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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0342676336102362,0.0254706781751602,0.850916923712294,0.588156221300602,0.377416999532401,0,0,0,0.032404058578668,0,0.274342920456472,0.541826132739306,0.39488922725419,0.501074154996811,0,0,0,0.0656939631255499,0,0.0943257785523457,0.165795549095301,0.149578685266771,0.28535904381024,0.109812129893149,0.0990452042849908,0.292722602136872,0.326450924050738,0.216293844171574,0.371855321441455,0.138771381856642,0.104796384789156,0.223799672996739,0.282905586573266,0.254104399297836,0.357682244950033,0.0285414980763901,0.0789870938765965,0.154187968871398,0.110660147363526,0.195175748476722,0.210270953277894,0.21039020075097,0.182267080928499,0.401456015417603,0.130052656369234,0.190544668373194,0.289898101694364,0.39423921055891,0.33580230146073,0.353714680949688,0.455281923549906,0.304828471182237,0.293219649463291,0.496148552190872,0.299852197236831,0.301587969986764,0,0.18924842580987,0,0.267983322146663,0.183710518706332,0.197212289927417,0.110190682492892,0.280239649989794,0.432590746050352,0.33735429485416,0.464096826824654,0.381229950060804,0.326544175202668,0,0.677365751160542,0.656778051334362,0.773118648094874,0.125277242771084,0.912237464726375,0.881810872456986,0.835360880413691,0.242078598014947,0.8094605290061,0.724646261177117,0.70370476703251,0.231290788101556,0.217562041184835,0.144059266752742,0.191087562954052,0.198548821842283,0.861365189803307,0.744151644420716,0.714448876940803,0.154467468535165,0.99151786295129,0.941010609835162,0.812452748347466,0.214083386736107,0.17097476142748,0.290135276828031,0.204743961790246,0.139936884827901,0.07899056079585,0.115891660309884,0.260340471002481,0.743135979153491,0.698500763646648,0.670531213020956,0,0,0,0,0,0,0,0,0,0,0,0.027549189648299,0,0,0,0,0,0.092892723212638,0.0186263052418409,0.13718235424895,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.13043262107049,1.26477514692984,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0351404276532009,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.370206346697763,0.317990581448934,0.374893641966348,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.779382205680047,0.66891390391059,0.750936195856818,0,0,0,0,0,0.638933982102663,0.601148601595643,0.894045460515775,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.541731010020753,0.648499276463506,0.37140500040934,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0329917985786174,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0411414099807427,0,0,0,0.0613516771671337,0.111291581162215,0.187529586342753,0,0,0,0,0,0,0,0,0,0.0604810747382799,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0458873451077849,0,0,0,0,0,0,0,0,0,0.0193242389715322,0,0,0,0.0489174175730049,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0126796920113676,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.036392272307665,0,0,0,0,0,0.0497540124621019,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0266602233572113,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0352989626615976,0,0,0,0,0,0.0881268324752877,0.248905129112398,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0342643952743103,0,0,0,0,0,0,0,0,0.0440642112897698,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0519552566855515,0,0,0,0,0.0312868713390618,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0473659963914933,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0390109377342095,0.0271284845789754,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0271819376754428,0.0508240440617333,0,0,0,0,0,0.0141538448872959,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C297_Eosinophils_CD4_Basophils_Natural_Neutrophils_CD8_Peripheral
|full_id=C297_Eosinophils_CD4_Basophils_Natural_Neutrophils_CD8_Peripheral
|gostat_on_coexpression_clusters=GO:0003713!transcription coactivator activity!0.0112437650335631!1390;5914$GO:0008140!cAMP response element binding protein binding!0.0112437650335631!1390$GO:0003712!transcription cofactor activity!0.0112437650335631!1390;5914$GO:0016563!transcription activator activity!0.0112437650335631!1390;5914$GO:0008134!transcription factor binding!0.0175123136485932!1390;5914$GO:0003708!retinoic acid receptor activity!0.0378801066558398!5914
|gostat_on_coexpression_clusters=GO:0003713!transcription coactivator activity!0.0112437650335631!1390;5914$GO:0008140!cAMP response element binding protein binding!0.0112437650335631!1390$GO:0003712!transcription cofactor activity!0.0112437650335631!1390;5914$GO:0016563!transcription activator activity!0.0112437650335631!1390;5914$GO:0008134!transcription factor binding!0.0175123136485932!1390;5914$GO:0003708!retinoic acid receptor activity!0.0378801066558398!5914

Revision as of 15:48, 12 September 2012


Full id: C297_Eosinophils_CD4_Basophils_Natural_Neutrophils_CD8_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:35416142..35416169,+p3@CREM
Hg19::chr10:35416172..35416184,+p13@CREM
Hg19::chr11:3862855..3862867,+p@chr11:3862855..3862867
+
Hg19::chr12:106697097..106697117,-p@chr12:106697097..106697117
-
Hg19::chr14:52314051..52314062,-p@chr14:52314051..52314062
-
Hg19::chr17:38497640..38497647,+p27@RARA
Hg19::chr17:62097904..62097915,-p4@ICAM2
Hg19::chr17:76837188..76837205,+p@chr17:76837188..76837205
+
Hg19::chr19:41769066..41769091,+p@chr19:41769066..41769091
+
Hg19::chr19:59085102..59085126,+p@chr19:59085102..59085126
+
Hg19::chr1:185536411..185536432,+p@chr1:185536411..185536432
+
Hg19::chr1:198650975..198650986,-p@chr1:198650975..198650986
-
Hg19::chr1:198651031..198651051,-p@chr1:198651031..198651051
-
Hg19::chr1:198651180..198651193,+p@chr1:198651180..198651193
+
Hg19::chr1:198651195..198651213,+p@chr1:198651195..198651213
+
Hg19::chr1:45273151..45273188,+p@chr1:45273151..45273188
+
Hg19::chr20:34356239..34356262,+p@chr20:34356239..34356262
+
Hg19::chr20:42839727..42839752,+p1@LOC100505783
Hg19::chr20:43150543..43150551,-p@chr20:43150543..43150551
-
Hg19::chr20:43150846..43150896,+p@chr20:43150846..43150896
+
Hg19::chr20:43150918..43150934,+p@chr20:43150918..43150934
+
Hg19::chr20:5590658..5590681,+p@chr20:5590658..5590681
+
Hg19::chr22:39097139..39097148,+p@chr22:39097139..39097148
+
Hg19::chr22:47158371..47158384,-p@chr22:47158371..47158384
-
Hg19::chr2:170441202..170441230,-p@chr2:170441202..170441230
-
Hg19::chr2:197034975..197035000,-p@chr2:197034975..197035000
-
Hg19::chr2:197035024..197035040,-p@chr2:197035024..197035040
-
Hg19::chr2:55845186..55845202,+p@chr2:55845186..55845202
+
Hg19::chr2:97204412..97204438,-p@chr2:97204412..97204438
-
Hg19::chr4:152020461..152020473,-p@chr4:152020461..152020473
-
Hg19::chr6:108145154..108145165,-p@chr6:108145154..108145165
-
Hg19::chr7:36816762..36816783,-p@chr7:36816762..36816783
-
Hg19::chr7:66146955..66146980,-p@chr7:66146955..66146980
-
Hg19::chr7:66309834..66309894,-p1@LOC729156
Hg19::chr7:75796016..75796041,+p@chr7:75796016..75796041
+
Hg19::chr8:118532766..118532792,-p@chr8:118532766..118532792
-
Hg19::chr8:64080945..64080978,-p@chr8:64080945..64080978
-
Hg19::chr9:100684655..100684671,+p@chr9:100684655..100684671
+
Hg19::chr9:132650707..132650725,-p8@FNBP1
Hg19::chr9:132650755..132650788,-p4@FNBP1
Hg19::chr9:132650792..132650809,-p12@FNBP1
Hg19::chr9:33159824..33159848,+p@chr9:33159824..33159848
+


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
6.41827216562196e-050.040627662808387273Notch up reg. targets (Netpath):NetPath_3



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:0003713transcription coactivator activity0.0112437650335631
GO:0008140cAMP response element binding protein binding0.0112437650335631
GO:0003712transcription cofactor activity0.0112437650335631
GO:0016563transcription activator activity0.0112437650335631
GO:0008134transcription factor binding0.0175123136485932
GO:0003708retinoic acid receptor activity0.0378801066558398



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
leukocyte3.18e-45140
hematopoietic stem cell2.61e-39172
angioblastic mesenchymal cell2.61e-39172
hematopoietic lineage restricted progenitor cell1.97e-36124
hematopoietic cell2.55e-36182
hematopoietic oligopotent progenitor cell1.35e-35165
hematopoietic multipotent progenitor cell1.35e-35165
nongranular leukocyte7.36e-35119
CD14-positive, CD16-negative classical monocyte1.89e-2242
lymphocyte4.38e-2253
common lymphoid progenitor4.38e-2253
lymphoid lineage restricted progenitor cell4.69e-2252
classical monocyte4.21e-2145
myeloid leukocyte7.93e-1876
myeloid cell7.58e-15112
common myeloid progenitor7.58e-15112
granulocyte monocyte progenitor cell9.34e-1571
myeloid lineage restricted progenitor cell4.57e-1470
macrophage dendritic cell progenitor8.17e-1365
monopoietic cell5.18e-1263
monocyte5.18e-1263
monoblast5.18e-1263
promonocyte5.18e-1263
T cell1.18e-1125
pro-T cell1.18e-1125
mature alpha-beta T cell2.85e-1118
alpha-beta T cell2.85e-1118
immature T cell2.85e-1118
mature T cell2.85e-1118
immature alpha-beta T cell2.85e-1118
lymphocyte of B lineage8.74e-1024
pro-B cell8.74e-1024
mesenchymal cell1.45e-08358
connective tissue cell3.12e-08365
B cell1.69e-0714
CD8-positive, alpha-beta T cell3.78e-0711
intermediate monocyte9.17e-079
CD14-positive, CD16-positive monocyte9.17e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.73e-20102
blood island1.73e-20102
hemolymphoid system4.66e-17112
bone marrow2.10e-1380
bone element4.82e-1286
immune system2.37e-09115
skeletal element1.70e-07101
skeletal system1.70e-07101
adult organism2.44e-07115
connective tissue3.08e-07375
blood9.12e-0715
haemolymphatic fluid9.12e-0715
organism substance9.12e-0715


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#46784.278699909715950.0004663231207055730.00429170958788943
BATF#10538105.799476617215155.93965793861152e-060.00017815391598238
BCL11A#53335117.430095384278041.60966870389735e-078.91368980733483e-06
BCL3#60254.112750333778370.007083034499878040.0295389945347108
BCLAF1#9774147.217549203373953.07699218625634e-092.57292223331005e-07
BRCA1#672178.169807641304864.96860992546389e-126.49457637053221e-10
BRF2#552904102.3405315614627.88423726816163e-084.71874989140133e-06
CCNT2#905172.564653019246780.0001085459125704390.00151071782555226
CEBPB#1051203.79578458372612.93067916697899e-081.99269011406327e-06
CHD2#1106133.201721353417120.0001096654379979560.0015250797175857
CTCF#10664172.169627579577990.000844294016354890.00636658648188364
CTCFL#140690104.701541514041513.63874760731806e-050.000704145194294406
E2F4#187492.714584353275240.004824661988887480.0226382816720918
E2F6#1876192.269665688148820.0001824568162161910.00221011452433342
EBF1#1879173.604998485516031.11799004160593e-064.60417042410418e-05
EGR1#1958252.969154223101272.39834497378206e-081.68673906206616e-06
ELF1#1997272.737348687804852.16864782773001e-081.53657673324488e-06
ELK4#2005124.638766188133725.72957160997209e-060.000172397213878961
EP300#2033182.903117882667091.07598646932828e-050.000279053764266642
ETS1#2113153.474557472215129.80106808828958e-060.000257189384440421
FOS#2353132.785081405133980.0004405220379280360.00410416423899787
FOSL2#2355135.240300187126245.30749507015305e-072.47459588228444e-05
FOXA1#3169133.429963255762165.39654083920658e-050.000914950208938143
GABPB1#2553213.533841918091093.76526773060242e-082.4951827190126e-06
GATA1#262392.905780316528670.003069829661269730.0161826135671992
GTF2B#295986.084539035109384.18112365998534e-050.000757585659134645
GTF2F1#2962144.246553625585882.13268969595545e-067.75813232866217e-05
HEY1#23462282.693407362070471.22115425605082e-089.09024442962877e-07
HMGN3#9324163.115637227943081.76253764855585e-050.000402443527497866
IRF1#3659152.727558483415680.0001686044960766620.00206120624672252
IRF4#3662136.78306345065892.69676201628614e-081.85538292634327e-06
JUND#3727182.997713117944736.81826711745991e-060.000198188978424825
MAX#4149203.072645480479589.91561689780469e-074.20282919314052e-05
MEF2A#4205125.355208831326871.29637386153801e-065.15190219654369e-05
MEF2C#420898.85243310556236.12772843712137e-072.81183580951019e-05
MXI1#4601194.506425260629214.80064081371731e-093.87161487215306e-07
MYC#4609253.108501114053229.1160011331437e-096.96463820295826e-07
NFKB1#4790283.658708949462566.95021977783518e-128.85212199240645e-10
NFYB#480183.192341572102180.003041821609101670.0160471186054943
NRF1#489992.616488453080910.006131293458304640.0271091891745429
PAX5#5079264.12877866215775.12966171779913e-126.68000922874343e-10
PBX3#509094.695967004302319.65983251816607e-050.00137503509385954
POLR2A#5430402.045193501483881.34958418921476e-111.66213706529953e-09
POU2F2#5452214.553062028871263.75602121697042e-103.73595333218261e-08
RAD21#5885122.958581112987520.0004535969171531480.0042173247067175
REST#5978112.527388473271620.002986984463435450.0158797490647358
RFX5#5993236.597665452987791.26053327826328e-142.1688440699924e-12
RXRA#625694.301703672671410.0001872675035127390.0022647094487456
SIN3A#25942303.863489090582241.04916321365618e-131.64032270765026e-11
SIX5#14791272.84778589257650.01038085244441590.0385440076949073
SMC3#9126113.940339554625276.90500969681743e-050.00110099588965789
SP1#6667283.79892091876062.70412291122094e-123.63469617406698e-10
SP2#666874.35892174897410.0009897172147747680.00710412894803175
SPI1#6688224.297502790178573.34981793693828e-103.3639580338067e-08
SRF#6722206.570084886746581.69092484396929e-122.32366447078038e-10
STAT1#677273.451097916199870.003716320439153190.0187411294227291
STAT3#6774133.256024880071559.23444819976633e-050.00134378784385592
TAF1#6872342.706275564650951.14184188233196e-111.42306472970009e-09
TAF7#6879112.994375320337220.0007547943065901110.00593554420495178
TBP#6908343.000719127649464.66216504574772e-136.82905827788002e-11
TCF12#6938215.317232451093212.04337792876457e-112.45296951152003e-09
TCF7L2#6934123.077193303753530.000316052753437910.00323832370414029
USF1#7391142.120499759069320.003707991434821470.0187018359714743
USF2#7392103.093380329778470.001079963216966110.00762354027825098
YY1#7528222.572518011828214.28712985869587e-060.000135638762590833
ZEB1#693583.216844193817880.002901896662633210.0156820441658258
ZNF263#10127122.349097610574480.003410825010177240.0173826747298053



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

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