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FF:11818-124E9

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Name:CD4+CD25+ regulatory T cells, pool2 (Balb_cAJcl)
Species:Mouse (Mus musculus)
Library ID:CNhs13221
Sample type:primary cells
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 numberBLTreg
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004975
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13221 CAGE DRX008790 DRR009662
Accession ID Mm9

Library idBAMCTSS
CNhs13221 DRZ001087 DRZ002472
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs13221

00
10
100
1000
1000-0.0355
1001-0.0631
1002-0.116
1003-0.148
10040
10050.0998
1006-0.143
1007-0.199
10080
1009-0.19
1010.151
10100
10110.0347
10120.083
1013-0.0691
1014-0.0874
1015-0.109
1016-0.594
10170
10180
10190
1020.799
10200.0527
10210
1022-0.315
10230.0527
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.0989
103-0.0887
10300
1031-1.093
1032-0.655
10330.522
10340
10350
10360.373
10370
1038-0.184
1039-0.181
1040
1040-0.121
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



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: CNhs13221

Jaspar motifP-value
MA0002.23.37776e-5
MA0003.10.419
MA0004.10.0505
MA0006.10.609
MA0007.10.446
MA0009.10.65
MA0014.10.815
MA0017.10.706
MA0018.22.00102e-5
MA0019.10.917
MA0024.10.721
MA0025.10.734
MA0027.10.75
MA0028.16.97893e-8
MA0029.10.427
MA0030.10.248
MA0031.10.00804
MA0035.20.627
MA0038.10.00785
MA0039.20.541
MA0040.10.239
MA0041.10.0862
MA0042.10.444
MA0043.10.0223
MA0046.19.58241e-10
MA0047.20.161
MA0048.10.3
MA0050.12.13614e-10
MA0051.15.99243e-7
MA0052.10.0903
MA0055.10.138
MA0057.10.88
MA0058.10.0407
MA0059.10.0439
MA0060.10.00526
MA0061.11.54223e-11
MA0062.22.5443e-24
MA0065.20.932
MA0066.10.111
MA0067.10.0178
MA0068.10.0102
MA0069.10.622
MA0070.10.784
MA0071.10.801
MA0072.10.0942
MA0073.10.732
MA0074.10.481
MA0076.11.5439e-10
MA0077.10.0717
MA0078.10.645
MA0079.20.0852
MA0080.21.28881e-13
MA0081.10.00164
MA0083.10.341
MA0084.10.677
MA0087.10.829
MA0088.10.998
MA0090.10.0632
MA0091.10.821
MA0092.10.597
MA0093.10.063
MA0099.20.92
MA0100.10.25
MA0101.15.72993e-12
MA0102.20.964
MA0103.10.183
MA0104.20.0711
MA0105.14.364e-11
MA0106.10.942
MA0107.16.07129e-12
MA0108.20.00199
MA0111.10.293
MA0112.20.292
MA0113.10.143
MA0114.10.111
MA0115.10.853
MA0116.10.0237
MA0117.10.244
MA0119.10.54
MA0122.10.404
MA0124.10.686
MA0125.10.165
MA0131.10.584
MA0135.10.945
MA0136.11.69552e-25
MA0137.21.53488e-6
MA0138.20.00179
MA0139.10.416
MA0140.10.18
MA0141.10.731
MA0142.10.26
MA0143.10.586
MA0144.10.00603
MA0145.10.299
MA0146.10.691
MA0147.10.0338
MA0148.10.143
MA0149.10.185
MA0150.10.933
MA0152.10.932
MA0153.16.53611e-5
MA0154.10.126
MA0155.10.588
MA0156.13.68403e-29
MA0157.10.00938
MA0159.10.133
MA0160.10.887
MA0162.10.825
MA0163.10.0197
MA0164.10.262
MA0258.10.148
MA0259.10.184



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: CNhs13221

Novel motifP-value
10.383
100.0343
1000.54
1010.895
1020.507
1030.644
1040.845
1050.659
1060.684
1070.472
1080.577
1090.291
110.336
1100.0805
1110.141
1120.206
1130.627
1140.323
1150.647
1160.758
1174.1361e-4
1180.321
1190.785
120.282
1200.105
1210.313
1220.846
1230.66
1240.315
1250.293
1260.526
1270.954
1280.497
1290.583
130.0889
1300.808
1310.765
1320.993
1330.821
1340.514
1350.848
1360.273
1370.327
1380.558
1390.401
140.725
1400.668
1410.251
1420.328
1432.66668e-4
1440.382
1450.224
1460.987
1470.365
1480.165
1490.135
150.12
1500.796
1510.249
1520.499
1530.372
1540.306
1550.104
1560.114
1570.939
1580.0569
1590.537
1600.387
1610.273
1620.721
1630.368
1640.031
1650.576
1660.464
1670.0936
1680.63
1690.889
170.671
180.391
190.0814
20.0386
200.0169
210.2
220.789
230.828
240.281
250.164
260.364
270.742
280.257
290.0417
30.293
300.0908
310.526
320.133
330.127
340.462
350.0582
360.0315
370.126
380.659
390.636
40.885
400.321
410.42
420.262
430.558
440.657
450.462
460.513
470.581
480.343
490.232
50.0428
500.49
510.794
520.106
530.685
540.59
550.543
560.854
570.905
580.331
590.809
60.729
600.961
610.217
620.0933
630.826
640.971
650.527
660.278
670.797
680.88
690.855
70.435
700.0124
710.0974
720.292
730.181
740.548
750.00563
760.0207
770.0516
780.19
790.795
80.583
800.233
810.728
820.311
830.0441
840.488
850.997
860.102
870.744
880.389
890.851
90.913
900.141
910.905
920.556
930.247
940.375
950.0712
960.278
970.498
980.534
990.0369



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: CNhs13221


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000791 (mature alpha-beta T cell)
0000084 (T cell)
0000789 (alpha-beta T cell)
0002419 (mature T cell)
0000624 (CD4-positive, alpha-beta T cell)
0000815 (regulatory T cell)
0000792 (CD4-positive, CD25-positive, alpha-beta regulatory T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0011455 (CD4-positiveCD25-positive regulatory T cells (Balb_cAJcl) sample)

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
CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
CL:0000790 (immature alpha-beta T cell)

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