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Coexpression cluster:C3741: Difference between revisions

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|full_id=C3741_granulocyte_Eosinophils_Neutrophils_immature_CD8_Natural_CD14CD16
|full_id=C3741_granulocyte_Eosinophils_Neutrophils_immature_CD8_Natural_CD14CD16
|id=C3741
|id=C3741
|ontology_enrichment_celltype=CL:0000988!2.00e-36!182;CL:0000037!5.33e-36!172;CL:0000566!5.33e-36!172;CL:0000738!3.24e-33!140;CL:0002032!4.42e-32!165;CL:0000837!4.42e-32!165;CL:0002031!1.83e-25!124;CL:0002087!9.37e-24!119;CL:0000763!6.69e-23!112;CL:0000049!6.69e-23!112;CL:0000766!2.60e-20!76;CL:0002057!1.61e-19!42;CL:0000557!2.32e-17!71;CL:0000860!3.83e-17!45;CL:0000839!2.77e-16!70;CL:0002009!3.26e-15!65;CL:0002194!3.46e-14!63;CL:0000576!3.46e-14!63;CL:0000040!3.46e-14!63;CL:0000559!3.46e-14!63;CL:0000791!5.10e-10!18;CL:0000789!5.10e-10!18;CL:0002420!5.10e-10!18;CL:0002419!5.10e-10!18;CL:0000790!5.10e-10!18;CL:0000084!6.60e-09!25;CL:0000827!6.60e-09!25;CL:0000542!1.47e-08!53;CL:0000051!1.47e-08!53;CL:0000838!1.54e-08!52;CL:0000134!9.73e-08!358;CL:0000219!1.67e-07!390;CL:0002320!1.84e-07!365;CL:0002393!8.16e-07!9;CL:0002397!8.16e-07!9;CL:0000094!8.85e-07!8
|ontology_enrichment_celltype=CL:0000988!5.07e-38!177;CL:0000037!2.87e-37!168;CL:0000566!2.87e-37!168;CL:0002032!1.95e-33!161;CL:0000837!1.95e-33!161;CL:0000738!7.78e-33!136;CL:0000763!1.01e-25!108;CL:0000049!1.01e-25!108;CL:0002031!1.76e-25!120;CL:0002087!2.37e-24!115;CL:0000766!4.96e-22!72;CL:0000860!1.79e-19!42;CL:0002057!1.79e-19!42;CL:0000557!4.38e-19!67;CL:0000839!7.94e-18!66;CL:0002009!1.36e-17!61;CL:0002194!2.06e-16!59;CL:0000576!2.06e-16!59;CL:0000040!2.06e-16!59;CL:0000559!2.06e-16!59;CL:0000473!2.15e-16!48;CL:0000234!2.15e-16!48;CL:0000791!6.10e-09!18;CL:0000789!6.10e-09!18;CL:0002420!6.10e-09!18;CL:0002419!6.10e-09!18;CL:0000790!6.10e-09!18;CL:0000325!7.94e-09!87;CL:0000134!2.09e-08!354;CL:0002320!5.15e-08!361;CL:0002242!5.35e-08!55;CL:0000219!7.52e-08!386;CL:0000542!1.55e-07!53;CL:0000051!1.55e-07!53;CL:0000838!1.89e-07!52;CL:0000084!2.86e-07!25;CL:0000827!2.86e-07!25;CL:0002393!7.19e-07!9;CL:0002397!7.19e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.43e-21!102;UBERON:0003061!1.43e-21!102;UBERON:0002193!1.86e-21!112;UBERON:0002371!4.62e-14!80;UBERON:0001474!8.70e-14!86;UBERON:0002405!3.36e-13!115;UBERON:0003081!3.65e-09!216;UBERON:0004765!1.07e-08!101;UBERON:0001434!1.07e-08!101;UBERON:0000178!7.12e-07!15;UBERON:0000179!7.12e-07!15;UBERON:0000463!7.12e-07!15
|ontology_enrichment_uberon=UBERON:0002390!2.80e-21!98;UBERON:0003061!2.80e-21!98;UBERON:0002193!2.97e-21!108;UBERON:0002405!8.74e-17!93;UBERON:0002371!4.86e-15!76;UBERON:0001474!2.02e-13!82;UBERON:0004765!1.83e-10!90;UBERON:0001434!3.00e-08!100;UBERON:0003081!8.33e-08!203
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129620231662309!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.027384424398351!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296249242255042!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115198414273819!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325208615000859!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320488902483503!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046208892484825!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761868010947046!FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225879087430447!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156698456618157!MAX#4149;3:6.45255550900712:0.00372191383426551:0.018641519227741!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269524076381229!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767165887716384!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276579384778281!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239613141840455!SMARCC2#6601;2:62.7702496179317:0.000335837541708507:0.00341690570077884!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374949605469722!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.00064660473085482!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190175955646361!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421470522147656!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329231889776351!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156362020557406!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388887624901898
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}}
}}

Revision as of 15:22, 19 October 2012


Full id: C3741_granulocyte_Eosinophils_Neutrophils_immature_CD8_Natural_CD14CD16



Phase1 CAGE Peaks

Hg19::chr18:77439775..77439861,+p1@CTDP1
Hg19::chr18:77439863..77439883,+p2@CTDP1
Hg19::chr22:24059459..24059470,-p2@GUSBP11


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
hematopoietic cell5.07e-38177
hematopoietic stem cell2.87e-37168
angioblastic mesenchymal cell2.87e-37168
hematopoietic oligopotent progenitor cell1.95e-33161
hematopoietic multipotent progenitor cell1.95e-33161
leukocyte7.78e-33136
myeloid cell1.01e-25108
common myeloid progenitor1.01e-25108
hematopoietic lineage restricted progenitor cell1.76e-25120
nongranular leukocyte2.37e-24115
myeloid leukocyte4.96e-2272
classical monocyte1.79e-1942
CD14-positive, CD16-negative classical monocyte1.79e-1942
granulocyte monocyte progenitor cell4.38e-1967
myeloid lineage restricted progenitor cell7.94e-1866
macrophage dendritic cell progenitor1.36e-1761
monopoietic cell2.06e-1659
monocyte2.06e-1659
monoblast2.06e-1659
promonocyte2.06e-1659
defensive cell2.15e-1648
phagocyte2.15e-1648
mature alpha-beta T cell6.10e-0918
alpha-beta T cell6.10e-0918
immature T cell6.10e-0918
mature T cell6.10e-0918
immature alpha-beta T cell6.10e-0918
stuff accumulating cell7.94e-0987
mesenchymal cell2.09e-08354
connective tissue cell5.15e-08361
nucleate cell5.35e-0855
motile cell7.52e-08386
lymphocyte1.55e-0753
common lymphoid progenitor1.55e-0753
lymphoid lineage restricted progenitor cell1.89e-0752
T cell2.86e-0725
pro-T cell2.86e-0725
intermediate monocyte7.19e-079
CD14-positive, CD16-positive monocyte7.19e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.80e-2198
blood island2.80e-2198
hemolymphoid system2.97e-21108
immune system8.74e-1793
bone marrow4.86e-1576
bone element2.02e-1382
skeletal element1.83e-1090
skeletal system3.00e-08100
lateral plate mesoderm8.33e-08203


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
ATF3#467322.46317452600878.81932387510763e-050.00129620231662309
BCLAF1#9774214.43509840674790.006201147435546130.027384424398351
BRCA1#672213.45615376214920.007119807716084560.0296249242255042
CEBPB#105137.971147625824820.001974187055288560.0115198414273819
E2F1#186934.907389214879320.008460985347239390.0325208615000859
EGR1#195834.988179094810140.008056488137383440.0320488902483503
ELF1#199734.258097958807540.01295179875054610.046208892484825
ETS1#211339.728760922202340.001085840092584840.00761868010947046
FOXA2#3170216.42030916844350.004810682352105480.0225879087430447
JUND#372736.994663941871030.002921845042734990.0156698456618157
MAX#414936.452555509007120.003721913834265510.018641519227741
NFKB1#479035.488063424193840.006049381815655430.0269524076381229
REST#597839.650028716128020.001112636247114590.00767165887716384
SIN3A#2594235.408884726815140.006318961977991520.0276579384778281
SIX5#147912317.0867153554590.0002004060546325010.00239613141840455
SMARCC2#6601262.77024961793170.0003358375417085070.00341690570077884
SRF#6722313.79717826216780.0003806615025800190.00374949605469722
THAP1#55145331.36914460285133.23800758564397e-050.00064660473085482
USF1#739136.361499277207960.00388404057290560.0190175955646361
USF2#7392312.99219738506960.0004558979393427810.00421470522147656
YY1#752834.911170749853860.008441455341808260.0329231889776351
ZBTB33#10009221.10981668665410.002928597060603240.0156362020557406
ZNF143#7702313.50087655222790.0004062804962997170.00388887624901898



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.