Personal tools

FF:827-18D1: 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=NR1H4:3.33335646352;HNF4A_NR2F1,2:2.59146499905;ARID5B:2.50994909726;SNAI1..3:1.85440023102;ESRRA:1.84522338717;RXRA_VDR{dimer}:1.75839442272;ZEB1:1.72388351606;PDX1:1.69750201453;NR6A1:1.6388059904;JUN:1.62373352832;HNF1A:1.58687252738;IRF1,2:1.57950022476;STAT2,4,6:1.53893328807;TBX4,5:1.51349057557;POU1F1:1.48500446448;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.4185560291;FOXM1:1.26946251815;DMAP1_NCOR{1,2}_SMARC:1.25219279942;MYOD1:1.13674372401;NKX3-2:1.0925091738;TLX1..3_NFIC{dimer}:1.06114847368;NKX6-1,2:1.01298780643;T:0.95904982766;RBPJ:0.9378541313;SPZ1:0.93298098936;HAND1,2:0.906481044327;AR:0.881544096425;ATF6:0.825403076371;SRF:0.749865409516;CDX1,2,4:0.655925910231;LMO2:0.651627021875;FOX{I1,J2}:0.648178905536;ZNF423:0.637227223435;FOSL2:0.626058838934;EVI1:0.531808121523;ADNP_IRX_SIX_ZHX:0.52715572156;bHLH_family:0.448468013324;NR5A1,2:0.423132311845;TOPORS:0.41988562993;GTF2A1,2:0.397113453271;ETS1,2:0.390396805973;ZNF148:0.388980478551;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.38766304405;IRF7:0.37320326993;TFCP2:0.368867134483;TBP:0.368304201989;IKZF1:0.338546294567;NFIX:0.329910626401;TFAP4:0.314932543949;GATA6:0.300541474965;GLI1..3:0.281449189935;FOXQ1:0.254876344287;NKX2-1,4:0.242464186399;XCPE1{core}:0.232961051226;NKX2-2,8:0.230798432515;ESR1:0.218288270886;UFEwm:0.21547622625;TLX2:0.20777600957;SP1:0.174699599199;FOS_FOS{B,L1}_JUN{B,D}:0.142891141712;FOXA2:0.099542133161;MYBL2:0.0940210159969;NFKB1_REL_RELA:0.0822793937918;PAX8:0.0595869546914;EBF1:0.0475305661787;EN1,2:0.0158571669196;ZBTB6:0.0133409140159;NFE2L1:-0.00247536141077;SPI1:-0.00327857322652;SPIB:-0.0161680757232;TP53:-0.0350036786184;TEAD1:-0.0688480570414;FOXP1:-0.0936419842133;BACH2:-0.0954935855986;FOXN1:-0.11878853965;ATF5_CREB3:-0.123649497924;GFI1:-0.156502876412;MAFB:-0.167175988118;ZNF238:-0.17371614617;MAZ:-0.180765723636;HLF:-0.189925700587;CDC5L:-0.220022784368;E2F1..5:-0.222390817455;PITX1..3:-0.228280071072;ELF1,2,4:-0.252897565331;STAT1,3:-0.258394024252;YY1:-0.268124045504;PBX1:-0.307316134458;POU2F1..3:-0.316244086118;REST:-0.326081117105;PPARG:-0.344548731038;GTF2I:-0.359227169014;HIC1:-0.392088702183;ONECUT1,2:-0.410027934246;POU6F1:-0.423603388654;TFAP2B:-0.429524816556;LEF1_TCF7_TCF7L1,2:-0.440771293582;RXR{A,B,G}:-0.452087086113;FOXO1,3,4:-0.49224850468;MYFfamily:-0.516945334747;STAT5{A,B}:-0.524643830659;MTF1:-0.53306686264;ATF2:-0.540666312974;RUNX1..3:-0.545846145704;TAL1_TCF{3,4,12}:-0.547559598136;MYB:-0.553655582243;PAX5:-0.574191265314;NKX3-1:-0.591358827291;GCM1,2:-0.592902711744;TFAP2{A,C}:-0.593776568203;SMAD1..7,9:-0.6129011669;RFX2..5_RFXANK_RFXAP:-0.616315726127;KLF4:-0.61961300055;GZF1:-0.633424410907;PRDM1:-0.638145399085;NFE2L2:-0.663044313938;OCT4_SOX2{dimer}:-0.674579781885;HMGA1,2:-0.715158841113;FOX{D1,D2}:-0.719230603752;CREB1:-0.725120268201;NKX2-3_NKX2-5:-0.727632767527;MEF2{A,B,C,D}:-0.741855516918;BPTF:-0.752416983621;MED-1{core}:-0.75991421289;ZFP161:-0.773189997559;ALX4:-0.798339460262;ZBTB16:-0.810656475456;POU5F1:-0.830303294467;CUX2:-0.830871541542;ELK1,4_GABP{A,B1}:-0.831899433521;TGIF1:-0.83876174032;CEBPA,B_DDIT3:-0.848274734044;ZNF384:-0.871585156852;PAX6:-0.878447972994;NFE2:-0.895150610485;ATF4:-0.912366128492;PAX4:-0.913389006751;LHX3,4:-0.914679682926;RFX1:-0.925739303783;GFI1B:-0.93142159488;DBP:-0.93315666516;PATZ1:-0.952686227246;SOX17:-0.973586086417;SOX{8,9,10}:-0.983892488893;AHR_ARNT_ARNT2:-0.987417473884;IKZF2:-0.991288487969;PRRX1,2:-0.996081942029;CRX:-0.996225345496;PAX2:-1.01509092486;MZF1:-1.02367777432;HOXA9_MEIS1:-1.02701047279;EGR1..3:-1.03977939923;NFY{A,B,C}:-1.04626843903;FOX{F1,F2,J1}:-1.04851236996;HOX{A5,B5}:-1.05350838483;RREB1:-1.08052623644;BREu{core}:-1.0807309989;NANOG:-1.08372057682;TFDP1:-1.08419070029;MTE{core}:-1.0866408488;HBP1_HMGB_SSRP1_UBTF:-1.10118915198;VSX1,2:-1.10363556369;PAX1,9:-1.126527257;GATA4:-1.12957316882;EP300:-1.14311979835;HMX1:-1.14332154749;HOX{A4,D4}:-1.14806224977;HES1:-1.20045622446;NR3C1:-1.20358523863;ZIC1..3:-1.25155839657;NHLH1,2:-1.26552032762;SOX2:-1.26713770429;NFATC1..3:-1.29187421989;FOXL1:-1.29484888992;NRF1:-1.34657435835;HIF1A:-1.35401150327;AIRE:-1.36223725938;SREBF1,2:-1.38673695254;RORA:-1.39215613535;ZNF143:-1.53876184234;ALX1:-1.59207136521;SOX5:-1.61605941859;FOXD3:-1.69867678656;POU3F1..4:-1.69987309012;TEF:-1.73726997303;NFIL3:-2.0127747262;NANOG{mouse}:-2.07404234069;HSF1,2:-2.08113770088;FOXP3:-2.10256417817
|top_motifs=NR1H4:3.33335646352;HNF4A_NR2F1,2:2.59146499905;ARID5B:2.50994909726;SNAI1..3:1.85440023102;ESRRA:1.84522338717;RXRA_VDR{dimer}:1.75839442272;ZEB1:1.72388351606;PDX1:1.69750201453;NR6A1:1.6388059904;JUN:1.62373352832;HNF1A:1.58687252738;IRF1,2:1.57950022476;STAT2,4,6:1.53893328807;TBX4,5:1.51349057557;POU1F1:1.48500446448;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.4185560291;FOXM1:1.26946251815;DMAP1_NCOR{1,2}_SMARC:1.25219279942;MYOD1:1.13674372401;NKX3-2:1.0925091738;TLX1..3_NFIC{dimer}:1.06114847368;NKX6-1,2:1.01298780643;T:0.95904982766;RBPJ:0.9378541313;SPZ1:0.93298098936;HAND1,2:0.906481044327;AR:0.881544096425;ATF6:0.825403076371;SRF:0.749865409516;CDX1,2,4:0.655925910231;LMO2:0.651627021875;FOX{I1,J2}:0.648178905536;ZNF423:0.637227223435;FOSL2:0.626058838934;EVI1:0.531808121523;ADNP_IRX_SIX_ZHX:0.52715572156;bHLH_family:0.448468013324;NR5A1,2:0.423132311845;TOPORS:0.41988562993;GTF2A1,2:0.397113453271;ETS1,2:0.390396805973;ZNF148:0.388980478551;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.38766304405;IRF7:0.37320326993;TFCP2:0.368867134483;TBP:0.368304201989;IKZF1:0.338546294567;NFIX:0.329910626401;TFAP4:0.314932543949;GATA6:0.300541474965;GLI1..3:0.281449189935;FOXQ1:0.254876344287;NKX2-1,4:0.242464186399;XCPE1{core}:0.232961051226;NKX2-2,8:0.230798432515;ESR1:0.218288270886;UFEwm:0.21547622625;TLX2:0.20777600957;SP1:0.174699599199;FOS_FOS{B,L1}_JUN{B,D}:0.142891141712;FOXA2:0.099542133161;MYBL2:0.0940210159969;NFKB1_REL_RELA:0.0822793937918;PAX8:0.0595869546914;EBF1:0.0475305661787;EN1,2:0.0158571669196;ZBTB6:0.0133409140159;NFE2L1:-0.00247536141077;SPI1:-0.00327857322652;SPIB:-0.0161680757232;TP53:-0.0350036786184;TEAD1:-0.0688480570414;FOXP1:-0.0936419842133;BACH2:-0.0954935855986;FOXN1:-0.11878853965;ATF5_CREB3:-0.123649497924;GFI1:-0.156502876412;MAFB:-0.167175988118;ZNF238:-0.17371614617;MAZ:-0.180765723636;HLF:-0.189925700587;CDC5L:-0.220022784368;E2F1..5:-0.222390817455;PITX1..3:-0.228280071072;ELF1,2,4:-0.252897565331;STAT1,3:-0.258394024252;YY1:-0.268124045504;PBX1:-0.307316134458;POU2F1..3:-0.316244086118;REST:-0.326081117105;PPARG:-0.344548731038;GTF2I:-0.359227169014;HIC1:-0.392088702183;ONECUT1,2:-0.410027934246;POU6F1:-0.423603388654;TFAP2B:-0.429524816556;LEF1_TCF7_TCF7L1,2:-0.440771293582;RXR{A,B,G}:-0.452087086113;FOXO1,3,4:-0.49224850468;MYFfamily:-0.516945334747;STAT5{A,B}:-0.524643830659;MTF1:-0.53306686264;ATF2:-0.540666312974;RUNX1..3:-0.545846145704;TAL1_TCF{3,4,12}:-0.547559598136;MYB:-0.553655582243;PAX5:-0.574191265314;NKX3-1:-0.591358827291;GCM1,2:-0.592902711744;TFAP2{A,C}:-0.593776568203;SMAD1..7,9:-0.6129011669;RFX2..5_RFXANK_RFXAP:-0.616315726127;KLF4:-0.61961300055;GZF1:-0.633424410907;PRDM1:-0.638145399085;NFE2L2:-0.663044313938;OCT4_SOX2{dimer}:-0.674579781885;HMGA1,2:-0.715158841113;FOX{D1,D2}:-0.719230603752;CREB1:-0.725120268201;NKX2-3_NKX2-5:-0.727632767527;MEF2{A,B,C,D}:-0.741855516918;BPTF:-0.752416983621;MED-1{core}:-0.75991421289;ZFP161:-0.773189997559;ALX4:-0.798339460262;ZBTB16:-0.810656475456;POU5F1:-0.830303294467;CUX2:-0.830871541542;ELK1,4_GABP{A,B1}:-0.831899433521;TGIF1:-0.83876174032;CEBPA,B_DDIT3:-0.848274734044;ZNF384:-0.871585156852;PAX6:-0.878447972994;NFE2:-0.895150610485;ATF4:-0.912366128492;PAX4:-0.913389006751;LHX3,4:-0.914679682926;RFX1:-0.925739303783;GFI1B:-0.93142159488;DBP:-0.93315666516;PATZ1:-0.952686227246;SOX17:-0.973586086417;SOX{8,9,10}:-0.983892488893;AHR_ARNT_ARNT2:-0.987417473884;IKZF2:-0.991288487969;PRRX1,2:-0.996081942029;CRX:-0.996225345496;PAX2:-1.01509092486;MZF1:-1.02367777432;HOXA9_MEIS1:-1.02701047279;EGR1..3:-1.03977939923;NFY{A,B,C}:-1.04626843903;FOX{F1,F2,J1}:-1.04851236996;HOX{A5,B5}:-1.05350838483;RREB1:-1.08052623644;BREu{core}:-1.0807309989;NANOG:-1.08372057682;TFDP1:-1.08419070029;MTE{core}:-1.0866408488;HBP1_HMGB_SSRP1_UBTF:-1.10118915198;VSX1,2:-1.10363556369;PAX1,9:-1.126527257;GATA4:-1.12957316882;EP300:-1.14311979835;HMX1:-1.14332154749;HOX{A4,D4}:-1.14806224977;HES1:-1.20045622446;NR3C1:-1.20358523863;ZIC1..3:-1.25155839657;NHLH1,2:-1.26552032762;SOX2:-1.26713770429;NFATC1..3:-1.29187421989;FOXL1:-1.29484888992;NRF1:-1.34657435835;HIF1A:-1.35401150327;AIRE:-1.36223725938;SREBF1,2:-1.38673695254;RORA:-1.39215613535;ZNF143:-1.53876184234;ALX1:-1.59207136521;SOX5:-1.61605941859;FOXD3:-1.69867678656;POU3F1..4:-1.69987309012;TEF:-1.73726997303;NFIL3:-2.0127747262;NANOG{mouse}:-2.07404234069;HSF1,2:-2.08113770088;FOXP3:-2.10256417817
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011431
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:04, 7 March 2012


Name:intestine, neonate N20
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage20 days neonate
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

CNhs11187

00
10
100
1000
10000
10010
10020.0569
1003-0.102
10040
10050
1006-0.0711
1007-0.0345
10081.889
10090.0728
101-0.0836
10100
1011-0.111
10120
10130.229
1014-0.0874
1015-0.303
1016-0.163
10170
10180.278
10190
1020
10200
10210
10220
10230
10240
10250.505
10260
1027-0.048
10280
10290.63
1030.226
10300
1031-0.105
10320.416
1033-0.0752
10340
10350
1036-0.223
10370
10380.108
10390.166
1040
1040-0.147
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: CNhs11187

Jaspar motifP-value
MA0002.20.015
MA0003.10.083
MA0004.10.676
MA0006.10.0735
MA0007.10.483
MA0009.10.663
MA0014.10.601
MA0017.13.71966e-18
MA0018.20.0109
MA0019.10.311
MA0024.10.0241
MA0025.10.0778
MA0027.10.653
MA0028.10.167
MA0029.10.591
MA0030.10.632
MA0031.10.663
MA0035.27.80492e-5
MA0038.10.379
MA0039.20.018
MA0040.10.186
MA0041.10.263
MA0042.10.852
MA0043.10.0396
MA0046.17.8573e-29
MA0047.20.0613
MA0048.10.493
MA0050.12.32909e-7
MA0051.12.8158e-5
MA0052.12.67406e-4
MA0055.10.364
MA0057.10.167
MA0058.10.461
MA0059.10.991
MA0060.15.27906e-4
MA0061.10.377
MA0062.20.108
MA0065.29.89822e-15
MA0066.10.216
MA0067.10.279
MA0068.10.295
MA0069.10.197
MA0070.10.217
MA0071.10.354
MA0072.10.306
MA0073.10.891
MA0074.10.0854
MA0076.10.0872
MA0077.10.676
MA0078.10.718
MA0079.20.264
MA0080.20.00559
MA0081.10.384
MA0083.10.586
MA0084.10.65
MA0087.10.894
MA0088.10.728
MA0090.10.779
MA0091.10.759
MA0092.10.308
MA0093.10.619
MA0099.20.0175
MA0100.10.18
MA0101.10.896
MA0102.20.124
MA0103.14.82241e-5
MA0104.20.149
MA0105.10.0933
MA0106.10.505
MA0107.10.868
MA0108.20.487
MA0111.10.962
MA0112.21.12886e-5
MA0113.10.743
MA0114.11.28767e-22
MA0115.11.25129e-11
MA0116.10.223
MA0117.10.768
MA0119.10.0461
MA0122.10.651
MA0124.10.383
MA0125.10.0724
MA0131.10.342
MA0135.10.984
MA0136.10.0828
MA0137.20.68
MA0138.20.405
MA0139.10.0467
MA0140.10.0461
MA0141.15.01623e-5
MA0142.10.39
MA0143.10.332
MA0144.10.0882
MA0145.10.00446
MA0146.10.264
MA0147.10.262
MA0148.10.00327
MA0149.10.0417
MA0150.10.698
MA0152.10.057
MA0153.14.93591e-28
MA0154.10.0103
MA0155.10.202
MA0156.10.448
MA0157.10.327
MA0159.10.00177
MA0160.10.00418
MA0162.10.214
MA0163.10.0125
MA0164.10.947
MA0258.10.00886
MA0259.10.265



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: CNhs11187

Novel motifP-value
10.15
100.148
1000.913
1010.907
1020.658
1030.116
1040.976
1050.386
1060.00801
1070.014
1080.605
1090.075
110.165
1100.184
1110.0902
1120.0104
1130.582
1140.0572
1150.685
1160.275
1170.296
1180.648
1190.0581
120.704
1200.643
1210.718
1220.605
1230.292
1240.978
1250.343
1260.152
1270.11
1280.0623
1290.487
130.00752
1300.948
1310.0409
1320.729
1330.984
1340.99
1350.86
1360.299
1370.524
1380.913
1390.0825
140.625
1400.129
1410.149
1420.26
1430.732
1440.46
1450.079
1460.255
1470.442
1480.322
1490.451
150.159
1500.336
1510.3
1520.0621
1530.962
1540.66
1550.314
1560.302
1570.986
1580.689
1590.611
1600.192
1610.336
1620.917
1630.346
1640.0769
1650.345
1660.498
1670.961
1680.867
1690.00933
170.0435
180.0394
190.0635
20.304
200.818
210.798
220.289
230.192
240.601
250.753
260.00307
270.456
280.64
290.291
30.225
300.497
310.565
320.0046
330.194
340.757
350.444
360.588
370.0299
380.32
390.249
40.383
400.308
410.299
420.465
430.208
440.103
450.418
460.225
470.296
480.278
490.156
50.479
500.495
510.538
520.0835
530.948
540.571
550.768
560.406
570.76
580.425
590.0427
60.873
600.0381
610.215
620.378
630.138
640.649
650.163
660.478
670.647
680.106
690.882
70.0749
700.0524
710.0735
720.438
730.125
740.855
750.144
760.745
770.097
780.0676
790.446
80.158
800.923
810.593
820.0987
830.34
840.483
850.0251
860.297
870.244
880.67
890.259
90.652
900.117
910.212
920.157
930.404
940.701
950.336
960.726
970.446
980.627
990.0656



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: CNhs11187


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)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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:827-18D1&oldid=724485"