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|fonse_treatment=EFO:0000369,FF:0000409,FF:0011446,FF:11815-124E6
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|fonse_treatment_closure=EFO:0000369,FF:0000409,FF:0011446,FF:11815-124E6
|fonse_treatment_closure=EFO:0000369,FF:0000409,FF:0011446,FF:11815-124E6
|top_motifs=bHLH_family:4.27806574288;ELK1,4_GABP{A,B1}:3.29622530588;NFKB1_REL_RELA:3.0368120466;NFE2L1:2.73923889277;RUNX1..3:2.63761958163;ATF5_CREB3:2.63618719897;YY1:2.526062295;HIF1A:2.49296998598;SPZ1:2.44434719098;PAX8:2.37607860047;FOXP3:2.24279793077;ATF4:2.07283006779;AIRE:2.03848953424;ZBTB16:1.90959499916;PPARG:1.88418838333;ELF1,2,4:1.79536933758;STAT1,3:1.7826930518;STAT5{A,B}:1.77662816515;ALX4:1.76887533098;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.58038648192;CREB1:1.5436978613;NFE2:1.4773821359;HSF1,2:1.42531971049;AHR_ARNT_ARNT2:1.41720821976;ETS1,2:1.28133622296;HES1:1.24573701228;SPI1:1.2135001643;TBX4,5:1.20836556026;PDX1:1.17374287389;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.15781861508;SPIB:1.09885995158;NFATC1..3:1.08000704272;NANOG{mouse}:1.01452725455;CDX1,2,4:0.992848600045;NKX3-1:0.992688796684;ALX1:0.959450004025;CEBPA,B_DDIT3:0.95779428837;FOXD3:0.881731078867;RORA:0.87545093325;MYB:0.697209279301;FOS_FOS{B,L1}_JUN{B,D}:0.634652053773;CRX:0.605327503595;TLX2:0.552634498234;HLF:0.53585654989;STAT2,4,6:0.506019092742;JUN:0.501638657524;PITX1..3:0.453641243999;NR6A1:0.450366128346;NRF1:0.42860022145;IKZF2:0.424246891956;POU3F1..4:0.41525763824;BPTF:0.412566905183;FOSL2:0.405266677156;PAX2:0.400358514089;PAX4:0.370381928959;ATF2:0.344267377985;PAX6:0.338197131695;NANOG:0.322022757488;CUX2:0.263948563076;HOX{A5,B5}:0.257288719653;PAX1,9:0.201483690822;NKX6-1,2:0.191610732498;FOXQ1:0.187764300102;HMGA1,2:0.179679967179;EN1,2:0.151420477555;HOX{A4,D4}:0.134934474103;NKX2-2,8:0.121163147457;NFIX:0.0962077198221;ZNF384:0.0910553591698;IRF7:0.0795453480643;EP300:0.0739484972905;RFX2..5_RFXANK_RFXAP:0.0102665477761;EVI1:0.00513553043514;FOXP1:0.00503289177905;OCT4_SOX2{dimer}:-0.00762940323665;NFIL3:-0.0266292488552;IRF1,2:-0.0279763641331;NKX2-1,4:-0.0610109937943;SOX17:-0.0967022004744;RXRA_VDR{dimer}:-0.0994725564984;ZEB1:-0.126255745219;ARID5B:-0.142324396276;E2F1..5:-0.150384800815;SRF:-0.181910269547;DMAP1_NCOR{1,2}_SMARC:-0.206549452392;NR5A1,2:-0.209818022333;LHX3,4:-0.294369814267;VSX1,2:-0.297809883142;ZIC1..3:-0.304133626477;FOX{F1,F2,J1}:-0.329864718707;ZNF143:-0.343196813906;NR1H4:-0.348259662678;GATA6:-0.362737485876;HMX1:-0.37475795454;TAL1_TCF{3,4,12}:-0.385796924718;LMO2:-0.406052926758;RXR{A,B,G}:-0.433110353535;SNAI1..3:-0.436253456177;MYOD1:-0.440890840724;ATF6:-0.444735871248;NKX2-3_NKX2-5:-0.454483941874;POU6F1:-0.468231447617;TFDP1:-0.488929457724;ESRRA:-0.48963196895;BACH2:-0.490302513253;AR:-0.490916345603;MEF2{A,B,C,D}:-0.500408881894;UFEwm:-0.504448722572;RBPJ:-0.531103214932;PRRX1,2:-0.559507551655;ZFP161:-0.565096152849;TEF:-0.573930479475;HNF4A_NR2F1,2:-0.574501617097;TP53:-0.597875428197;NKX3-2:-0.601956747648;POU5F1:-0.604942766729;FOX{I1,J2}:-0.616914113469;PBX1:-0.621699095457;EGR1..3:-0.633444895969;FOX{D1,D2}:-0.642312262595;FOXA2:-0.642804082089;SOX2:-0.678509043182;HNF1A:-0.684062354872;KLF4:-0.691850907009;BREu{core}:-0.70171892602;FOXM1:-0.703542636058;POU1F1:-0.718999491281;ADNP_IRX_SIX_ZHX:-0.734827310798;MAFB:-0.760900959534;PRDM1:-0.782560349542;HAND1,2:-0.783856934917;FOXO1,3,4:-0.813449157629;ESR1:-0.840423291411;LEF1_TCF7_TCF7L1,2:-0.870253458983;SMAD1..7,9:-0.890438453548;TBP:-0.937193988191;MTE{core}:-0.93869689804;ONECUT1,2:-0.956118595878;HOXA9_MEIS1:-0.978117344467;RREB1:-0.981414138043;RFX1:-0.985661684349;POU2F1..3:-0.987375991942;NR3C1:-1.00949584099;MED-1{core}:-1.05583384762;REST:-1.06492083382;IKZF1:-1.17832447895;ZNF148:-1.22641747148;MZF1:-1.23355371805;ZBTB6:-1.26939356366;NHLH1,2:-1.29762224151;ZNF238:-1.31312941751;GLI1..3:-1.37397243822;HBP1_HMGB_SSRP1_UBTF:-1.40044858407;TFAP2B:-1.40254153893;TFCP2:-1.40793988998;GZF1:-1.43552306821;TGIF1:-1.487271121;FOXN1:-1.50028854138;GCM1,2:-1.5143779432;NFE2L2:-1.52209440305;TEAD1:-1.55706908433;CDC5L:-1.60571795851;DBP:-1.60632729581;MYFfamily:-1.65525713129;SOX{8,9,10}:-1.66455981985;GATA4:-1.68812366229;SOX5:-1.6952575371;FOXL1:-1.71962328264;PAX5:-1.78163646853;HIC1:-1.81997913439;SREBF1,2:-1.83872432186;GFI1B:-1.87840932453;TFAP2{A,C}:-1.90219656468;TOPORS:-1.90871214918;T:-1.9115835318;NFY{A,B,C}:-1.94473792193;GTF2I:-2.00797428668;MYBL2:-2.03389864945;MAZ:-2.08313453337;PATZ1:-2.19843069761;TFAP4:-2.26416493512;GTF2A1,2:-2.34234236337;MTF1:-2.37850984412;ZNF423:-2.39979684322;GFI1:-2.58829369125;TLX1..3_NFIC{dimer}:-2.61597559713;EBF1:-2.68538747653;SP1:-3.31393482679;XCPE1{core}:-3.59382810729
}}
}}

Revision as of 15:16, 15 February 2012


Name:CD4+CD25-CD44- naive conventional T cells stimulated with alphaCD3_CD28 , 06hr, 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 numberB6Ts3/28-6
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

CNhs13218

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.087
10040
10050
1006-0.436
1007-0.122
10080
1009-0.2
1010.71
10100
10110.153
10120
1013-0.331
1014-0.0243
10150.212
1016-0.61
10170
10180
10190
1020.307
10200.128
10210
1022-0.223
10230
1024-0.307
1025-0.0611
10260
1027-0.048
10280
1029-0.115
103-0.0887
10300
1031-1.193
1032-0.602
10330.661
10340
10350
10360.631
10370
1038-0.481
1039-0.348
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: CNhs13218

Jaspar motifP-value
MA0002.20.0067
MA0003.10.273
MA0004.10.00463
MA0006.10.137
MA0007.10.346
MA0009.10.924
MA0014.10.73
MA0017.10.244
MA0018.20.00188
MA0019.10.521
MA0024.10.369
MA0025.10.71
MA0027.10.43
MA0028.14.55556e-8
MA0029.10.535
MA0030.10.246
MA0031.10.873
MA0035.20.622
MA0038.10.00635
MA0039.20.0351
MA0040.10.278
MA0041.10.143
MA0042.10.532
MA0043.10.0386
MA0046.11.16911e-9
MA0047.20.844
MA0048.10.0996
MA0050.10.111
MA0051.10.458
MA0052.10.0737
MA0055.10.00747
MA0057.10.707
MA0058.10.00283
MA0059.16.4326e-7
MA0060.11.93449e-10
MA0061.15.04248e-5
MA0062.21.33131e-17
MA0065.20.133
MA0066.10.194
MA0067.10.0792
MA0068.10.218
MA0069.10.848
MA0070.10.463
MA0071.10.134
MA0072.10.123
MA0073.10.763
MA0074.10.259
MA0076.11.44856e-9
MA0077.10.432
MA0078.10.211
MA0079.20.0259
MA0080.29.31245e-8
MA0081.10.00453
MA0083.10.428
MA0084.10.214
MA0087.10.913
MA0088.10.354
MA0090.10.127
MA0091.10.238
MA0092.10.667
MA0093.10.00678
MA0099.20.0132
MA0100.10.244
MA0101.11.49296e-7
MA0102.20.565
MA0103.10.229
MA0104.25.43602e-6
MA0105.14.6811e-6
MA0106.10.711
MA0107.14.38625e-6
MA0108.22.23758e-4
MA0111.10.256
MA0112.20.067
MA0113.10.31
MA0114.10.972
MA0115.10.0397
MA0116.10.0317
MA0117.10.344
MA0119.10.467
MA0122.10.55
MA0124.10.987
MA0125.10.0709
MA0131.10.23
MA0135.10.334
MA0136.18.7591e-18
MA0137.22.4542e-4
MA0138.20.0365
MA0139.10.471
MA0140.10.915
MA0141.10.102
MA0142.10.291
MA0143.10.711
MA0144.10.073
MA0145.10.213
MA0146.10.924
MA0147.18.67113e-8
MA0148.10.896
MA0149.10.0678
MA0150.10.0537
MA0152.10.227
MA0153.11.60579e-4
MA0154.10.206
MA0155.10.797
MA0156.11.00072e-15
MA0157.10.72
MA0159.10.0913
MA0160.10.133
MA0162.10.775
MA0163.10.00446
MA0164.10.157
MA0258.10.024
MA0259.10.0107



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: CNhs13218

Novel motifP-value
10.128
100.0433
1000.527
1010.608
1020.386
1030.429
1040.477
1050.525
1060.521
1070.687
1080.821
1090.147
110.135
1100.026
1110.00892
1120.0772
1130.924
1140.0657
1150.841
1160.704
1175.12485e-4
1180.545
1190.476
120.491
1200.176
1210.525
1220.971
1230.669
1240.259
1250.0755
1260.131
1270.558
1280.44
1290.423
130.0637
1300.541
1310.454
1320.686
1330.067
1340.438
1350.749
1360.249
1370.621
1380.328
1390.00777
140.196
1400.098
1410.475
1420.28
1430.0136
1440.546
1450.0301
1460.857
1470.792
1480.252
1490.491
150.157
1500.768
1510.703
1520.214
1530.177
1540.419
1550.321
1560.0196
1570.534
1580.0166
1590.925
1600.781
1610.0543
1620.391
1630.938
1640.0135
1650.307
1660.065
1670.021
1680.82
1690.703
170.521
180.0957
190.277
20.164
200.00557
210.124
220.772
230.49
240.517
250.192
260.0317
270.509
280.661
290.0207
30.307
300.112
310.814
320.543
330.173
340.364
350.0741
360.045
370.175
381
390.89
40.625
400.394
410.146
420.414
430.54
440.296
450.477
460.167
470.466
480.189
490.149
50.0903
500.751
510.939
520.231
530.727
540.842
550.41
560.932
570.364
580.32
590.975
60.767
600.76
610.144
620.0844
630.588
640.529
650.775
660.357
670.568
680.0895
690.645
70.31
700.00239
710.0106
720.451
730.251
740.811
750.0104
760.00696
770.518
780.0329
790.6
80.0832
800.242
810.677
820.158
830.268
840.414
850.919
860.193
870.96
880.449
890.626
90.978
900.0183
910.937
920.0735
930.158
940.208
950.182
960.0389
970.537
980.527
990.264



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: CNhs13218


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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