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|fonse_treatment_closure=FF:0000343,FF:0011450,FF:11813-124E4
|top_motifs=RUNX1..3:3.4129784072;BPTF:3.30645131961;ALX4:3.0323448171;ETS1,2:2.98626760595;ELF1,2,4:2.71183412215;ATF5_CREB3:2.41979518713;SPI1:2.27597634828;FOXO1,3,4:2.21518381411;CREB1:2.16089625416;NFKB1_REL_RELA:2.1036542732;ATF4:2.10123198406;ELK1,4_GABP{A,B1}:2.07553135184;NFATC1..3:2.01324107493;SPZ1:1.93744966577;PDX1:1.92103557532;YY1:1.68398478358;PPARG:1.65820789511;IRF7:1.59948770336;TLX2:1.59289608623;IRF1,2:1.55659477548;SPIB:1.53770885968;FOX{D1,D2}:1.53006691351;ZBTB16:1.52857740965;DMAP1_NCOR{1,2}_SMARC:1.46005034668;PAX2:1.44705840947;AIRE:1.39083708429;STAT5{A,B}:1.2875964855;FOX{I1,J2}:1.07961364882;ATF6:1.02624021252;PAX8:0.982749941088;NFE2L1:0.94204099997;CRX:0.939137883943;TAL1_TCF{3,4,12}:0.913027061597;FOXD3:0.896716427582;NFIX:0.831760689593;FOXQ1:0.802938791618;STAT2,4,6:0.778616544612;CDX1,2,4:0.74340686461;STAT1,3:0.636496049889;RFX2..5_RFXANK_RFXAP:0.59399713651;PITX1..3:0.588144973648;JUN:0.576708863005;NRF1:0.499439051981;FOXP1:0.488589386747;LEF1_TCF7_TCF7L1,2:0.425587553184;FOXP3:0.424501271059;MYB:0.399162913934;POU1F1:0.370565356524;bHLH_family:0.322209567316;ALX1:0.298091565732;SREBF1,2:0.272095908637;AHR_ARNT_ARNT2:0.253615790535;RORA:0.22924031674;OCT4_SOX2{dimer}:0.193883189485;TEF:0.14247667817;NKX2-2,8:0.134122991704;HOX{A4,D4}:0.131892359123;NANOG{mouse}:0.128135248949;PBX1:0.118710959885;PAX4:0.114890819748;POU6F1:0.100114866808;NKX2-1,4:0.065736568343;FOS_FOS{B,L1}_JUN{B,D}:0.014206053881;HOX{A5,B5}:-0.0186322900868;ATF2:-0.0280106713243;E2F1..5:-0.0487957384909;NKX3-1:-0.06333666164;ZEB1:-0.0894282677565;NR1H4:-0.129709932668;CEBPA,B_DDIT3:-0.144244608531;POU3F1..4:-0.146618038315;NANOG:-0.169221941714;NR5A1,2:-0.174018904807;AR:-0.183540433596;RXRA_VDR{dimer}:-0.183868025753;LMO2:-0.186687587755;NKX6-1,2:-0.200859588156;ARID5B:-0.204121997683;HLF:-0.256744065327;SOX2:-0.266813682856;EP300:-0.268872133603;NFIL3:-0.269047319984;ZNF384:-0.282538202256;POU2F1..3:-0.293089084956;GATA6:-0.304756327176;FOX{F1,F2,J1}:-0.305924705882;HMX1:-0.325826138773;FOXM1:-0.367660160465;TGIF1:-0.376741539773;SOX17:-0.395453936863;ZNF148:-0.396690696666;HBP1_HMGB_SSRP1_UBTF:-0.407606914506;SRF:-0.446530943636;VSX1,2:-0.48381760414;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.521648666266;CUX2:-0.542668870574;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.56131409661;SNAI1..3:-0.566734039611;PRRX1,2:-0.570604384053;ZNF143:-0.577609033799;EN1,2:-0.57793334082;TBX4,5:-0.602166693881;POU5F1:-0.604297835197;MYOD1:-0.617537976817;PAX6:-0.621850213454;HIF1A:-0.625450474694;NFY{A,B,C}:-0.641708742406;HNF4A_NR2F1,2:-0.661201827868;HSF1,2:-0.661524121756;EGR1..3:-0.686586114024;ZFP161:-0.691807015715;SMAD1..7,9:-0.696516076268;NR6A1:-0.711284065319;FOXN1:-0.749416298136;MEF2{A,B,C,D}:-0.755495943569;HOXA9_MEIS1:-0.761992542913;HES1:-0.774017509471;NKX2-3_NKX2-5:-0.787636983179;HNF1A:-0.799865354715;FOSL2:-0.807367088303;NHLH1,2:-0.822645919612;SOX{8,9,10}:-0.824569575723;RFX1:-0.828614796273;EVI1:-0.853091139873;ZNF238:-0.881418165822;MZF1:-0.886854058874;RBPJ:-0.892572459235;TFDP1:-0.965067556854;TFCP2:-1.01704848116;MED-1{core}:-1.02606395062;LHX3,4:-1.03597768804;T:-1.06069841729;HMGA1,2:-1.06660745941;MTE{core}:-1.09972790014;REST:-1.13030154043;FOXL1:-1.14701453127;BACH2:-1.1608361565;FOXA2:-1.19171141856;RREB1:-1.19285158154;MYFfamily:-1.195979256;BREu{core}:-1.21947905265;ESRRA:-1.23684954244;CDC5L:-1.25731879848;MTF1:-1.25945279215;IKZF2:-1.27709790293;PRDM1:-1.27982226196;TBP:-1.2810476607;GATA4:-1.28692963137;MAFB:-1.29392988042;PAX1,9:-1.32175558385;NKX3-2:-1.36102152484;NR3C1:-1.36247002168;NFE2:-1.36854154188;GZF1:-1.37580691054;SOX5:-1.46129326075;RXR{A,B,G}:-1.46826118306;TFAP2B:-1.51116581578;KLF4:-1.52049547679;TP53:-1.56366449682;EBF1:-1.57483732301;ADNP_IRX_SIX_ZHX:-1.58414328953;HAND1,2:-1.61411347116;GLI1..3:-1.6397337311;ONECUT1,2:-1.66341077399;ZBTB6:-1.6972840682;UFEwm:-1.73984391637;GTF2I:-1.76942698941;NFE2L2:-1.81590818659;PATZ1:-1.83499210792;MAZ:-1.84376710993;DBP:-1.84700860588;IKZF1:-1.86911083652;HIC1:-1.91526384123;TOPORS:-1.92497115799;TEAD1:-1.94835854686;ZIC1..3:-1.96581275943;ESR1:-2.02898151474;GFI1:-2.11299206447;TFAP2{A,C}:-2.1304424847;MYBL2:-2.18131695777;SP1:-2.2659719576;XCPE1{core}:-2.29745553756;PAX5:-2.30051379057;GTF2A1,2:-2.34404809153;GCM1,2:-2.45331027958;GFI1B:-2.47197356995;TFAP4:-2.5519895483;TLX1..3_NFIC{dimer}:-2.80967447779;ZNF423:-3.14910372738
}}
}}

Revision as of 15:16, 15 February 2012


Name:CD4+CD25-CD44- naive conventional T cells, pool1 (C57BL_6J)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueblood
dev stageNA
sexNA
ageNA
cell typeT cell
cell lineNA
companyNA
collaborationMorikawa (University of Kyoto)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB6nT
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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

CNhs13217

00
10
100
1000
1000-0.00116
1001-0.0287
1002-0.116
1003-0.141
10040
10050.0686
1006-0.143
1007-0.181
10080
1009-0.19
1010.205
10100
10110.0686
10120
1013-0.101
1014-0.0874
1015-0.123
1016-0.594
10170
10180
10190
1020.694
10200.148
10210.0649
1022-0.124
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.115
103-0.0887
10300
1031-1.148
1032-0.683
10330.405
10340
10350
10360.416
10370
1038-0.154
1039-0.184
1040
1040-0.216
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: CNhs13217

Jaspar motifP-value
MA0002.22.27047e-5
MA0003.10.262
MA0004.10.0589
MA0006.10.442
MA0007.10.245
MA0009.10.672
MA0014.10.725
MA0017.10.878
MA0018.20.00117
MA0019.10.613
MA0024.10.684
MA0025.10.589
MA0027.10.918
MA0028.14.67099e-8
MA0029.10.0807
MA0030.10.3
MA0031.10.0053
MA0035.20.888
MA0038.10.00614
MA0039.20.342
MA0040.10.32
MA0041.10.0673
MA0042.10.503
MA0043.10.0498
MA0046.13.63424e-10
MA0047.20.139
MA0048.10.334
MA0050.14.43777e-10
MA0051.12.78516e-7
MA0052.10.00911
MA0055.10.134
MA0057.10.889
MA0058.10.0481
MA0059.10.0244
MA0060.15.23444e-4
MA0061.18.67915e-5
MA0062.21.01941e-23
MA0065.20.858
MA0066.10.134
MA0067.10.0779
MA0068.10.0251
MA0069.10.962
MA0070.10.914
MA0071.10.941
MA0072.10.0916
MA0073.10.803
MA0074.10.408
MA0076.13.52052e-11
MA0077.10.102
MA0078.10.56
MA0079.20.0551
MA0080.25.54865e-14
MA0081.10.00305
MA0083.10.176
MA0084.10.798
MA0087.10.913
MA0088.10.68
MA0090.10.0886
MA0091.10.642
MA0092.10.727
MA0093.10.076
MA0099.20.46
MA0100.10.166
MA0101.11.3357e-5
MA0102.20.781
MA0103.10.159
MA0104.20.0433
MA0105.12.28159e-6
MA0106.10.948
MA0107.14.49873e-5
MA0108.22.48672e-5
MA0111.10.208
MA0112.20.0977
MA0113.10.31
MA0114.10.345
MA0115.10.56
MA0116.10.0283
MA0117.10.446
MA0119.10.507
MA0122.10.411
MA0124.10.455
MA0125.10.121
MA0131.10.385
MA0135.10.925
MA0136.19.63199e-28
MA0137.22.24288e-4
MA0138.20.00614
MA0139.10.3
MA0140.10.569
MA0141.10.985
MA0142.10.2
MA0143.10.577
MA0144.10.0231
MA0145.10.215
MA0146.10.744
MA0147.10.0215
MA0148.10.173
MA0149.10.11
MA0150.10.784
MA0152.10.904
MA0153.11.38088e-5
MA0154.10.359
MA0155.10.483
MA0156.11.12574e-31
MA0157.10.00374
MA0159.10.164
MA0160.10.938
MA0162.10.833
MA0163.10.0101
MA0164.10.301
MA0258.10.0624
MA0259.10.13



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: CNhs13217

Novel motifP-value
10.248
100.0278
1000.596
1010.868
1020.512
1030.277
1040.929
1050.887
1060.98
1070.413
1080.426
1090.215
110.256
1100.0484
1110.103
1120.11
1130.398
1140.117
1150.724
1160.668
1174.83597e-4
1180.206
1190.688
120.232
1200.0779
1210.489
1220.925
1230.375
1240.342
1250.252
1260.396
1270.69
1280.724
1290.277
130.0573
1300.841
1310.446
1320.899
1330.834
1340.489
1350.803
1360.344
1370.334
1380.383
1390.313
140.669
1400.228
1410.171
1420.266
1432.16595e-4
1440.495
1450.0841
1460.908
1470.388
1480.3
1490.377
150.0762
1500.724
1510.194
1520.239
1530.256
1540.189
1550.143
1560.465
1570.941
1580.0581
1590.605
1600.439
1610.08
1620.397
1630.706
1640.0278
1650.611
1660.56
1670.0811
1680.68
1690.731
170.677
180.29
190.164
20.0434
200.0156
210.0849
220.703
230.72
240.316
250.121
260.308
270.878
280.28
290.024
30.233
300.107
310.694
320.236
330.0803
340.404
350.0489
360.0415
370.151
380.517
390.436
40.937
400.447
410.299
420.219
430.516
440.692
450.435
460.404
470.521
480.286
490.2
50.0394
500.563
510.82
520.0625
530.727
540.663
550.546
560.872
570.567
580.262
590.639
60.578
600.943
610.151
620.0642
630.76
640.863
650.472
660.239
670.624
680.996
690.853
70.384
700.00883
710.089
720.567
730.239
740.83
750.00524
760.0124
770.101
780.119
790.691
80.475
800.147
810.902
820.163
830.0439
840.591
850.939
860.188
870.925
880.434
890.767
90.958
900.0368
910.937
920.469
930.174
940.292
950.139
960.233
970.556
980.428
990.117



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: CNhs13217


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000624 (CD4-positive, alpha-beta T cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000789 (alpha-beta T cell)
0000790 (immature alpha-beta T cell)
0000791 (mature alpha-beta T cell)
0000805 (immature single positive thymocyte)
0000806 (DN2 thymocyte)
0000807 (DN3 thymocyte)
0000808 (DN4 thymocyte)
0000809 (double-positive, alpha-beta thymocyte)
0000810 (CD4-positive, alpha-beta thymocyte)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000893 (thymocyte)
0000894 (DN1 thymic pro-T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)
0000898 (naive T cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002419 (mature T cell)
0002420 (immature T cell)
0002425 (early T lineage precursor)
0002427 (resting double-positive thymocyte)
0002428 (double-positive blast)
0002429 (CD69-positive double-positive thymocyte)
0002431 (CD4-positive, CD8-intermediate double-positive thymocyte)
0002432 (CD24-positive, CD4 single-positive thymocyte)
0002433 (CD69-positive, CD4-positive single-positive thymocyte)
0002436 (mature CD4 single-positive thymocyte)
0002489 (double negative thymocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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