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Difference between revisions of "Coexpression cluster:C4333"

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|gostat_on_coexpression_clusters=GO:0008296!3'-5'-exodeoxyribonuclease activity!0.00191754554170662!11277$GO:0008853!exodeoxyribonuclease III activity!0.00191754554170662!11277$GO:0032405!MutLalpha complex binding!0.00191754554170662!11277$GO:0032407!MutSalpha complex binding!0.00191754554170662!11277$GO:0016895!exodeoxyribonuclease activity, producing 5'-phosphomonoesters!0.00191754554170662!11277$GO:0032404!mismatch repair complex binding!0.00191754554170662!11277$GO:0004529!exodeoxyribonuclease activity!0.00191754554170662!11277$GO:0016796!exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters!0.00461409395973154!11277$GO:0008408!3'-5' exonuclease activity!0.00503355704697986!11277$GO:0004536!deoxyribonuclease activity!0.00838926174496644!11277$GO:0003697!single-stranded DNA binding!0.00922818791946309!11277$GO:0004527!exonuclease activity!0.00922818791946309!11277$GO:0006298!mismatch repair!0.00922818791946309!11277$GO:0045005!maintenance of fidelity during DNA-dependent DNA replication!0.00922818791946309!11277$GO:0032403!protein complex binding!0.0112975391498881!11277$GO:0042803!protein homodimerization activity!0.0153803131991051!11277$GO:0043566!structure-specific DNA binding!0.0153803131991051!11277$GO:0006261!DNA-dependent DNA replication!0.0153803131991051!11277$GO:0005635!nuclear envelope!0.0165268456375839!11277$GO:0006310!DNA recombination!0.0165268456375839!11277$GO:0004518!nuclease activity!0.0196548418024928!11277$GO:0006260!DNA replication!0.0255872483221476!11277$GO:0042802!identical protein binding!0.0255872483221476!11277$GO:0046983!protein dimerization activity!0.0255872483221476!11277$GO:0006281!DNA repair!0.0263087248322147!11277$GO:0000287!magnesium ion binding!0.0278399204573701!11277$GO:0006974!response to DNA damage stimulus!0.0278399204573701!11277$GO:0009719!response to endogenous stimulus!0.0316994247363375!11277$GO:0031967!organelle envelope!0.0348993288590604!11277$GO:0031975!envelope!0.0348993288590604!11277
 
|gostat_on_coexpression_clusters=GO:0008296!3'-5'-exodeoxyribonuclease activity!0.00191754554170662!11277$GO:0008853!exodeoxyribonuclease III activity!0.00191754554170662!11277$GO:0032405!MutLalpha complex binding!0.00191754554170662!11277$GO:0032407!MutSalpha complex binding!0.00191754554170662!11277$GO:0016895!exodeoxyribonuclease activity, producing 5'-phosphomonoesters!0.00191754554170662!11277$GO:0032404!mismatch repair complex binding!0.00191754554170662!11277$GO:0004529!exodeoxyribonuclease activity!0.00191754554170662!11277$GO:0016796!exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters!0.00461409395973154!11277$GO:0008408!3'-5' exonuclease activity!0.00503355704697986!11277$GO:0004536!deoxyribonuclease activity!0.00838926174496644!11277$GO:0003697!single-stranded DNA binding!0.00922818791946309!11277$GO:0004527!exonuclease activity!0.00922818791946309!11277$GO:0006298!mismatch repair!0.00922818791946309!11277$GO:0045005!maintenance of fidelity during DNA-dependent DNA replication!0.00922818791946309!11277$GO:0032403!protein complex binding!0.0112975391498881!11277$GO:0042803!protein homodimerization activity!0.0153803131991051!11277$GO:0043566!structure-specific DNA binding!0.0153803131991051!11277$GO:0006261!DNA-dependent DNA replication!0.0153803131991051!11277$GO:0005635!nuclear envelope!0.0165268456375839!11277$GO:0006310!DNA recombination!0.0165268456375839!11277$GO:0004518!nuclease activity!0.0196548418024928!11277$GO:0006260!DNA replication!0.0255872483221476!11277$GO:0042802!identical protein binding!0.0255872483221476!11277$GO:0046983!protein dimerization activity!0.0255872483221476!11277$GO:0006281!DNA repair!0.0263087248322147!11277$GO:0000287!magnesium ion binding!0.0278399204573701!11277$GO:0006974!response to DNA damage stimulus!0.0278399204573701!11277$GO:0009719!response to endogenous stimulus!0.0316994247363375!11277$GO:0031967!organelle envelope!0.0348993288590604!11277$GO:0031975!envelope!0.0348993288590604!11277
 
|id=C4333
 
|id=C4333
|ontology_enrichment_celltype=CL:0000738!1.49e-57!140;CL:0002087!3.03e-52!119;CL:0002031!1.50e-48!124;CL:0000037!1.65e-45!172;CL:0000566!1.65e-45!172;CL:0000988!1.33e-44!182;CL:0002032!4.32e-42!165;CL:0000837!4.32e-42!165;CL:0000766!5.73e-32!76;CL:0002009!1.14e-30!65;CL:0002194!1.14e-30!63;CL:0000576!1.14e-30!63;CL:0000040!1.14e-30!63;CL:0000559!1.14e-30!63;CL:0000557!2.51e-29!71;CL:0000839!1.39e-28!70;CL:0002057!3.86e-26!42;CL:0000860!1.39e-25!45;CL:0000763!3.56e-22!112;CL:0000049!3.56e-22!112;CL:0000542!9.09e-19!53;CL:0000051!9.09e-19!53;CL:0000838!1.66e-18!52;CL:0000134!1.88e-15!358;CL:0002320!1.59e-14!365;CL:0000219!3.24e-13!390;CL:0000945!5.73e-12!24;CL:0000826!5.73e-12!24;CL:0000048!7.03e-11!430;CL:0000723!2.27e-10!436;CL:0000034!1.47e-09!444;CL:0000236!5.08e-08!14;CL:0000084!6.15e-07!25;CL:0000827!6.15e-07!25;CL:0002393!9.91e-07!9;CL:0002397!9.91e-07!9
+
|ontology_enrichment_celltype=CL:0000738!1.48e-56!136;CL:0002087!2.74e-51!115;CL:0002031!6.17e-48!120;CL:0000037!2.24e-45!168;CL:0000566!2.24e-45!168;CL:0000988!8.26e-44!177;CL:0002032!9.80e-42!161;CL:0000837!9.80e-42!161;CL:0000766!4.19e-31!72;CL:0002009!2.08e-30!61;CL:0002194!4.42e-30!59;CL:0000576!4.42e-30!59;CL:0000040!4.42e-30!59;CL:0000559!4.42e-30!59;CL:0000557!3.79e-29!67;CL:0000839!5.70e-28!66;CL:0000473!1.35e-26!48;CL:0000234!1.35e-26!48;CL:0000860!3.16e-26!42;CL:0002057!3.16e-26!42;CL:0000763!6.49e-22!108;CL:0000049!6.49e-22!108;CL:0000542!1.03e-18!53;CL:0000051!1.03e-18!53;CL:0002242!1.98e-18!55;CL:0000838!2.24e-18!52;CL:0000945!2.62e-11!24;CL:0000826!2.62e-11!24;CL:0000325!9.70e-11!87;CL:0000134!4.17e-10!354;CL:0002320!4.92e-09!361;CL:0000219!1.62e-08!386;CL:0000236!1.41e-07!14;CL:0000084!1.99e-07!25;CL:0000827!1.99e-07!25
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!4.01e-37!112;UBERON:0002390!3.78e-36!102;UBERON:0003061!3.78e-36!102;UBERON:0002371!4.13e-28!80;UBERON:0001474!5.32e-25!86;UBERON:0002405!4.22e-22!115;UBERON:0004765!4.65e-19!101;UBERON:0001434!4.65e-19!101;UBERON:0002384!4.63e-13!375;UBERON:0003081!5.49e-13!216;UBERON:0002204!1.88e-09!167;UBERON:0007023!2.01e-09!115
+
|ontology_enrichment_uberon=UBERON:0002390!4.02e-35!98;UBERON:0003061!4.02e-35!98;UBERON:0002193!5.83e-34!108;UBERON:0002405!3.11e-29!93;UBERON:0002371!3.23e-28!76;UBERON:0001474!9.10e-25!82;UBERON:0004765!1.15e-20!90;UBERON:0001434!8.68e-18!100;UBERON:0003081!8.83e-13!203;UBERON:0007023!2.45e-09!114;UBERON:0002384!2.19e-08!371;UBERON:0002204!2.80e-07!167
 
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129931071546391!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.029637912952296!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323507088382307!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321726595258743!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463959152703921!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376888320789893!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246857942525534!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00137132786678213!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187124131775312!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324954941495427!MEF2C#4208;2:27.5409029950827:0.00172911993836969:0.0106509912853667!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295474653854669!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270331345447451!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460613302964609!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173411085681!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.0088417932714359!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370859489133412!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024737429787601!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109285408373603!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287599372335363!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00560994635799984!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630679256201579!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190882929459173!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330490761149765!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0378227804718644
 
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129931071546391!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.029637912952296!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323507088382307!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321726595258743!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463959152703921!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376888320789893!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246857942525534!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00137132786678213!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187124131775312!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324954941495427!MEF2C#4208;2:27.5409029950827:0.00172911993836969:0.0106509912853667!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295474653854669!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270331345447451!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460613302964609!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173411085681!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.0088417932714359!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370859489133412!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024737429787601!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109285408373603!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287599372335363!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00560994635799984!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630679256201579!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190882929459173!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330490761149765!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0378227804718644
 
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361435
 
}}
 
}}

Revision as of 06:52, 19 October 2012


Full id: C4333_CD14_Mesenchymal_Eosinophils_CD14CD16_Smooth_xeroderma_Monocytederived



Phase1 CAGE Peaks

  Short description
Hg19::chr3:48507621..48507689,+ p1@TREX1
Hg19::chr6:37401042..37401063,+ p2@FTSJD2
Hg19::chr6:37401066..37401079,+ p4@FTSJD2


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:00082963'-5'-exodeoxyribonuclease activity0.00191754554170662
GO:0008853exodeoxyribonuclease III activity0.00191754554170662
GO:0032405MutLalpha complex binding0.00191754554170662
GO:0032407MutSalpha complex binding0.00191754554170662
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.00191754554170662
GO:0032404mismatch repair complex binding0.00191754554170662
GO:0004529exodeoxyribonuclease activity0.00191754554170662
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.00461409395973154
GO:00084083'-5' exonuclease activity0.00503355704697986
GO:0004536deoxyribonuclease activity0.00838926174496644
GO:0003697single-stranded DNA binding0.00922818791946309
GO:0004527exonuclease activity0.00922818791946309
GO:0006298mismatch repair0.00922818791946309
GO:0045005maintenance of fidelity during DNA-dependent DNA replication0.00922818791946309
GO:0032403protein complex binding0.0112975391498881
GO:0042803protein homodimerization activity0.0153803131991051
GO:0043566structure-specific DNA binding0.0153803131991051
GO:0006261DNA-dependent DNA replication0.0153803131991051
GO:0005635nuclear envelope0.0165268456375839
GO:0006310DNA recombination0.0165268456375839
GO:0004518nuclease activity0.0196548418024928
GO:0006260DNA replication0.0255872483221476
GO:0042802identical protein binding0.0255872483221476
GO:0046983protein dimerization activity0.0255872483221476
GO:0006281DNA repair0.0263087248322147
GO:0000287magnesium ion binding0.0278399204573701
GO:0006974response to DNA damage stimulus0.0278399204573701
GO:0009719response to endogenous stimulus0.0316994247363375
GO:0031967organelle envelope0.0348993288590604
GO:0031975envelope0.0348993288590604



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
leukocyte1.48e-56136
nongranular leukocyte2.74e-51115
hematopoietic lineage restricted progenitor cell6.17e-48120
hematopoietic stem cell2.24e-45168
angioblastic mesenchymal cell2.24e-45168
hematopoietic cell8.26e-44177
hematopoietic oligopotent progenitor cell9.80e-42161
hematopoietic multipotent progenitor cell9.80e-42161
myeloid leukocyte4.19e-3172
macrophage dendritic cell progenitor2.08e-3061
monopoietic cell4.42e-3059
monocyte4.42e-3059
monoblast4.42e-3059
promonocyte4.42e-3059
granulocyte monocyte progenitor cell3.79e-2967
myeloid lineage restricted progenitor cell5.70e-2866
defensive cell1.35e-2648
phagocyte1.35e-2648
classical monocyte3.16e-2642
CD14-positive, CD16-negative classical monocyte3.16e-2642
myeloid cell6.49e-22108
common myeloid progenitor6.49e-22108
lymphocyte1.03e-1853
common lymphoid progenitor1.03e-1853
nucleate cell1.98e-1855
lymphoid lineage restricted progenitor cell2.24e-1852
lymphocyte of B lineage2.62e-1124
pro-B cell2.62e-1124
stuff accumulating cell9.70e-1187
mesenchymal cell4.17e-10354
connective tissue cell4.92e-09361
motile cell1.62e-08386
B cell1.41e-0714
T cell1.99e-0725
pro-T cell1.99e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.02e-3598
blood island4.02e-3598
hemolymphoid system5.83e-34108
immune system3.11e-2993
bone marrow3.23e-2876
bone element9.10e-2582
skeletal element1.15e-2090
skeletal system8.68e-18100
lateral plate mesoderm8.83e-13203
adult organism2.45e-09114
connective tissue2.19e-08371
musculoskeletal system2.80e-07167


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467322.46317452600878.81932387510763e-050.00129931071546391
BRCA1#672213.45615376214920.007119807716084560.029637912952296
E2F6#187635.017155731697390.00791769806886330.0323507088382307
EGR1#195834.988179094810140.008056488137383440.0321726595258743
ELF1#199734.258097958807540.01295179875054610.0463959152703921
FOSL2#2355211.28680040304110.0100534586973120.0376888320789893
HNF4A#3172215.42152690863580.005444210486686610.0246857942525534
IRF4#3662321.91451268674419.49854535978121e-050.00137132786678213
MAX#414936.452555509007120.003721913834265510.0187124131775312
MEF2A#4205212.4954872730960.008235029478029740.0324954941495427
MEF2C#4208227.54090299508270.001729119938369690.0106509912853667
MYC#460935.22228187160940.007020843755740150.0295474653854669
NFKB1#479035.488063424193840.006049381815655430.0270331345447451
NR3C1#290829.982015554115360.01278474365547170.0460613302964609
PAX5#507936.669565531177830.003370290999677260.0173411085681
POU2F2#545239.106124057742520.001324165192682130.0088417932714359
SIX5#147912211.3911435703060.009873820081429030.0370859489133412
SP1#666735.69838137814090.005403962701712170.024737429787601
SPI1#668838.204323508522730.001810593189410520.0109285408373603
STAT1#6772213.80439166479950.006770931708444080.0287599372335363
STAT2#6773243.50918079096040.0006968990898868230.00560994635799984
TCF12#6938310.63446490218640.0008313523990202070.00630679256201579
USF1#739136.361499277207960.00388404057290560.0190882929459173
YY1#752834.911170749853860.008441455341808260.0330490761149765
ZEB1#6935211.25895467836260.01010222676646330.0378227804718644



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.