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{{f5samples
{{f5samples
|id=FF:11820-124F2
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|name=CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool2 (Balb_cAJcl)
|sample_id=11820
|rna_tube_id=124F2
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|sample_species=Mouse (Mus musculus)
|sample_strain=Balb/cAJcl
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|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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|rna_concentration=0.15194
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|ancestors_in_disease_facet=
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|sample_description=
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|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=EFO:0000369,FF:0000409,FF:0011449,FF:11820-124F2
|fonse_treatment=EFO:0000369,FF:0000409,FF:0011449,FF:11820-124F2
|fonse_treatment_closure=EFO:0000369,FF:0000409,FF:0011449,FF:11820-124F2
|fonse_treatment_closure=EFO:0000369,FF:0000409,FF:0011449,FF:11820-124F2
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|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011449
|name=CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool2 (Balb_cAJcl)
|namespace=
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|rna_lot_number=BLTsPI-2
|rna_od260/230=2.180252583
|rna_od260/280=2.121787709
|rna_position=F2
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|rna_sample_type=total RNA
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|sample_collaboration=Morikawa (University of Kyoto)
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|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11820
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=Balb/cAJcl
|sample_tissue=blood
|top_motifs=NFKB1_REL_RELA:5.46529720824;ATF4:4.38342448979;ATF5_CREB3:4.25735638358;NFATC1..3:3.87920364287;NFE2L1:3.80482773942;SPZ1:3.80466451654;RUNX1..3:3.58986533379;CREB1:3.52507916189;FOXP3:3.26908399123;AIRE:3.12828141939;bHLH_family:2.67915316537;ALX4:2.560184551;NANOG{mouse}:2.51256324647;STAT5{A,B}:2.39870300357;PAX2:2.37304254953;STAT1,3:2.34677381476;TBX4,5:2.24361241637;ZBTB16:2.05875920214;ETS1,2:2.01488922568;FOS_FOS{B,L1}_JUN{B,D}:2.01277834021;FOSL2:1.88442489356;HIF1A:1.8815113182;SPI1:1.74844879301;PPARG:1.72875179691;NFE2:1.71441282046;PDX1:1.66723444196;SPIB:1.52716461248;ELF1,2,4:1.52455796953;CRX:1.51803499089;TLX2:1.47002674788;JUN:1.42507839235;HSF1,2:1.41395009302;ELK1,4_GABP{A,B1}:1.38754974544;HES1:1.36368148773;PAX8:1.35581587987;HMX1:1.30170906303;BPTF:1.24404397015;AHR_ARNT_ARNT2:1.21008461759;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.20557527579;RORA:1.1543420093;PAX4:1.07322319596;STAT2,4,6:1.01987308483;YY1:0.999720966624;ZNF384:0.993646678547;IRF7:0.961436652112;NR1H4:0.958585151275;MTE{core}:0.84020048956;ATF6:0.840126116473;EGR1..3:0.829148125319;EP300:0.814736486163;IRF1,2:0.800245329426;BACH2:0.762993912183;ATF2:0.76227498265;DMAP1_NCOR{1,2}_SMARC:0.718396883425;CEBPA,B_DDIT3:0.665342805225;FOX{D1,D2}:0.653481831699;FOXN1:0.640828935529;MYB:0.594826891601;IKZF2:0.524306810572;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.485284159339;ALX1:0.459887948427;EVI1:0.30994229002;NKX3-1:0.306532489351;FOXD3:0.280453370012;NR6A1:0.245841629101;PITX1..3:0.231738276056;TFDP1:0.221151583388;RFX2..5_RFXANK_RFXAP:0.218558297932;MAFB:0.213325585373;HLF:0.139480359995;NANOG:0.127588456686;SRF:0.124394492441;FOXM1:0.112860528527;HOX{A5,B5}:0.0757870617959;NKX6-1,2:0.0604406485991;HMGA1,2:0.0470729213834;POU3F1..4:0.0436366329204;E2F1..5:0.041817128621;FOXP1:0.026888304532;NRF1:0.0249466727007;MYOD1:0.0228151872821;NKX2-1,4:-0.0837622378798;SMAD1..7,9:-0.0943404858122;ZNF148:-0.102826851788;ZIC1..3:-0.128863260949;SOX17:-0.150076280015;TFAP2B:-0.155595968183;TBP:-0.171185041467;HOX{A4,D4}:-0.206232439355;ZFP161:-0.265108991584;GATA6:-0.27528907055;SOX2:-0.285034406516;NFIL3:-0.327701272157;MED-1{core}:-0.331155902542;SNAI1..3:-0.351701101537;RREB1:-0.352595571569;RXR{A,B,G}:-0.362892961154;OCT4_SOX2{dimer}:-0.389770836528;FOXQ1:-0.3924307417;MEF2{A,B,C,D}:-0.407612571127;POU6F1:-0.409845427792;TP53:-0.412862261742;NR5A1,2:-0.417917433025;MZF1:-0.437875037428;LEF1_TCF7_TCF7L1,2:-0.444541928186;POU5F1:-0.457999428863;EN1,2:-0.458289763762;LMO2:-0.463239865904;RXRA_VDR{dimer}:-0.473826303171;CDX1,2,4:-0.479012891027;FOX{F1,F2,J1}:-0.488127856254;CUX2:-0.489932511547;CDC5L:-0.4906615689;PAX1,9:-0.504170117094;FOXL1:-0.51646467646;HBP1_HMGB_SSRP1_UBTF:-0.521225904605;GLI1..3:-0.527614395186;TAL1_TCF{3,4,12}:-0.5681818791;AR:-0.59390114564;PAX5:-0.62348345794;POU2F1..3:-0.628823351483;FOX{I1,J2}:-0.63233572629;ZEB1:-0.639370755609;NFIX:-0.676277566316;SP1:-0.681816540776;FOXO1,3,4:-0.683935161658;ZNF143:-0.685297902605;HNF1A:-0.715605723799;NKX2-2,8:-0.72448789736;MAZ:-0.729026985306;RBPJ:-0.730667806384;HNF4A_NR2F1,2:-0.738402363067;ESRRA:-0.764118981166;NFE2L2:-0.80039088387;NHLH1,2:-0.822494742511;UFEwm:-0.859868493966;VSX1,2:-0.863680567233;LHX3,4:-0.873694415436;MYFfamily:-0.89316808101;ZBTB6:-0.907634911557;BREu{core}:-0.908195840088;HOXA9_MEIS1:-0.946698959782;NFY{A,B,C}:-0.999741852594;FOXA2:-1.0386553079;REST:-1.03931693398;TFCP2:-1.04443486477;TGIF1:-1.0550724659;KLF4:-1.05719266512;PRDM1:-1.06068501888;ESR1:-1.07410745122;POU1F1:-1.07534690362;ARID5B:-1.08698856754;PBX1:-1.09596717954;NKX2-3_NKX2-5:-1.1128185582;TEF:-1.14318357472;RFX1:-1.154991569;NKX3-2:-1.19978154892;GCM1,2:-1.20214458761;PAX6:-1.21386525567;GZF1:-1.24694680943;HAND1,2:-1.34938641221;ZNF238:-1.3534122882;MTF1:-1.36337784832;PRRX1,2:-1.3680505279;SREBF1,2:-1.38740425773;SOX{8,9,10}:-1.39930750025;T:-1.43336877203;IKZF1:-1.4703320256;TFAP2{A,C}:-1.50932474791;GATA4:-1.51540099029;PATZ1:-1.53092491785;HIC1:-1.65785421138;GTF2A1,2:-1.67621170419;DBP:-1.77300711527;ADNP_IRX_SIX_ZHX:-1.77969821922;GTF2I:-1.79497261577;SOX5:-1.82330649516;ONECUT1,2:-1.84784459381;TEAD1:-1.88630439129;TOPORS:-1.90020611972;MYBL2:-1.995965657;EBF1:-2.23507167739;XCPE1{core}:-2.24617319568;NR3C1:-2.29882582042;TFAP4:-2.30936405468;GFI1B:-2.79760142976;GFI1:-2.87243582194;TLX1..3_NFIC{dimer}:-3.01850076725;ZNF423:-3.38977131832
}}
}}

Revision as of 15:03, 21 March 2012


Name:CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool2 (Balb_cAJcl)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/cAJcl
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 numberBLTsPI-2
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

CNhs13226

00
10
100
1000
1000-0.0355
1001-0.0668
1002-0.116
1003-0.14
10040
1005-0.101
1006-0.436
1007-0.246
10080
1009-0.19
1010.657
10100
10110.0913
10120
1013-0.183
1014-0.0851
10150.176
1016-0.448
10170
10180
10190
1020.836
10200.037
10210
1022-0.296
10230.167
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.0989
103-0.0887
10300
1031-1.056
1032-0.717
10330.929
10340
10350
10360.583
10370
1038-0.183
1039-0.482
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: CNhs13226

Jaspar motifP-value
MA0002.20.0123
MA0003.10.132
MA0004.10.0237
MA0006.10.189
MA0007.10.939
MA0009.10.648
MA0014.10.91
MA0017.10.137
MA0018.22.07019e-9
MA0019.10.94
MA0024.10.92
MA0025.10.173
MA0027.10.744
MA0028.10.00249
MA0029.10.934
MA0030.10.961
MA0031.10.326
MA0035.20.892
MA0038.10.0248
MA0039.20.132
MA0040.10.96
MA0041.10.0585
MA0042.10.0987
MA0043.12.05521e-4
MA0046.15.92568e-11
MA0047.20.667
MA0048.10.265
MA0050.11.28568e-4
MA0051.10.00394
MA0052.10.532
MA0055.10.157
MA0057.10.829
MA0058.10.00664
MA0059.13.67959e-4
MA0060.10.00516
MA0061.15.00318e-11
MA0062.25.74142e-11
MA0065.20.385
MA0066.10.614
MA0067.19.17826e-4
MA0068.17.04658e-4
MA0069.10.679
MA0070.10.95
MA0071.10.631
MA0072.10.158
MA0073.10.522
MA0074.10.583
MA0076.10.00342
MA0077.10.798
MA0078.10.5
MA0079.20.326
MA0080.24.44885e-10
MA0081.18.28542e-4
MA0083.10.619
MA0084.10.341
MA0087.10.889
MA0088.10.0725
MA0090.10.0295
MA0091.10.877
MA0092.10.0846
MA0093.10.0243
MA0099.21.90857e-6
MA0100.10.263
MA0101.11.39184e-15
MA0102.20.401
MA0103.10.553
MA0104.21.26819e-4
MA0105.11.50427e-6
MA0106.10.582
MA0107.16.78646e-16
MA0108.20.475
MA0111.10.409
MA0112.20.389
MA0113.10.952
MA0114.10.00388
MA0115.10.268
MA0116.10.97
MA0117.10.0353
MA0119.10.0251
MA0122.10.632
MA0124.10.483
MA0125.10.114
MA0131.10.526
MA0135.10.88
MA0136.11.50298e-16
MA0137.20.00564
MA0138.22.57295e-4
MA0139.10.212
MA0140.10.721
MA0141.10.524
MA0142.10.585
MA0143.10.226
MA0144.10.183
MA0145.10.0226
MA0146.10.958
MA0147.17.41537e-6
MA0148.10.622
MA0149.10.246
MA0150.10.0778
MA0152.10.0654
MA0153.15.21671e-6
MA0154.10.739
MA0155.10.336
MA0156.11.56159e-14
MA0157.10.259
MA0159.10.679
MA0160.10.971
MA0162.10.0189
MA0163.10.748
MA0164.10.0466
MA0258.10.849
MA0259.10.0203



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: CNhs13226

Novel motifP-value
10.972
100.228
1000.474
1010.463
1020.434
1030.16
1040.493
1050.425
1060.215
1070.971
1080.77
1090.722
110.702
1100.407
1110.129
1120.296
1130.91
1140.975
1150.462
1160.543
1172.80937e-4
1180.66
1190.899
120.295
1200.162
1210.373
1220.981
1230.648
1240.221
1250.579
1260.452
1270.502
1280.191
1290.513
130.259
1300.461
1310.305
1320.612
1330.196
1340.454
1350.253
1360.954
1370.872
1380.976
1390.143
140.0871
1400.992
1410.847
1420.562
1430.0167
1440.36
1450.192
1460.854
1470.662
1480.244
1490.115
150.486
1501
1510.973
1520.673
1530.467
1540.165
1550.22
1560.00111
1570.983
1580.0143
1590.714
1600.119
1610.322
1620.203
1630.767
1640.0701
1650.807
1660.0774
1670.133
1680.709
1690.212
170.921
180.29
190.0105
20.00773
200.00328
210.167
220.356
230.683
240.533
250.357
260.55
270.122
280.421
290.251
30.984
300.12
310.444
320.0509
330.223
340.298
350.278
360.157
370.371
380.446
390.589
40.788
400.914
410.151
420.787
430.686
440.728
450.32
460.883
470.646
480.794
490.696
50.205
500.635
510.658
520.497
530.641
540.564
550.992
560.757
570.63
580.74
590.428
60.654
600.458
610.243
620.264
630.699
640.592
650.791
660.668
670.621
680.157
690.523
70.689
700.0204
710.235
720.818
730.369
740.668
750.042
760.0327
770.02
780.0608
790.857
80.989
800.415
810.877
820.803
830.243
840.284
850.582
860.129
870.423
880.544
890.322
90.819
900.524
910.554
920.622
930.258
940.486
950.482
960.567
970.502
980.852
990.0483



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: CNhs13226


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

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11820-124F2&oldid=727487"