Personal tools

FF:475-3I5: 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=HOX{A4,D4}:2.68569107211;NKX2-3_NKX2-5:2.55736200275;TBP:2.32951102147;MYOD1:2.30375529371;ZNF148:2.23144087114;TFAP4:2.16868216543;LHX3,4:2.16643522216;SMAD1..7,9:2.08138674102;EP300:2.04394080423;VSX1,2:1.93282657623;HMX1:1.91462650712;LEF1_TCF7_TCF7L1,2:1.85323421896;TFCP2:1.80488591949;NKX3-2:1.78212765743;GLI1..3:1.77729332567;ESR1:1.73803220282;MAZ:1.73773887965;PATZ1:1.70869986244;TGIF1:1.69573676233;GTF2I:1.69092665135;TFAP2{A,C}:1.67708137463;RREB1:1.63545460541;MYFfamily:1.61174194701;HOX{A5,B5}:1.58406998915;NANOG:1.56547922005;MAFB:1.54679858982;MZF1:1.52212700371;XCPE1{core}:1.51977862057;SOX{8,9,10}:1.5159654057;TBX4,5:1.4846203676;KLF4:1.43798453665;NHLH1,2:1.43055545245;T:1.41018349147;SP1:1.30023624957;PAX5:1.28388265298;MTF1:1.27341348513;PRDM1:1.26568770542;PRRX1,2:1.25352938978;HIC1:1.24871630303;ZNF238:1.24159751596;ZNF423:1.23568411323;PPARG:1.21430524939;EN1,2:1.19549819391;GTF2A1,2:1.18837826061;TOPORS:1.18509984788;MED-1{core}:1.14943540208;HAND1,2:1.14892217482;POU5F1:1.13170143425;REST:1.12906505493;FOXL1:1.11542136744;TAL1_TCF{3,4,12}:1.11469384426;ZIC1..3:1.10665695993;FOS_FOS{B,L1}_JUN{B,D}:1.078195146;ATF2:1.07798293529;ZBTB6:1.07737777143;GFI1B:1.07162478685;MTE{core}:1.04390083216;TFAP2B:1.03674304599;EGR1..3:1.03609204182;GCM1,2:1.01408569945;SOX2:1.01154909249;NKX2-1,4:1.00868261943;MEF2{A,B,C,D}:1.00128238137;ALX1:0.997125735133;LMO2:0.976492872008;RFX2..5_RFXANK_RFXAP:0.971025072725;BREu{core}:0.951249773624;EBF1:0.868217456185;POU6F1:0.849924091578;ADNP_IRX_SIX_ZHX:0.839405087081;ATF6:0.829794325232;TLX1..3_NFIC{dimer}:0.815340469772;TEAD1:0.790667648071;ZFP161:0.787775321524;HIF1A:0.781853251546;SOX5:0.761245714818;HOXA9_MEIS1:0.754892898835;IKZF1:0.736648821572;RFX1:0.736567579381;HES1:0.724704941662;PAX1,9:0.720572858967;TFDP1:0.715685035853;FOSL2:0.712462996483;TLX2:0.705409400647;PAX2:0.671631217492;TP53:0.668382436487;OCT4_SOX2{dimer}:0.661010208808;UFEwm:0.632327870657;SNAI1..3:0.628764451978;GFI1:0.625231921669;POU2F1..3:0.594510463046;AHR_ARNT_ARNT2:0.589856958085;FOXP3:0.562546389054;CRX:0.537999967687;CDC5L:0.520609837959;CUX2:0.517118415739;RXRA_VDR{dimer}:0.500421929583;NFATC1..3:0.487573473824;PAX6:0.463799301415;FOXM1:0.446051829919;SPZ1:0.433853532928;HSF1,2:0.431450692837;NR3C1:0.419192414055;SRF:0.413359280494;ZEB1:0.403884221948;HMGA1,2:0.378799896481;ZNF384:0.373987041466;NFE2L2:0.372929776738;GATA4:0.313918890353;DBP:0.300811685671;MYBL2:0.286808872327;NFE2L1:0.253322040887;POU3F1..4:0.225161117918;JUN:0.195012153572;FOXQ1:0.183995593076;SOX17:0.166211920348;PAX4:0.152062031825;RBPJ:0.112849138372;IKZF2:0.0987136402802;FOXA2:0.0418340446791;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0331973210569;NKX6-1,2:0.0314137494615;FOX{F1,F2,J1}:0.021143416032;PITX1..3:0.0209400051872;RORA:0.00600310770537;ZNF143:-0.0126391636251;BACH2:-0.0400508329885;NANOG{mouse}:-0.0426439883084;NFE2:-0.0467209596886;FOXN1:-0.0763305035385;bHLH_family:-0.0934174599822;HLF:-0.130276631385;NR5A1,2:-0.137712024458;NRF1:-0.195176484059;RXR{A,B,G}:-0.210654342965;POU1F1:-0.219678866509;PAX8:-0.224760791666;HBP1_HMGB_SSRP1_UBTF:-0.266083329327;NFIX:-0.280872870914;GZF1:-0.310496966396;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.323209981856;NKX2-2,8:-0.338612128001;RUNX1..3:-0.346608785582;NFKB1_REL_RELA:-0.359799999423;NFY{A,B,C}:-0.411425648207;PBX1:-0.428339641763;SPIB:-0.434825630321;NR1H4:-0.459290173593;EVI1:-0.473645816773;ONECUT1,2:-0.484201264973;ATF5_CREB3:-0.502365199483;FOX{I1,J2}:-0.52526014969;E2F1..5:-0.547903127463;SPI1:-0.56298482944;STAT2,4,6:-0.586921628762;CEBPA,B_DDIT3:-0.608628305221;MYB:-0.612894052749;STAT5{A,B}:-0.640098285708;ALX4:-0.647716429468;FOX{D1,D2}:-0.686138955155;BPTF:-0.734758009289;NKX3-1:-0.736319367236;ETS1,2:-0.75975990109;TEF:-0.763716425727;HNF4A_NR2F1,2:-0.77456273727;AIRE:-0.832969666159;FOXD3:-0.834088590866;FOXP1:-0.858480837273;HNF1A:-0.862245966836;CREB1:-0.867769540971;SREBF1,2:-0.869641948776;ATF4:-0.873359394194;NFIL3:-0.873909663536;IRF7:-0.888315671246;DMAP1_NCOR{1,2}_SMARC:-0.913054470374;AR:-0.918501340411;GATA6:-0.951601437774;ESRRA:-0.968095613284;FOXO1,3,4:-0.998486495493;IRF1,2:-1.08746881907;ELF1,2,4:-1.16426446057;YY1:-1.17503639464;ELK1,4_GABP{A,B1}:-1.1751415719;ARID5B:-1.29606726052;STAT1,3:-1.35339722579;CDX1,2,4:-1.44183473779;NR6A1:-1.53816732902;PDX1:-1.61374068992;ZBTB16:-1.71748275825
|top_motifs=HOX{A4,D4}:2.68569107211;NKX2-3_NKX2-5:2.55736200275;TBP:2.32951102147;MYOD1:2.30375529371;ZNF148:2.23144087114;TFAP4:2.16868216543;LHX3,4:2.16643522216;SMAD1..7,9:2.08138674102;EP300:2.04394080423;VSX1,2:1.93282657623;HMX1:1.91462650712;LEF1_TCF7_TCF7L1,2:1.85323421896;TFCP2:1.80488591949;NKX3-2:1.78212765743;GLI1..3:1.77729332567;ESR1:1.73803220282;MAZ:1.73773887965;PATZ1:1.70869986244;TGIF1:1.69573676233;GTF2I:1.69092665135;TFAP2{A,C}:1.67708137463;RREB1:1.63545460541;MYFfamily:1.61174194701;HOX{A5,B5}:1.58406998915;NANOG:1.56547922005;MAFB:1.54679858982;MZF1:1.52212700371;XCPE1{core}:1.51977862057;SOX{8,9,10}:1.5159654057;TBX4,5:1.4846203676;KLF4:1.43798453665;NHLH1,2:1.43055545245;T:1.41018349147;SP1:1.30023624957;PAX5:1.28388265298;MTF1:1.27341348513;PRDM1:1.26568770542;PRRX1,2:1.25352938978;HIC1:1.24871630303;ZNF238:1.24159751596;ZNF423:1.23568411323;PPARG:1.21430524939;EN1,2:1.19549819391;GTF2A1,2:1.18837826061;TOPORS:1.18509984788;MED-1{core}:1.14943540208;HAND1,2:1.14892217482;POU5F1:1.13170143425;REST:1.12906505493;FOXL1:1.11542136744;TAL1_TCF{3,4,12}:1.11469384426;ZIC1..3:1.10665695993;FOS_FOS{B,L1}_JUN{B,D}:1.078195146;ATF2:1.07798293529;ZBTB6:1.07737777143;GFI1B:1.07162478685;MTE{core}:1.04390083216;TFAP2B:1.03674304599;EGR1..3:1.03609204182;GCM1,2:1.01408569945;SOX2:1.01154909249;NKX2-1,4:1.00868261943;MEF2{A,B,C,D}:1.00128238137;ALX1:0.997125735133;LMO2:0.976492872008;RFX2..5_RFXANK_RFXAP:0.971025072725;BREu{core}:0.951249773624;EBF1:0.868217456185;POU6F1:0.849924091578;ADNP_IRX_SIX_ZHX:0.839405087081;ATF6:0.829794325232;TLX1..3_NFIC{dimer}:0.815340469772;TEAD1:0.790667648071;ZFP161:0.787775321524;HIF1A:0.781853251546;SOX5:0.761245714818;HOXA9_MEIS1:0.754892898835;IKZF1:0.736648821572;RFX1:0.736567579381;HES1:0.724704941662;PAX1,9:0.720572858967;TFDP1:0.715685035853;FOSL2:0.712462996483;TLX2:0.705409400647;PAX2:0.671631217492;TP53:0.668382436487;OCT4_SOX2{dimer}:0.661010208808;UFEwm:0.632327870657;SNAI1..3:0.628764451978;GFI1:0.625231921669;POU2F1..3:0.594510463046;AHR_ARNT_ARNT2:0.589856958085;FOXP3:0.562546389054;CRX:0.537999967687;CDC5L:0.520609837959;CUX2:0.517118415739;RXRA_VDR{dimer}:0.500421929583;NFATC1..3:0.487573473824;PAX6:0.463799301415;FOXM1:0.446051829919;SPZ1:0.433853532928;HSF1,2:0.431450692837;NR3C1:0.419192414055;SRF:0.413359280494;ZEB1:0.403884221948;HMGA1,2:0.378799896481;ZNF384:0.373987041466;NFE2L2:0.372929776738;GATA4:0.313918890353;DBP:0.300811685671;MYBL2:0.286808872327;NFE2L1:0.253322040887;POU3F1..4:0.225161117918;JUN:0.195012153572;FOXQ1:0.183995593076;SOX17:0.166211920348;PAX4:0.152062031825;RBPJ:0.112849138372;IKZF2:0.0987136402802;FOXA2:0.0418340446791;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0331973210569;NKX6-1,2:0.0314137494615;FOX{F1,F2,J1}:0.021143416032;PITX1..3:0.0209400051872;RORA:0.00600310770537;ZNF143:-0.0126391636251;BACH2:-0.0400508329885;NANOG{mouse}:-0.0426439883084;NFE2:-0.0467209596886;FOXN1:-0.0763305035385;bHLH_family:-0.0934174599822;HLF:-0.130276631385;NR5A1,2:-0.137712024458;NRF1:-0.195176484059;RXR{A,B,G}:-0.210654342965;POU1F1:-0.219678866509;PAX8:-0.224760791666;HBP1_HMGB_SSRP1_UBTF:-0.266083329327;NFIX:-0.280872870914;GZF1:-0.310496966396;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.323209981856;NKX2-2,8:-0.338612128001;RUNX1..3:-0.346608785582;NFKB1_REL_RELA:-0.359799999423;NFY{A,B,C}:-0.411425648207;PBX1:-0.428339641763;SPIB:-0.434825630321;NR1H4:-0.459290173593;EVI1:-0.473645816773;ONECUT1,2:-0.484201264973;ATF5_CREB3:-0.502365199483;FOX{I1,J2}:-0.52526014969;E2F1..5:-0.547903127463;SPI1:-0.56298482944;STAT2,4,6:-0.586921628762;CEBPA,B_DDIT3:-0.608628305221;MYB:-0.612894052749;STAT5{A,B}:-0.640098285708;ALX4:-0.647716429468;FOX{D1,D2}:-0.686138955155;BPTF:-0.734758009289;NKX3-1:-0.736319367236;ETS1,2:-0.75975990109;TEF:-0.763716425727;HNF4A_NR2F1,2:-0.77456273727;AIRE:-0.832969666159;FOXD3:-0.834088590866;FOXP1:-0.858480837273;HNF1A:-0.862245966836;CREB1:-0.867769540971;SREBF1,2:-0.869641948776;ATF4:-0.873359394194;NFIL3:-0.873909663536;IRF7:-0.888315671246;DMAP1_NCOR{1,2}_SMARC:-0.913054470374;AR:-0.918501340411;GATA6:-0.951601437774;ESRRA:-0.968095613284;FOXO1,3,4:-0.998486495493;IRF1,2:-1.08746881907;ELF1,2,4:-1.16426446057;YY1:-1.17503639464;ELK1,4_GABP{A,B1}:-1.1751415719;ARID5B:-1.29606726052;STAT1,3:-1.35339722579;CDX1,2,4:-1.44183473779;NR6A1:-1.53816732902;PDX1:-1.61374068992;ZBTB16:-1.71748275825
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011365
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:02, 7 March 2012


Name:whole body, embryo E17
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 days embryo
sexmixture
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

CNhs10517

00
10.243
100
1000.176
10000.176
1001-0.0633
10020.0447
10030.335
10040.136
10050
10060.269
1007-0.0202
10080
10090.111
101-0.0674
10100
10110.246
10120
1013-0.0375
10140.481
10150.232
10160.274
10170.0968
10180.243
10190
1020
10200
10210
10220.0265
10230
10240.161
10250.176
10260.118
10270.0968
10280
1029-0.0179
1030.721
10300
10310.421
10320.0374
10330.0303
10340
10350
1036-0.0723
10370
1038-0.018
1039-0.00831
1040
10400.135
10410



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: CNhs10517

Jaspar motifP-value
MA0002.20.0306
MA0003.10.728
MA0004.10.196
MA0006.10.493
MA0007.10.107
MA0009.10.64
MA0014.10.207
MA0017.12.14197e-10
MA0018.20.53
MA0019.10.228
MA0024.10.398
MA0025.10.663
MA0027.10.963
MA0028.17.79861e-6
MA0029.10.595
MA0030.10.924
MA0031.10.249
MA0035.20.00787
MA0038.10.0527
MA0039.20.906
MA0040.10.733
MA0041.10.292
MA0042.10.641
MA0043.10.79
MA0046.11.34826e-14
MA0047.20.0035
MA0048.10.0089
MA0050.11.3185e-9
MA0051.11.02954e-5
MA0052.11.61395e-9
MA0055.12.5934e-4
MA0057.10.752
MA0058.10.0923
MA0059.10.0213
MA0060.10.0475
MA0061.10.048
MA0062.22.15916e-11
MA0065.28.43857e-5
MA0066.10.0771
MA0067.10.216
MA0068.10.405
MA0069.10.432
MA0070.10.162
MA0071.10.0113
MA0072.10.0127
MA0073.10.961
MA0074.10.313
MA0076.16.90427e-6
MA0077.10.153
MA0078.10.763
MA0079.20.0414
MA0080.24.01137e-10
MA0081.10.0936
MA0083.18.21615e-4
MA0084.10.66
MA0087.10.65
MA0088.10.0966
MA0090.10.595
MA0091.10.77
MA0092.10.775
MA0093.10.188
MA0099.20.477
MA0100.10.0302
MA0101.10.00421
MA0102.20.833
MA0103.10.532
MA0104.20.399
MA0105.10.0322
MA0106.10.155
MA0107.10.0324
MA0108.23.99907e-27
MA0111.10.892
MA0112.20.00144
MA0113.10.0874
MA0114.12.35562e-8
MA0115.11.41215e-7
MA0116.10.192
MA0117.10.345
MA0119.10.309
MA0122.10.957
MA0124.10.773
MA0125.10.00349
MA0131.10.311
MA0135.10.0145
MA0136.16.93788e-15
MA0137.24.89415e-5
MA0138.24.14627e-4
MA0139.10.235
MA0140.16.87162e-4
MA0141.17.67928e-5
MA0142.10.366
MA0143.10.345
MA0144.10.0161
MA0145.10.999
MA0146.10.047
MA0147.10.372
MA0148.15.23807e-4
MA0149.10.00321
MA0150.10.00377
MA0152.10.279
MA0153.15.60157e-15
MA0154.10.2
MA0155.10.503
MA0156.11.5869e-12
MA0157.10.287
MA0159.10.00412
MA0160.10.00161
MA0162.10.577
MA0163.10.00482
MA0164.10.472
MA0258.10.0189
MA0259.10.524



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: CNhs10517

Novel motifP-value
10.196
100.0344
1000.531
1010.364
1020.843
1030.0144
1040.65
1050.971
1060.424
1070.928
1080.464
1090.0502
110.0611
1100.0492
1110.00339
1120.00498
1130.974
1140.134
1150.915
1160.646
1170.00129
1180.137
1190.286
120.839
1200.825
1210.434
1220.549
1230.124
1240.58
1250.118
1260.0157
1270.35
1280.536
1290.144
131.6065e-5
1300.976
1310.882
1320.805
1330.38
1340.412
1350.785
1360.122
1370.363
1380.713
1390.0499
140.703
1400.376
1410.599
1420.0358
1430.264
1440.755
1450.0195
1460.953
1470.653
1480.292
1490.63
150.0141
1500.282
1510.54
1520.495
1530.681
1540.313
1550.128
1562.73725e-6
1570.691
1580.0108
1590.681
1600.852
1610.0746
1620.742
1630.35
1640.0012
1650.0372
1660.779
1670.00963
1680.263
1690.0387
170.232
180.695
190.436
20.0836
200.0167
210.719
220.413
230.556
240.231
250.357
260.0024
270.654
280.235
290.00573
30.0423
300.126
310.958
320.4
330.116
340.581
350.23
360.0846
370.0167
380.679
390.508
40.846
400.225
410.483
420.268
430.171
440.21
450.6
460.279
470.305
480.117
490.0723
50.0464
500.902
510.695
520.706
530.421
540.85
550.815
560.915
570.506
580.41
590.703
60.891
600.325
610.0767
620.268
630.587
640.772
650.79
660.779
670.957
680.807
690.979
70.0733
700.0524
710.0206
720.373
730.0242
740.498
750.0203
760.015
770.806
780.0231
790.698
80.0777
800.515
810.939
820.264
830.237
840.751
850.433
860.327
870.605
880.361
890.677
90.944
900.0192
910.606
920.321
930.0459
940.567
950.0251
960.592
970.863
980.817
990.741



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: CNhs10517


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:475-3I5&oldid=724415"