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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11855
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11855
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11855
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11855
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520CD8%252b%2520T%2520Cells%252c%2520donor1.CNhs13511.11855-125A1.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520CD8%252b%2520T%2520Cells%252c%2520donor1.CNhs13511.11855-125A1.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520CD8%252b%2520T%2520Cells%252c%2520donor1.CNhs13511.11855-125A1.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520CD8%252b%2520T%2520Cells%252c%2520donor1.CNhs13511.11855-125A1.mm10.nobarcode.ctss.bed.gz

Revision as of 17:15, 4 August 2017


Name:Mouse CD8+ T Cells, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13511
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespleen
dev stageNA
sexNA
ageNA
cell typet cell, CD8+
cell lineNA
companyNA
collaborationKawamoto (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004722
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13511 CAGE DRX008815 DRR009687
Accession ID Mm9

Library idBAMCTSS
CNhs13511 DRZ001112 DRZ002497
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

CNhs13511

00
10
100
1000
1000-0.0355
1001-0.0299
1002-0.116
1003-0.156
10040
10050
1006-0.163
1007-0.036
10080
1009-0.19
1010.238
10100
10110.126
10120.126
1013-0.0562
1014-0.0874
1015-0.0796
1016-0.594
10170
10180
10190
1020.64
10200
10210.021
1022-0.275
10230.126
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.051
103-0.0887
10300
1031-1.034
1032-0.655
10330.459
10340
10350
10360.424
10370
1038-0.172
1039-0.309
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



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: CNhs13511

Jaspar motifP-value
MA0002.24.08878e-5
MA0003.10.245
MA0004.10.0544
MA0006.10.483
MA0007.10.379
MA0009.10.722
MA0014.10.504
MA0017.10.619
MA0018.21.35058e-6
MA0019.10.774
MA0024.10.951
MA0025.10.217
MA0027.10.973
MA0028.13.39625e-5
MA0029.10.206
MA0030.10.0744
MA0031.10.00127
MA0035.20.829
MA0038.10.00198
MA0039.20.131
MA0040.10.269
MA0041.10.0977
MA0042.10.383
MA0043.10.0237
MA0046.12.42124e-11
MA0047.20.115
MA0048.10.418
MA0050.13.15153e-9
MA0051.13.54723e-6
MA0052.10.00527
MA0055.10.294
MA0057.10.945
MA0058.10.0287
MA0059.10.0215
MA0060.10.00925
MA0061.12.66576e-6
MA0062.23.29484e-19
MA0065.20.708
MA0066.10.15
MA0067.10.0114
MA0068.10.196
MA0069.10.884
MA0070.10.706
MA0071.10.972
MA0072.10.0614
MA0073.10.956
MA0074.10.579
MA0076.12.24672e-6
MA0077.10.122
MA0078.10.82
MA0079.20.0503
MA0080.25.55285e-14
MA0081.10.00336
MA0083.10.121
MA0084.10.962
MA0087.10.878
MA0088.10.609
MA0090.10.0221
MA0091.10.869
MA0092.10.762
MA0093.10.0628
MA0099.20.938
MA0100.10.124
MA0101.11.3603e-6
MA0102.20.799
MA0103.10.179
MA0104.20.0483
MA0105.13.23462e-6
MA0106.10.528
MA0107.18.26197e-7
MA0108.20.00275
MA0111.10.433
MA0112.20.385
MA0113.10.399
MA0114.10.0497
MA0115.10.312
MA0116.10.114
MA0117.10.107
MA0119.10.187
MA0122.10.416
MA0124.10.495
MA0125.10.131
MA0131.10.389
MA0135.10.827
MA0136.11.07412e-26
MA0137.20.0159
MA0138.27.32612e-4
MA0139.10.882
MA0140.10.857
MA0141.10.535
MA0142.10.0875
MA0143.10.429
MA0144.10.119
MA0145.10.0981
MA0146.10.557
MA0147.10.0199
MA0148.10.167
MA0149.10.127
MA0150.10.595
MA0152.10.542
MA0153.14.10783e-6
MA0154.10.608
MA0155.10.372
MA0156.11.56024e-28
MA0157.10.00148
MA0159.10.36
MA0160.10.996
MA0162.10.73
MA0163.10.0107
MA0164.10.346
MA0258.10.0955
MA0259.10.188



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: CNhs13511

Novel motifP-value
10.465
100.0326
1000.498
1010.969
1020.431
1030.552
1040.932
1050.696
1060.715
1070.323
1080.852
1090.506
110.47
1100.138
1110.205
1120.113
1130.34
1140.382
1150.826
1160.637
1172.10715e-4
1180.0875
1190.568
120.361
1200.137
1210.313
1220.956
1230.558
1240.757
1250.568
1260.464
1270.87
1280.42
1290.377
130.106
1300.867
1310.357
1320.997
1330.673
1340.853
1350.817
1360.473
1370.25
1380.385
1390.437
140.512
1400.309
1410.23
1420.246
1435.31175e-4
1440.429
1450.137
1460.918
1470.572
1480.243
1490.26
150.113
1500.55
1510.353
1520.375
1530.353
1540.182
1550.1
1560.187
1570.621
1580.00902
1590.732
1600.401
1610.105
1620.186
1630.549
1640.0336
1650.928
1660.358
1670.089
1680.548
1690.887
170.895
180.29
190.131
20.0258
200.0136
210.0509
220.722
230.792
240.413
250.168
260.292
270.74
280.258
290.0349
30.477
300.104
310.643
320.11
330.112
340.38
350.0317
360.068
370.189
380.7
390.463
40.772
400.413
410.203
420.293
430.644
440.37
450.3
460.56
470.819
480.487
490.211
50.158
500.448
510.75
520.172
530.679
540.623
550.923
560.936
570.807
580.301
590.558
60.793
600.885
610.149
620.0875
630.942
640.864
650.58
660.314
670.851
680.537
690.97
70.493
700.0275
710.11
720.736
730.252
740.807
750.00989
760.0207
770.0475
780.0337
790.829
80.548
800.191
810.905
820.224
830.15
840.944
850.864
860.118
870.808
880.386
890.74
90.939
900.0443
910.81
920.506
930.0418
940.491
950.279
960.34
970.488
980.523
990.0243



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: CNhs13511


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)
0000625 (CD8-positive, alpha-beta T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000030 (CD8-positive T cell 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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