009!8.64e-91!61;CL:0002194!1.64e-89!59;CL:0000576!1.64e-89!59;CL:0000040!1.64e-89!59;CL:0000559!1.64e-89!59;CL:0000557!6.84e-82!67;CL:0000839!4.02e-79!66;CL:0000763!5.07e-68!108;CL:0000049!5.07e-68!108;CL:0000738!7.78e-68!136;CL:0002087!6.01e-57!115;CL:0000325!1.14e-55!87;CL:0000037!7.57e-53!168;CL:0000566!7.57e-53!168;CL:0000988!1.33e-49!177;CL:0002031!1.55e-48!120;CL:0002032!2.37e-48!161;CL:0000837!2.37e-48!161;CL:0002393!2.07e-31!9;CL:0002397!2.07e-31!9;CL:0000094!2.79e-22!8;CL:0000134!3.94e-19!354;CL:0002320!1.55e-18!361;CL:0000219!1.94e-16!386;CL:0000081!6.62e-16!11;CL:0000048!7.16e-14!427;CL:0000723!1.62e-13!433;CL:0000034!4.65e-13!441;CL:0000226!3.00e-12!3;CL:0000842!3.00e-12!3;CL:0000767!1.98e-11!3;CL:0000875!6.51e-11!3;CL:0002396!6.51e-11!3;CL:0000623!2.30e-10!3;CL:0000825!2.30e-10!3;CL:0000771!9.59e-09!2;CL:0002371!2.33e-07!588
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!8.91e-69!102;UBERON:0003061!8.91e-69!102;UBERON:0002193!8.52e-61!112;UBERON:0002371!3.25e-60!80;UBERON:0001474!8.71e-57!86;UBERON:0004765!1.02e-45!101;UBERON:0001434!1.02e-45!101;UBERON:0002405!1.10e-42!115;UBERON:0003081!1.59e-25!216;UBERON:0002204!8.44e-25!167;UBERON:0002384!2.20e-18!375;UBERON:0000178!1.17e-10!15;UBERON:0000179!1.17e-10!15;UBERON:0000463!1.17e-10!15;UBERON:0000926!1.91e-08!448;UBERON:0004120!1.91e-08!448;UBERON:0006603!1.91e-08!448
|ontology_enrichment_uberon=UBERON:0002371!3.84e-71!76;UBERON:0002390!1.59e-65!98;UBERON:0003061!1.59e-65!98;UBERON:0001474!2.86e-65!82;UBERON:0004765!1.20e-58!90;UBERON:0002193!1.54e-58!108;UBERON:0002405!1.88e-56!93;UBERON:0001434!7.68e-52!100;UBERON:0002204!3.75e-27!167;UBERON:0003081!2.54e-26!203;UBERON:0002384!1.01e-17!371;UBERON:0000926!3.07e-13!315;UBERON:0004120!3.07e-13!315;UBERON:0006603!3.07e-13!315
|tf_chipseq_enrich=BRCA1#672;2:10.0921153216119:0.013771396990026:0.0484592631482926!FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234520697651095!FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353335203432319!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112803437157404!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386614656259458!NR2C2#7182;2:16.3073054526204:0.00541182534464822:0.024548541833292!PRDM1#639;2:65.9154778887304:0.000341517512076895:0.0034672642601146!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00517906349081605!SMARCC1#6599;2:21.8316796598157:0.00305120745616205:0.0160901315583998!SMARCC2#6601;2:47.0776872134488:0.000666928296709587:0.00544890279121118!STAT1#6772;2:10.3532937485996:0.0131077747617126:0.0464827302413671!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.015713634507577
|tf_chipseq_enrich=BRCA1#672;2:10.0921153216119:0.013771396990026:0.0484592631482926!FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234520697651095!FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353335203432319!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112803437157404!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386614656259458!NR2C2#7182;2:16.3073054526204:0.00541182534464822:0.024548541833292!PRDM1#639;2:65.9154778887304:0.000341517512076895:0.0034672642601146!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00517906349081605!SMARCC1#6599;2:21.8316796598157:0.00305120745616205:0.0160901315583998!SMARCC2#6601;2:47.0776872134488:0.000666928296709587:0.00544890279121118!STAT1#6772;2:10.3532937485996:0.0131077747617126:0.0464827302413671!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.015713634507577
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}}
}}

Revision as of 12:01, 19 October 2012


Full id: C2069_CD14_Neutrophils_Peripheral_Eosinophils_Basophils_immature_CD14CD16



Phase1 CAGE Peaks

Hg19::chr10:70815943..70815956,-p@chr10:70815943..70815956
-
Hg19::chr11:47396114..47396124,-p@chr11:47396114..47396124
-
Hg19::chr9:132536258..132536280,+p@chr9:132536258..132536280
+
Hg19::chr9:132536282..132536289,+p@chr9:132536282..132536289
+


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
classical monocyte8.61e-12642
CD14-positive, CD16-negative classical monocyte8.61e-12642
defensive cell7.56e-10948
phagocyte7.56e-10948
myeloid leukocyte2.11e-10272
macrophage dendritic cell progenitor8.64e-9161
monopoietic cell1.64e-8959
monocyte1.64e-8959
monoblast1.64e-8959
promonocyte1.64e-8959
granulocyte monocyte progenitor cell6.84e-8267
myeloid lineage restricted progenitor cell4.02e-7966
myeloid cell5.07e-68108
common myeloid progenitor5.07e-68108
leukocyte7.78e-68136
nongranular leukocyte6.01e-57115
stuff accumulating cell1.14e-5587
hematopoietic stem cell7.57e-53168
angioblastic mesenchymal cell7.57e-53168
hematopoietic cell1.33e-49177
hematopoietic lineage restricted progenitor cell1.55e-48120
hematopoietic oligopotent progenitor cell2.37e-48161
hematopoietic multipotent progenitor cell2.37e-48161
intermediate monocyte2.07e-319
CD14-positive, CD16-positive monocyte2.07e-319
granulocyte2.79e-228
mesenchymal cell3.94e-19354
connective tissue cell1.55e-18361
motile cell1.94e-16386
blood cell6.62e-1611
multi fate stem cell7.16e-14427
somatic stem cell1.62e-13433
stem cell4.65e-13441
single nucleate cell3.00e-123
mononuclear cell3.00e-123
basophil1.98e-113
non-classical monocyte6.51e-113
CD14-low, CD16-positive monocyte6.51e-113
natural killer cell2.30e-103
pro-NK cell2.30e-103
eosinophil9.59e-092
somatic cell2.33e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow3.84e-7176
hematopoietic system1.59e-6598
blood island1.59e-6598
bone element2.86e-6582
skeletal element1.20e-5890
hemolymphoid system1.54e-58108
immune system1.88e-5693
skeletal system7.68e-52100
musculoskeletal system3.75e-27167
lateral plate mesoderm2.54e-26203
connective tissue1.01e-17371
mesoderm3.07e-13315
mesoderm-derived structure3.07e-13315
presumptive mesoderm3.07e-13315


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
BRCA1#672210.09211532161190.0137713969900260.0484592631482926
FOS#235336.74846648167080.005032452776317940.0234520697651095
FOXA2#3170212.31523187633260.009361916285467240.0353335203432319
JUN#372539.384621894252250.001918994502030470.0112803437157404
JUND#372735.245997956403270.01043432751748420.0386614656259458
NR2C2#7182216.30730545262040.005411825344648220.024548541833292
PRDM1#639265.91547788873040.0003415175120768950.0034672642601146
SMARCB1#6598313.68953683586810.0006305783409379340.00517906349081605
SMARCC1#6599221.83167965981570.003051207456162050.0160901315583998
SMARCC2#6601247.07768721344880.0006669282967095870.00544890279121118
STAT1#6772210.35329374859960.01310777476171260.0464827302413671
TFAP2C#702238.106921457395170.002947011739866440.015713634507577



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.