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|top_motifs=JUN:5.6915083538;SOX17:5.358292647;HLF:4.77768514715;RFX2..5_RFXANK_RFXAP:4.75200277899;RFX1:4.5617862975;MYB:4.53705025272;ATF2:3.64593667106;HSF1,2:3.57284584026;ESR1:2.90129344504;PPARG:2.53309877243;NFE2L1:2.28758296935;FOXN1:2.28286887152;HBP1_HMGB_SSRP1_UBTF:2.20473348062;NFIL3:2.18174138979;HOXA9_MEIS1:1.68794996479;TBX4,5:1.40970850168;NR1H4:1.17709342086;NR3C1:1.07325017827;ZBTB6:1.03155343269;PAX5:1.02489809041;NRF1:1.00725451332;BREu{core}:0.91469774455;REST:0.850647514045;bHLH_family:0.715522171398;TFAP2{A,C}:0.70922832969;ATF5_CREB3:0.705145086545;ATF4:0.690382436545;HIC1:0.678025160783;PAX6:0.659244820276;STAT1,3:0.637957662372;GLI1..3:0.635984491192;CUX2:0.635516946133;NKX3-2:0.619466382383;NFY{A,B,C}:0.619434338994;HIF1A:0.616409008276;PRRX1,2:0.611993703609;RBPJ:0.60363292854;PATZ1:0.594233728141;ESRRA:0.58795523654;HES1:0.582834868648;TFAP2B:0.574009740051;ZEB1:0.567484714213;AR:0.428232907826;HNF1A:0.373954313919;AHR_ARNT_ARNT2:0.364109717386;FOXO1,3,4:0.356702000803;POU6F1:0.338550358847;OCT4_SOX2{dimer}:0.33190447989;MTE{core}:0.27085953884;HAND1,2:0.263080264516;GFI1:0.259346090379;SMAD1..7,9:0.24472218164;NHLH1,2:0.242630198895;SNAI1..3:0.23245277771;HOX{A5,B5}:0.208787940472;GCM1,2:0.205770771382;EGR1..3:0.205008033758;TGIF1:0.201610650806;MED-1{core}:0.186010233914;ADNP_IRX_SIX_ZHX:0.152861042483;GFI1B:0.125343647105;MAFB:0.0985094212922;RXR{A,B,G}:0.092448243681;NKX3-1:0.0870878807663;SOX5:0.0852711609666;XCPE1{core}:0.0546830572024;TBP:0.0544795573188;ZNF148:0.0232576968407;TFDP1:0.00650892769952;ZFP161:-0.0275441838531;HNF4A_NR2F1,2:-0.0276050954865;CREB1:-0.0292891341986;LMO2:-0.0403505706201;SOX2:-0.0684292740425;NR5A1,2:-0.0822077570055;NKX6-1,2:-0.0903890151831;DMAP1_NCOR{1,2}_SMARC:-0.126734063972;GTF2I:-0.141856621769;MZF1:-0.207266382651;MTF1:-0.234193669917;PBX1:-0.234897622789;TEAD1:-0.235560413264;FOXM1:-0.252790933489;GTF2A1,2:-0.275064127433;FOS_FOS{B,L1}_JUN{B,D}:-0.284135458077;TFCP2:-0.290315557553;T:-0.301673963751;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.31608697632;TLX1..3_NFIC{dimer}:-0.345923877175;ZNF143:-0.356435078844;PAX1,9:-0.365752084598;MYOD1:-0.36758738694;SREBF1,2:-0.380814092409;TEF:-0.389092282625;ATF6:-0.397420134221;MYFfamily:-0.440822601272;SP1:-0.493464337915;PRDM1:-0.500855766048;SOX{8,9,10}:-0.5095813323;ZIC1..3:-0.534012299047;FOX{D1,D2}:-0.550192122694;POU2F1..3:-0.591857996659;FOX{I1,J2}:-0.593661946616;STAT2,4,6:-0.602039582263;PDX1:-0.615112770108;FOXQ1:-0.660721634612;MAZ:-0.687032423596;RREB1:-0.688497889341;MEF2{A,B,C,D}:-0.696544524034;MYBL2:-0.701923421365;NKX2-3_NKX2-5:-0.702291554617;NFIX:-0.715447577596;PITX1..3:-0.730018561914;GZF1:-0.777148534573;E2F1..5:-0.797300097811;SRF:-0.801091698281;FOSL2:-0.833371549656;EBF1:-0.854185066778;NFKB1_REL_RELA:-0.869613248369;TLX2:-0.874972039792;FOXA2:-0.900157341363;ETS1,2:-0.959232453989;KLF4:-0.993774118396;SPZ1:-1.00393172389;NFATC1..3:-1.03859435952;ONECUT1,2:-1.03974409005;IRF1,2:-1.09540361293;POU5F1:-1.14296502993;TOPORS:-1.15012246377;ELK1,4_GABP{A,B1}:-1.15876946182;LHX3,4:-1.17167078176;RUNX1..3:-1.17963796366;HOX{A4,D4}:-1.20987221058;ZNF238:-1.21597543038;RXRA_VDR{dimer}:-1.23044328124;FOX{F1,F2,J1}:-1.23508671323;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.24914851985;ZNF423:-1.29149876422;ZBTB16:-1.30729917159;NFE2L2:-1.31071765576;FOXD3:-1.322178713;TFAP4:-1.32394111194;BACH2:-1.33265084232;SPIB:-1.33756203493;HMGA1,2:-1.35160798735;IKZF1:-1.36201305759;IKZF2:-1.39988076579;GATA6:-1.41406807988;NANOG{mouse}:-1.42636586363;RORA:-1.43342941647;HMX1:-1.44275679737;NFE2:-1.44823188932;GATA4:-1.48142461315;CRX:-1.4925297275;DBP:-1.49585109691;CEBPA,B_DDIT3:-1.5044029627;IRF7:-1.50560535752;EP300:-1.56408226507;ELF1,2,4:-1.56457301487;AIRE:-1.64124727198;FOXP1:-1.671932183;LEF1_TCF7_TCF7L1,2:-1.68408789204;ZNF384:-1.68926097361;TP53:-1.69317411013;NR6A1:-1.72270354223;EN1,2:-1.7240413086;EVI1:-1.8018519103;NKX2-1,4:-1.82518735913;PAX8:-1.87993882135;SPI1:-1.89897429862;YY1:-1.90871880648;ALX4:-1.93393674401;TAL1_TCF{3,4,12}:-1.94801974518;CDC5L:-1.94983862868;VSX1,2:-2.03040931956;NANOG:-2.21989727846;PAX2:-2.32093293547;POU3F1..4:-2.33605000546;ALX1:-2.48225940365;STAT5{A,B}:-2.49595688861;FOXL1:-2.50408861296;ARID5B:-2.7865703865;BPTF:-2.84279573865;UFEwm:-2.85443467645;POU1F1:-2.93210494152;NKX2-2,8:-3.02700115326;PAX4:-3.07286980634;CDX1,2,4:-3.15546092703;FOXP3:-3.46263248082
}}
}}

Revision as of 15:16, 15 February 2012


Name:Clontech Mouse Universal Reference Total RNA, pool1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuewhole body
dev stageUNDEFINED
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8092682.00000
catalog numberCat:636657
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
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

CNhs10609

00.715
10.323
100
1000
10000.0652
10010.0244
1002-0.0343
1003-0.00177
10040.236
10050.0354
10060.259
10070.0894
10080
10090.168
101-0.0613
10100.0354
10110.692
10120.0682
10130.0807
1014-0.0851
10150.122
1016-0.0769
10170
10180.0682
10190.0354
1020
10200
10210
10220.217
10230
10240.233
10250.373
10260.581
10270.131
10280.0354
1029-0.0307
1030.00251
10300
1031-0.0963
10320.053
10330.0322
10340.125
10350.247
1036-0.238
10370
10380.0329
10390.179
1040
10400.082
10410.225



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: CNhs10609

Jaspar motifP-value
MA0002.20.26
MA0003.10.159
MA0004.10.81
MA0006.10.0516
MA0007.10.746
MA0009.10.309
MA0014.10.913
MA0017.10.592
MA0018.22.88425e-14
MA0019.10.0969
MA0024.10.346
MA0025.10.00866
MA0027.10.0693
MA0028.10.0117
MA0029.10.672
MA0030.10.374
MA0031.10.913
MA0035.20.00266
MA0038.10.375
MA0039.20.468
MA0040.10.279
MA0041.10.0618
MA0042.10.353
MA0043.10.00211
MA0046.10.00346
MA0047.20.265
MA0048.10.835
MA0050.10.0197
MA0051.10.967
MA0052.10.0616
MA0055.10.0454
MA0057.10.364
MA0058.10.897
MA0059.10.478
MA0060.16.26947e-5
MA0061.12.34811e-4
MA0062.21.0206e-5
MA0065.20.523
MA0066.10.411
MA0067.10.411
MA0068.10.222
MA0069.10.197
MA0070.10.97
MA0071.10.755
MA0072.10.27
MA0073.10.942
MA0074.10.547
MA0076.10.0668
MA0077.15.72116e-5
MA0078.18.26167e-10
MA0079.20.686
MA0080.21.44718e-5
MA0081.10.00323
MA0083.10.387
MA0084.10.554
MA0087.10.0301
MA0088.10.402
MA0090.10.143
MA0091.10.994
MA0092.10.0993
MA0093.10.941
MA0099.20.134
MA0100.12.94888e-22
MA0101.10.00555
MA0102.20.495
MA0103.10.166
MA0104.24.70328e-4
MA0105.12.07987e-7
MA0106.11.70295e-4
MA0107.10.00145
MA0108.20.821
MA0111.10.0386
MA0112.20.0726
MA0113.10.611
MA0114.10.301
MA0115.10.917
MA0116.10.0201
MA0117.10.95
MA0119.10.341
MA0122.10.666
MA0124.10.619
MA0125.10.453
MA0131.10.492
MA0135.10.793
MA0136.12.5896e-5
MA0137.20.101
MA0138.20.37
MA0139.10.432
MA0140.13.39424e-7
MA0141.10.335
MA0142.10.498
MA0143.13.38138e-4
MA0144.10.227
MA0145.10.18
MA0146.10.0203
MA0147.10.00513
MA0148.10.133
MA0149.10.491
MA0150.10.659
MA0152.10.0808
MA0153.10.151
MA0154.10.0539
MA0155.10.244
MA0156.11.22068e-6
MA0157.10.381
MA0159.10.543
MA0160.10.0011
MA0162.10.582
MA0163.10.363
MA0164.10.726
MA0258.10.499
MA0259.10.16



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: CNhs10609

Novel motifP-value
10.915
100.389
1000.308
1010.3
1020.353
1030.547
1040.899
1050.929
1060.00252
1070.0468
1080.449
1090.947
110.656
1100.689
1110.862
1120.497
1130.856
1140.395
1150.904
1160.917
1170.514
1180.551
1190.667
120.867
1200.657
1210.0271
1220.615
1230.371
1240.855
1250.735
1260.924
1270.202
1280.0167
1290.444
130.00371
1300.934
1310.824
1320.683
1330.423
1340.969
1350.1
1360.00394
1370.385
1380.989
1390.333
140.649
1400.064
1410.142
1420.727
1430.529
1440.27
1450.834
1460.199
1470.368
1480.298
1490.389
150.671
1500.803
1510.372
1520.521
1530.806
1540.315
1550.462
1561.84924e-5
1570.987
1581.38689e-5
1590.0548
1600.0135
1610.23
1620.48
1630.733
1640.49
1650.477
1660.471
1670.639
1680.791
1690.543
170.49
180.473
190.426
20.074
200.275
210.531
220.949
230.499
240.0694
250.438
260.0485
270.0435
280.459
290.848
30.322
300.825
310.414
320.737
330.618
340.225
350.665
360.335
370.0688
380.73
390.497
40.992
400.0822
415.29361e-4
420.497
430.29
440.767
450.734
460.312
470.0627
480.245
490.815
50.347
500.578
510.656
520.662
530.983
540.489
550.807
560.157
570.48
580.402
590.5
60.756
600.347
610.345
620.6
630.578
640.691
650.527
660.152
670.257
680.785
690.425
70.442
700.814
710.00348
720.329
730.243
740.786
750.17
760.4
770.748
782.14088e-6
790.963
80.016
800.533
810.301
820.916
830.658
840.682
850.891
860.287
870.00114
880.282
890.874
90.971
900.629
910.52
920.518
930.683
940.418
950.9
960.774
970.154
980.956
990.912



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: CNhs10609


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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

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

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