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FF:11819-124F1

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Name:CD4+CD25-CD44- naive conventional T cells stimulated with alphaCD3_CD28, 06hr, 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 numberBLTs3/28-6
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

CNhs13225

00
10
100
1000
1000-0.0355
1001-0.0668
1002-0.116
1003-0.108
10040
1005-0.024
1006-0.424
1007-0.11
10080
1009-0.19
1010.699
10100
10110.0336
10120.0333
1013-0.254
1014-0.0874
10150.344
1016-0.594
10170
10180
10190
1020.235
10200.0333
10210
1022-0.224
10230
1024-0.307
1025-0.0611
10260
1027-0.048
10280
1029-0.0828
103-0.0887
10300
1031-1.193
1032-0.576
10330.655
10340
10350
10360.568
10370
1038-0.487
1039-0.284
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: CNhs13225

Jaspar motifP-value
MA0002.20.00766
MA0003.10.337
MA0004.10.00368
MA0006.10.152
MA0007.10.372
MA0009.10.975
MA0014.10.772
MA0017.10.232
MA0018.20.0152
MA0019.10.63
MA0024.10.387
MA0025.10.932
MA0027.10.615
MA0028.17.31614e-8
MA0029.10.935
MA0030.10.119
MA0031.10.753
MA0035.20.863
MA0038.10.00594
MA0039.20.0361
MA0040.10.23
MA0041.10.126
MA0042.10.414
MA0043.10.0756
MA0046.11.031e-8
MA0047.20.778
MA0048.10.0961
MA0050.10.17
MA0051.10.379
MA0052.10.0594
MA0055.10.0123
MA0057.10.708
MA0058.10.00272
MA0059.13.48309e-7
MA0060.12.43015e-10
MA0061.11.41286e-4
MA0062.21.30098e-16
MA0065.20.0681
MA0066.10.203
MA0067.10.15
MA0068.10.635
MA0069.10.774
MA0070.10.283
MA0071.10.0859
MA0072.10.104
MA0073.10.771
MA0074.10.222
MA0076.17.07843e-9
MA0077.10.585
MA0078.10.19
MA0079.20.0264
MA0080.22.67505e-7
MA0081.10.00542
MA0083.10.138
MA0084.10.0979
MA0087.10.956
MA0088.10.334
MA0090.10.112
MA0091.10.236
MA0092.10.582
MA0093.10.00552
MA0099.20.0206
MA0100.10.187
MA0101.18.20456e-7
MA0102.20.41
MA0103.10.223
MA0104.22.64744e-6
MA0105.11.92748e-5
MA0106.10.629
MA0107.12.73302e-5
MA0108.21.80337e-5
MA0111.10.248
MA0112.20.0822
MA0113.10.245
MA0114.10.858
MA0115.10.0448
MA0116.10.0328
MA0117.10.547
MA0119.10.485
MA0122.10.757
MA0124.10.651
MA0125.10.0935
MA0131.10.296
MA0135.10.26
MA0136.12.33575e-15
MA0137.22.3372e-4
MA0138.20.0562
MA0139.10.355
MA0140.10.839
MA0141.10.0816
MA0142.10.426
MA0143.10.638
MA0144.10.0774
MA0145.10.186
MA0146.10.857
MA0147.13.74731e-8
MA0148.10.947
MA0149.10.0885
MA0150.10.066
MA0152.10.477
MA0153.11.43941e-4
MA0154.10.221
MA0155.10.876
MA0156.12.74252e-14
MA0157.10.973
MA0159.10.07
MA0160.10.0974
MA0162.10.872
MA0163.10.00265
MA0164.10.137
MA0258.10.0269
MA0259.10.012



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: CNhs13225

Novel motifP-value
10.126
100.038
1000.482
1010.55
1020.366
1030.386
1040.413
1050.64
1060.554
1070.798
1080.882
1090.163
110.113
1100.0329
1110.00466
1120.0736
1130.927
1140.0434
1150.952
1160.722
1174.54775e-4
1180.504
1190.463
120.423
1200.198
1210.487
1220.978
1230.802
1240.264
1250.0715
1260.0884
1270.504
1280.427
1290.496
130.0812
1300.434
1310.415
1320.739
1330.155
1340.481
1350.661
1360.26
1370.643
1380.363
1390.00302
140.212
1400.075
1410.328
1420.261
1430.023
1440.303
1450.0263
1460.907
1470.9
1480.201
1490.501
150.131
1500.695
1510.64
1520.249
1530.233
1540.479
1550.281
1567.67826e-4
1570.65
1580.0161
1590.787
1600.794
1610.0814
1620.59
1630.899
1640.0142
1650.494
1660.0817
1670.0226
1680.857
1690.668
170.552
180.0878
190.322
20.169
200.008
210.191
220.823
230.416
240.42
250.186
260.0276
270.577
280.582
290.0216
30.308
300.137
310.858
320.472
330.217
340.388
350.064
360.0436
370.204
380.941
390.896
40.584
400.396
410.143
420.426
430.545
440.276
450.472
460.145
470.379
480.155
490.148
50.0818
500.782
510.968
520.241
530.684
540.766
550.319
560.895
570.388
580.348
590.957
60.787
600.712
610.0816
620.0866
630.54
640.507
650.764
660.309
670.357
680.103
690.698
70.288
700.00311
710.0116
720.364
730.234
740.904
750.00961
760.00511
770.491
780.0489
790.388
80.0769
800.285
810.624
820.176
830.364
840.301
850.813
860.204
870.98
880.369
890.581
90.938
900.0208
910.935
920.103
930.214
940.195
950.133
960.0361
970.554
980.473
990.313



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: CNhs13225


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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