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|library_id=CNhs13220
|library_id=CNhs13220
|library_id_phase_based=2:CNhs13220
|library_id_phase_based=2:CNhs13220
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11817
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11817
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm10.nobarcode.ctss.bed.gz

Revision as of 21:33, 18 May 2017


Name:CD4+CD25-CD44- naive conventional T cells, pool2 (Balb_cAJcl)
Species:Mouse (Mus musculus)
Library ID:CNhs13220
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 numberBLnT
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005686
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13220 CAGE DRX008796 DRR009668
Accession ID Mm9

Library idBAMCTSS
CNhs13220 DRZ001093 DRZ002478
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

CNhs13220

00
10
100
1000
1000-0.0173
1001-0.0631
1002-0.116
1003-0.157
10040
10050
1006-0.254
1007-0.265
10080
1009-0.19
1010.185
10100
10110.0364
10120
1013-0.139
1014-0.0874
1015-0.202
1016-0.594
10170
10180
10190
1020.636
10200.0364
10210.124
1022-0.137
10230.0364
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.089
103-0.0887
10300
1031-1.111
1032-0.659
10330.515
10340
10350
10360.293
10370
1038-0.223
1039-0.229
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: CNhs13220

Jaspar motifP-value
MA0002.24.71356e-5
MA0003.10.274
MA0004.10.0488
MA0006.10.493
MA0007.10.365
MA0009.10.803
MA0014.10.736
MA0017.10.983
MA0018.25.23107e-4
MA0019.10.698
MA0024.10.676
MA0025.10.792
MA0027.10.926
MA0028.14.47163e-8
MA0029.10.256
MA0030.10.293
MA0031.10.00665
MA0035.20.728
MA0038.10.00204
MA0039.20.354
MA0040.10.294
MA0041.10.0512
MA0042.10.397
MA0043.10.0297
MA0046.12.37414e-9
MA0047.20.143
MA0048.10.293
MA0050.11.56882e-8
MA0051.11.69982e-6
MA0052.10.0142
MA0055.10.144
MA0057.10.846
MA0058.10.0316
MA0059.10.019
MA0060.13.53943e-4
MA0061.16.26951e-5
MA0062.29.73059e-24
MA0065.20.756
MA0066.10.072
MA0067.10.0923
MA0068.10.0997
MA0069.10.689
MA0070.10.684
MA0071.10.913
MA0072.10.0895
MA0073.10.904
MA0074.10.273
MA0076.11.67357e-11
MA0077.10.143
MA0078.10.574
MA0079.20.0675
MA0080.21.16197e-13
MA0081.10.00318
MA0083.10.135
MA0084.10.602
MA0087.10.878
MA0088.10.645
MA0090.10.0789
MA0091.10.752
MA0092.10.745
MA0093.10.0598
MA0099.20.441
MA0100.10.138
MA0101.13.43622e-5
MA0102.20.82
MA0103.10.135
MA0104.20.0372
MA0105.11.00043e-6
MA0106.10.867
MA0107.17.88025e-5
MA0108.23.80426e-6
MA0111.10.227
MA0112.20.125
MA0113.10.237
MA0114.10.334
MA0115.10.745
MA0116.10.0162
MA0117.10.501
MA0119.10.566
MA0122.10.522
MA0124.10.642
MA0125.10.154
MA0131.10.487
MA0135.10.834
MA0136.11.00843e-26
MA0137.21.1018e-4
MA0138.20.00606
MA0139.10.248
MA0140.10.335
MA0141.10.924
MA0142.10.346
MA0143.10.573
MA0144.10.0202
MA0145.10.265
MA0146.10.791
MA0147.10.0161
MA0148.10.126
MA0149.10.111
MA0150.10.624
MA0152.10.732
MA0153.11.26494e-5
MA0154.10.187
MA0155.10.603
MA0156.11.03144e-30
MA0157.10.00633
MA0159.10.155
MA0160.10.899
MA0162.10.977
MA0163.10.00999
MA0164.10.276
MA0258.10.0939
MA0259.10.194



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: CNhs13220

Novel motifP-value
10.267
100.0248
1000.552
1010.9
1020.483
1030.318
1040.868
1050.85
1060.976
1070.449
1080.543
1090.246
110.243
1100.0622
1110.0663
1120.0828
1130.613
1140.112
1150.666
1160.75
1173.27666e-4
1180.21
1190.812
120.22
1200.0494
1210.442
1220.77
1230.307
1240.297
1250.249
1260.299
1270.759
1280.784
1290.349
130.118
1300.738
1310.313
1320.965
1330.928
1340.698
1350.779
1360.293
1370.445
1380.393
1390.335
140.654
1400.532
1410.0804
1420.392
1431.13569e-4
1440.419
1450.148
1460.932
1470.544
1480.231
1490.301
150.0813
1500.732
1510.292
1520.232
1530.479
1540.248
1550.0908
1560.891
1570.93
1580.0511
1590.834
1600.445
1610.105
1620.601
1630.832
1640.0165
1650.873
1660.423
1670.0758
1680.631
1690.769
170.635
180.25
190.144
20.0462
200.0122
210.101
220.789
230.689
240.269
250.142
260.281
270.904
280.228
290.0193
30.26
300.125
310.737
320.231
330.0873
340.438
350.0352
360.0323
370.133
380.534
390.576
40.966
400.411
410.275
420.243
430.566
440.602
450.447
460.418
470.516
480.255
490.224
50.0338
500.591
510.792
520.0732
530.731
540.629
550.441
560.904
570.639
580.344
590.795
60.646
600.974
610.183
620.0718
630.718
640.823
650.439
660.143
670.578
680.847
690.852
70.449
700.0114
710.0955
720.482
730.26
740.686
750.00566
760.0143
770.14
780.135
790.823
80.481
800.195
810.836
820.2
830.0724
840.675
850.99
860.174
870.971
880.416
890.96
90.928
900.0674
910.863
920.468
930.194
940.3
950.0922
960.191
970.507
980.45
990.0884



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: CNhs13220


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)
0000898 (naive T cell)
0000895 (naive thymus-derived CD4-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)
0000343 (control treatment sample)
0011451 (CD4-positiveCD25-CD44- naive conventional 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)
CL:0002425 (early T lineage precursor)
CL:0002427 (resting double-positive thymocyte)

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