Personal tools

FF:490-9F9: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 67: Line 67:
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=TBP:2.6850142093;NKX3-2:2.37811303976;HOX{A4,D4}:2.36068813716;NKX2-3_NKX2-5:2.04089288333;TLX2:1.9125918365;T:1.89297391386;ZNF148:1.79247478273;TFCP2:1.77535163857;TFAP4:1.74356531856;FOXL1:1.53756330703;ZNF238:1.50860345391;SMAD1..7,9:1.49987026851;MYOD1:1.45722980739;PAX1,9:1.4475552124;TBX4,5:1.44457629417;TAL1_TCF{3,4,12}:1.44112681751;MAZ:1.42718211063;TGIF1:1.41530869124;LEF1_TCF7_TCF7L1,2:1.38737691928;FOXA2:1.38608429473;GLI1..3:1.36998436728;EP300:1.36207484059;MYFfamily:1.35487343841;GTF2I:1.26364477379;FOSL2:1.26327795158;FOX{F1,F2,J1}:1.25620553355;EN1,2:1.21741988694;MEF2{A,B,C,D}:1.2155751139;FOS_FOS{B,L1}_JUN{B,D}:1.13592733587;GFI1:1.11095916258;MZF1:1.10995404591;VSX1,2:1.10605103645;TLX1..3_NFIC{dimer}:1.06794488151;SRF:1.04224635417;XCPE1{core}:1.03099766356;GATA6:1.0177631088;PATZ1:0.98894839485;PBX1:0.984819430629;TEAD1:0.980350132349;SP1:0.978892851237;SOX{8,9,10}:0.978687152584;GFI1B:0.970298572182;MAFB:0.959298424435;HMX1:0.956793664854;SNAI1..3:0.947303256636;TFAP2{A,C}:0.941306413622;EBF1:0.93915101267;NKX2-1,4:0.923441209423;ESR1:0.906699863218;NHLH1,2:0.899340281616;GCM1,2:0.885736199046;RREB1:0.858132083687;ADNP_IRX_SIX_ZHX:0.833565648055;MTF1:0.820600276349;FOX{D1,D2}:0.78016320146;NANOG:0.777465422361;ATF6:0.770559593889;NFE2L2:0.766288330025;SOX5:0.752080504062;HNF1A:0.75010612326;POU5F1:0.741598162313;CEBPA,B_DDIT3:0.740378339133;ZNF423:0.718503038254;HOXA9_MEIS1:0.715047339908;HMGA1,2:0.711822153046;TP53:0.698779860005;TOPORS:0.680909676045;DBP:0.667298369711;LMO2:0.666518004936;PAX6:0.664925260546;HSF1,2:0.662555915766;PRDM1:0.65129214323;KLF4:0.637963185875;HLF:0.627066920766;HOX{A5,B5}:0.624295870571;GTF2A1,2:0.621321911109;CUX2:0.606429362118;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.593744753066;HIC1:0.590984488617;HIF1A:0.546092114223;NFIX:0.54582649402;MTE{core}:0.500857397565;POU3F1..4:0.498836694549;NANOG{mouse}:0.473114494529;RXRA_VDR{dimer}:0.472376966676;POU6F1:0.465598148061;PRRX1,2:0.450935526355;NFATC1..3:0.448193933513;RBPJ:0.422950040181;EGR1..3:0.417758806707;MYBL2:0.407329504817;HNF4A_NR2F1,2:0.401070999458;IKZF1:0.358938649412;ATF2:0.358126034093;PAX2:0.351615411874;LHX3,4:0.326023627747;TFAP2B:0.319210724407;REST:0.31068353677;PAX5:0.304105817144;OCT4_SOX2{dimer}:0.282607174835;ZIC1..3:0.265136809059;MED-1{core}:0.2482325969;CRX:0.234358044809;NR5A1,2:0.212800242421;NFE2:0.208676365585;NR3C1:0.183479517535;ZBTB6:0.181952107495;CDC5L:0.17843678879;ALX1:0.168622165351;SOX2:0.167502354522;HES1:0.160097454574;GATA4:0.145619227697;ZFP161:0.1275879085;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.126370970424;GZF1:0.115673005405;STAT2,4,6:0.114628268515;ONECUT1,2:0.088977234119;IKZF2:0.0773840414383;ESRRA:0.0741397776927;ZNF384:0.0434722227975;HBP1_HMGB_SSRP1_UBTF:0.0417199004268;ZEB1:0.0374287407985;NFY{A,B,C}:0.029039270471;TFDP1:0.020528172937;RFX2..5_RFXANK_RFXAP:0.0201056889428;BREu{core}:0.00879290986179;NR1H4:-0.0423159962581;RFX1:-0.0482620595649;SPZ1:-0.0494209649773;POU2F1..3:-0.0632622962985;E2F1..5:-0.066528630355;BACH2:-0.100507260231;SOX17:-0.106780875378;FOXD3:-0.108392352686;PPARG:-0.108958842587;NKX3-1:-0.115249164652;DMAP1_NCOR{1,2}_SMARC:-0.120004676195;AHR_ARNT_ARNT2:-0.127735859425;FOXP3:-0.144299090205;FOXM1:-0.153033587977;RORA:-0.154243929092;FOXP1:-0.181996048593;PITX1..3:-0.21400065745;ZNF143:-0.241393937709;JUN:-0.248880145008;IRF7:-0.258849457933;HAND1,2:-0.275573521625;ALX4:-0.300475868102;NFIL3:-0.311321527905;CDX1,2,4:-0.312736101072;SPI1:-0.337161909565;SPIB:-0.344121076628;PAX4:-0.345212856024;AR:-0.362353832298;ETS1,2:-0.37020492736;NKX6-1,2:-0.387727079377;RUNX1..3:-0.39509254819;FOX{I1,J2}:-0.429232586644;NKX2-2,8:-0.46937050112;RXR{A,B,G}:-0.487090355836;NFKB1_REL_RELA:-0.50786999436;UFEwm:-0.510497707444;FOXN1:-0.531364177569;EVI1:-0.545723753035;PDX1:-0.547250780912;NRF1:-0.557141679838;NR6A1:-0.573925088548;STAT5{A,B}:-0.58128291293;MYB:-0.583879237319;bHLH_family:-0.587056108511;POU1F1:-0.601255808284;FOXQ1:-0.641751713859;YY1:-0.644974146427;NFE2L1:-0.654794184123;ATF5_CREB3:-0.660944167281;TEF:-0.723172495196;FOXO1,3,4:-0.728063218883;ARID5B:-0.742834194205;ATF4:-0.767628654357;ELF1,2,4:-0.774832604613;IRF1,2:-0.797203254906;SREBF1,2:-0.902893119351;CREB1:-0.908568198255;AIRE:-0.953418609683;PAX8:-1.01310150597;ELK1,4_GABP{A,B1}:-1.32600479299;STAT1,3:-1.36708256771;BPTF:-1.36737295946;ZBTB16:-1.51278459687
|top_motifs=TBP:2.6850142093;NKX3-2:2.37811303976;HOX{A4,D4}:2.36068813716;NKX2-3_NKX2-5:2.04089288333;TLX2:1.9125918365;T:1.89297391386;ZNF148:1.79247478273;TFCP2:1.77535163857;TFAP4:1.74356531856;FOXL1:1.53756330703;ZNF238:1.50860345391;SMAD1..7,9:1.49987026851;MYOD1:1.45722980739;PAX1,9:1.4475552124;TBX4,5:1.44457629417;TAL1_TCF{3,4,12}:1.44112681751;MAZ:1.42718211063;TGIF1:1.41530869124;LEF1_TCF7_TCF7L1,2:1.38737691928;FOXA2:1.38608429473;GLI1..3:1.36998436728;EP300:1.36207484059;MYFfamily:1.35487343841;GTF2I:1.26364477379;FOSL2:1.26327795158;FOX{F1,F2,J1}:1.25620553355;EN1,2:1.21741988694;MEF2{A,B,C,D}:1.2155751139;FOS_FOS{B,L1}_JUN{B,D}:1.13592733587;GFI1:1.11095916258;MZF1:1.10995404591;VSX1,2:1.10605103645;TLX1..3_NFIC{dimer}:1.06794488151;SRF:1.04224635417;XCPE1{core}:1.03099766356;GATA6:1.0177631088;PATZ1:0.98894839485;PBX1:0.984819430629;TEAD1:0.980350132349;SP1:0.978892851237;SOX{8,9,10}:0.978687152584;GFI1B:0.970298572182;MAFB:0.959298424435;HMX1:0.956793664854;SNAI1..3:0.947303256636;TFAP2{A,C}:0.941306413622;EBF1:0.93915101267;NKX2-1,4:0.923441209423;ESR1:0.906699863218;NHLH1,2:0.899340281616;GCM1,2:0.885736199046;RREB1:0.858132083687;ADNP_IRX_SIX_ZHX:0.833565648055;MTF1:0.820600276349;FOX{D1,D2}:0.78016320146;NANOG:0.777465422361;ATF6:0.770559593889;NFE2L2:0.766288330025;SOX5:0.752080504062;HNF1A:0.75010612326;POU5F1:0.741598162313;CEBPA,B_DDIT3:0.740378339133;ZNF423:0.718503038254;HOXA9_MEIS1:0.715047339908;HMGA1,2:0.711822153046;TP53:0.698779860005;TOPORS:0.680909676045;DBP:0.667298369711;LMO2:0.666518004936;PAX6:0.664925260546;HSF1,2:0.662555915766;PRDM1:0.65129214323;KLF4:0.637963185875;HLF:0.627066920766;HOX{A5,B5}:0.624295870571;GTF2A1,2:0.621321911109;CUX2:0.606429362118;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.593744753066;HIC1:0.590984488617;HIF1A:0.546092114223;NFIX:0.54582649402;MTE{core}:0.500857397565;POU3F1..4:0.498836694549;NANOG{mouse}:0.473114494529;RXRA_VDR{dimer}:0.472376966676;POU6F1:0.465598148061;PRRX1,2:0.450935526355;NFATC1..3:0.448193933513;RBPJ:0.422950040181;EGR1..3:0.417758806707;MYBL2:0.407329504817;HNF4A_NR2F1,2:0.401070999458;IKZF1:0.358938649412;ATF2:0.358126034093;PAX2:0.351615411874;LHX3,4:0.326023627747;TFAP2B:0.319210724407;REST:0.31068353677;PAX5:0.304105817144;OCT4_SOX2{dimer}:0.282607174835;ZIC1..3:0.265136809059;MED-1{core}:0.2482325969;CRX:0.234358044809;NR5A1,2:0.212800242421;NFE2:0.208676365585;NR3C1:0.183479517535;ZBTB6:0.181952107495;CDC5L:0.17843678879;ALX1:0.168622165351;SOX2:0.167502354522;HES1:0.160097454574;GATA4:0.145619227697;ZFP161:0.1275879085;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.126370970424;GZF1:0.115673005405;STAT2,4,6:0.114628268515;ONECUT1,2:0.088977234119;IKZF2:0.0773840414383;ESRRA:0.0741397776927;ZNF384:0.0434722227975;HBP1_HMGB_SSRP1_UBTF:0.0417199004268;ZEB1:0.0374287407985;NFY{A,B,C}:0.029039270471;TFDP1:0.020528172937;RFX2..5_RFXANK_RFXAP:0.0201056889428;BREu{core}:0.00879290986179;NR1H4:-0.0423159962581;RFX1:-0.0482620595649;SPZ1:-0.0494209649773;POU2F1..3:-0.0632622962985;E2F1..5:-0.066528630355;BACH2:-0.100507260231;SOX17:-0.106780875378;FOXD3:-0.108392352686;PPARG:-0.108958842587;NKX3-1:-0.115249164652;DMAP1_NCOR{1,2}_SMARC:-0.120004676195;AHR_ARNT_ARNT2:-0.127735859425;FOXP3:-0.144299090205;FOXM1:-0.153033587977;RORA:-0.154243929092;FOXP1:-0.181996048593;PITX1..3:-0.21400065745;ZNF143:-0.241393937709;JUN:-0.248880145008;IRF7:-0.258849457933;HAND1,2:-0.275573521625;ALX4:-0.300475868102;NFIL3:-0.311321527905;CDX1,2,4:-0.312736101072;SPI1:-0.337161909565;SPIB:-0.344121076628;PAX4:-0.345212856024;AR:-0.362353832298;ETS1,2:-0.37020492736;NKX6-1,2:-0.387727079377;RUNX1..3:-0.39509254819;FOX{I1,J2}:-0.429232586644;NKX2-2,8:-0.46937050112;RXR{A,B,G}:-0.487090355836;NFKB1_REL_RELA:-0.50786999436;UFEwm:-0.510497707444;FOXN1:-0.531364177569;EVI1:-0.545723753035;PDX1:-0.547250780912;NRF1:-0.557141679838;NR6A1:-0.573925088548;STAT5{A,B}:-0.58128291293;MYB:-0.583879237319;bHLH_family:-0.587056108511;POU1F1:-0.601255808284;FOXQ1:-0.641751713859;YY1:-0.644974146427;NFE2L1:-0.654794184123;ATF5_CREB3:-0.660944167281;TEF:-0.723172495196;FOXO1,3,4:-0.728063218883;ARID5B:-0.742834194205;ATF4:-0.767628654357;ELF1,2,4:-0.774832604613;IRF1,2:-0.797203254906;SREBF1,2:-0.902893119351;CREB1:-0.908568198255;AIRE:-0.953418609683;PAX8:-1.01310150597;ELK1,4_GABP{A,B1}:-1.32600479299;STAT1,3:-1.36708256771;BPTF:-1.36737295946;ZBTB16:-1.51278459687
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011374
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:02, 7 March 2012


Name:whole body, embryo E17.5
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage17.5 days embryo
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs10513

00
10.103
100
1000.0766
10000.0737
10010.0651
1002-0.0468
10030.0602
10040
10050.0479
10060.187
10070.00857
10080
10090.0353
101-0.0221
10100
10110.1
10120.0438
1013-0.0355
10140.401
10150.0117
10160.169
10170
10180.371
10190
1020
10200
10210
10220.247
10230
10240.16
10250.437
10260.145
10270.15
10280
1029-0.1
1030.442
10300
10310.344
1032-0.022
10330
10340.198
10350.129
1036-0.0113
10370
10380.0613
10390.0638
1040
10400.124
10410.198



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10513

Jaspar motifP-value
MA0002.20.368
MA0003.10.0865
MA0004.10.0685
MA0006.10.513
MA0007.10.132
MA0009.10.527
MA0014.10.214
MA0017.10.388
MA0018.21.83182e-4
MA0019.10.83
MA0024.10.475
MA0025.10.205
MA0027.10.505
MA0028.15.29781e-9
MA0029.10.549
MA0030.10.422
MA0031.10.755
MA0035.20.0998
MA0038.10.0126
MA0039.20.113
MA0040.10.831
MA0041.10.494
MA0042.10.7
MA0043.10.0627
MA0046.11.97535e-19
MA0047.20.0839
MA0048.10.003
MA0050.11.90546e-7
MA0051.11.39622e-5
MA0052.12.16537e-16
MA0055.13.31586e-5
MA0057.10.638
MA0058.10.0104
MA0059.10.00463
MA0060.10.0385
MA0061.10.106
MA0062.21.94351e-16
MA0065.20.66
MA0066.10.694
MA0067.10.0696
MA0068.10.351
MA0069.10.236
MA0070.10.21
MA0071.10.0247
MA0072.10.175
MA0073.10.986
MA0074.10.192
MA0076.14.3881e-10
MA0077.10.717
MA0078.10.0563
MA0079.20.012
MA0080.24.3656e-7
MA0081.10.0311
MA0083.15.08059e-10
MA0084.10.818
MA0087.10.113
MA0088.10.132
MA0090.10.0408
MA0091.10.763
MA0092.10.29
MA0093.10.0589
MA0099.20.683
MA0100.10.00591
MA0101.10.00669
MA0102.20.199
MA0103.10.804
MA0104.20.0822
MA0105.10.775
MA0106.10.289
MA0107.10.0361
MA0108.21.05129e-53
MA0111.10.647
MA0112.20.664
MA0113.10.15
MA0114.10.846
MA0115.10.169
MA0116.10.873
MA0117.10.165
MA0119.10.211
MA0122.10.73
MA0124.10.871
MA0125.10.0137
MA0131.10.231
MA0135.10.0571
MA0136.11.06296e-13
MA0137.20.00105
MA0138.22.11122e-6
MA0139.10.194
MA0140.10.00369
MA0141.10.0379
MA0142.10.783
MA0143.10.781
MA0144.10.0941
MA0145.10.0786
MA0146.10.255
MA0147.10.0633
MA0148.10.0449
MA0149.10.00532
MA0150.10.183
MA0152.10.932
MA0153.13.53897e-9
MA0154.10.377
MA0155.10.145
MA0156.11.26058e-12
MA0157.10.932
MA0159.10.0416
MA0160.10.0516
MA0162.10.965
MA0163.10.232
MA0164.10.16
MA0258.10.377
MA0259.10.207



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10513

Novel motifP-value
10.508
100.0806
1000.532
1010.1
1020.0485
1030.0386
1040.73
1050.462
1060.581
1070.024
1080.813
1090.372
110.313
1100.292
1110.018
1120.106
1130.633
1140.196
1150.863
1160.371
1170.00415
1180.144
1190.694
120.358
1200.384
1210.291
1220.248
1230.401
1240.646
1250.099
1260.124
1270.78
1280.532
1290.804
130.0371
1300.471
1310.0527
1320.943
1330.0828
1340.482
1350.739
1360.176
1370.55
1380.762
1390.696
140.389
1400.725
1410.838
1420.749
1430.144
1440.817
1450.359
1460.204
1470.95
1480.28
1490.858
150.0267
1500.88
1510.776
1520.534
1530.298
1540.415
1550.0295
1560.0797
1570.134
1580.00395
1590.0657
1600.126
1610.118
1620.274
1630.817
1640.0362
1650.395
1660.118
1670.00395
1680.00139
1690.639
170.966
180.245
190.444
20.0189
200.00368
210.342
220.834
230.274
240.156
250.695
260.511
270.464
280.819
290.0228
30.411
300.072
310.683
320.754
330.19
340.349
350.151
360.0629
370.257
380.702
390.711
40.914
400.211
410.205
420.619
430.999
440.205
450.201
460.737
470.827
480.415
490.515
50.536
500.683
510.857
520.199
530.14
540.476
550.743
560.586
570.529
580.833
590.133
60.91
600.804
610.308
620.792
630.865
640.951
650.87
660.999
670.916
680.53
690.771
70.794
700.0118
710.393
720.504
730.142
740.788
750.0411
760.0016
770.336
780.683
790.836
80.407
800.901
810.587
820.833
830.558
840.705
850.921
860.963
870.58
880.363
890.419
90.489
900.0119
910.505
920.684
930.0316
940.968
950.0238
960.866
970.576
980.748
990.138



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs10513


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000922 (embryo)
0001062 (anatomical entity)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:490-9F9&oldid=724424"