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FF:11813-124E4

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Name:CD4+CD25-CD44- naive conventional T cells, pool1 (C57BL_6J)
Species:Mouse (Mus musculus)
Library ID:CNhs13217
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
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 numberB6nT
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005225
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13217 CAGE DRX008795 DRR009667
Accession ID Mm9

Library idBAMCTSS
CNhs13217 DRZ001092 DRZ002477
Accession ID Mm10

Library idBAMCTSS
CNhs13217 DRZ012442 DRZ013827
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data

CNhs13217

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.00116
1001 -0.0287
1002 -0.116
1003 -0.141
1004 0
1005 0.0686
1006 -0.143
1007 -0.181
1008 0
1009 -0.19
101 0.205
1010 0
1011 0.0686
1012 0
1013 -0.101
1014 -0.0874
1015 -0.123
1016 -0.594
1017 0
1018 0
1019 0
102 0.694
1020 0.148
1021 0.0649
1022 -0.124
1023 0
1024 -0.307
1025 0
1026 0
1027 -0.048
1028 0
1029 -0.115
103 -0.0887
1030 0
1031 -1.148
1032 -0.683
1033 0.405
1034 0
1035 0
1036 0.416
1037 0
1038 -0.154
1039 -0.184
104 0
1040 -0.216
1041 0



Repeat families with enriched expression in this sample
Summary:Ranked list of repeat family expression in this sample relative to

the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA



link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs
Summary:Association of JASPAR motif to the promoter expression in this

sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon



link to dataset.
data

library id: CNhs13217
Jaspar motif P-value
MA0002.2 2.27047e-5
MA0003.1 0.262
MA0004.1 0.0589
MA0006.1 0.442
MA0007.1 0.245
MA0009.1 0.672
MA0014.1 0.725
MA0017.1 0.878
MA0018.2 0.00117
MA0019.1 0.613
MA0024.1 0.684
MA0025.1 0.589
MA0027.1 0.918
MA0028.1 4.67099e-8
MA0029.1 0.0807
MA0030.1 0.3
MA0031.1 0.0053
MA0035.2 0.888
MA0038.1 0.00614
MA0039.2 0.342
MA0040.1 0.32
MA0041.1 0.0673
MA0042.1 0.503
MA0043.1 0.0498
MA0046.1 3.63424e-10
MA0047.2 0.139
MA0048.1 0.334
MA0050.1 4.43777e-10
MA0051.1 2.78516e-7
MA0052.1 0.00911
MA0055.1 0.134
MA0057.1 0.889
MA0058.1 0.0481
MA0059.1 0.0244
MA0060.1 5.23444e-4
MA0061.1 8.67915e-5
MA0062.2 1.01941e-23
MA0065.2 0.858
MA0066.1 0.134
MA0067.1 0.0779
MA0068.1 0.0251
MA0069.1 0.962
MA0070.1 0.914
MA0071.1 0.941
MA0072.1 0.0916
MA0073.1 0.803
MA0074.1 0.408
MA0076.1 3.52052e-11
MA0077.1 0.102
MA0078.1 0.56
MA0079.2 0.0551
MA0080.2 5.54865e-14
MA0081.1 0.00305
MA0083.1 0.176
MA0084.1 0.798
MA0087.1 0.913
MA0088.1 0.68
MA0090.1 0.0886
MA0091.1 0.642
MA0092.1 0.727
MA0093.1 0.076
MA0099.2 0.46
MA0100.1 0.166
MA0101.1 1.3357e-5
MA0102.2 0.781
MA0103.1 0.159
MA0104.2 0.0433
MA0105.1 2.28159e-6
MA0106.1 0.948
MA0107.1 4.49873e-5
MA0108.2 2.48672e-5
MA0111.1 0.208
MA0112.2 0.0977
MA0113.1 0.31
MA0114.1 0.345
MA0115.1 0.56
MA0116.1 0.0283
MA0117.1 0.446
MA0119.1 0.507
MA0122.1 0.411
MA0124.1 0.455
MA0125.1 0.121
MA0131.1 0.385
MA0135.1 0.925
MA0136.1 9.63199e-28
MA0137.2 2.24288e-4
MA0138.2 0.00614
MA0139.1 0.3
MA0140.1 0.569
MA0141.1 0.985
MA0142.1 0.2
MA0143.1 0.577
MA0144.1 0.0231
MA0145.1 0.215
MA0146.1 0.744
MA0147.1 0.0215
MA0148.1 0.173
MA0149.1 0.11
MA0150.1 0.784
MA0152.1 0.904
MA0153.1 1.38088e-5
MA0154.1 0.359
MA0155.1 0.483
MA0156.1 1.12574e-31
MA0157.1 0.00374
MA0159.1 0.164
MA0160.1 0.938
MA0162.1 0.833
MA0163.1 0.0101
MA0164.1 0.301
MA0258.1 0.0624
MA0259.1 0.13



FANTOM5 phase1 novel unique motifs
Summary: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 in

169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon



link to dataset.
data

library id: CNhs13217
Novel motif P-value
1 0.248
10 0.0278
100 0.596
101 0.868
102 0.512
103 0.277
104 0.929
105 0.887
106 0.98
107 0.413
108 0.426
109 0.215
11 0.256
110 0.0484
111 0.103
112 0.11
113 0.398
114 0.117
115 0.724
116 0.668
117 4.83597e-4
118 0.206
119 0.688
12 0.232
120 0.0779
121 0.489
122 0.925
123 0.375
124 0.342
125 0.252
126 0.396
127 0.69
128 0.724
129 0.277
13 0.0573
130 0.841
131 0.446
132 0.899
133 0.834
134 0.489
135 0.803
136 0.344
137 0.334
138 0.383
139 0.313
14 0.669
140 0.228
141 0.171
142 0.266
143 2.16595e-4
144 0.495
145 0.0841
146 0.908
147 0.388
148 0.3
149 0.377
15 0.0762
150 0.724
151 0.194
152 0.239
153 0.256
154 0.189
155 0.143
156 0.465
157 0.941
158 0.0581
159 0.605
160 0.439
161 0.08
162 0.397
163 0.706
164 0.0278
165 0.611
166 0.56
167 0.0811
168 0.68
169 0.731
17 0.677
18 0.29
19 0.164
2 0.0434
20 0.0156
21 0.0849
22 0.703
23 0.72
24 0.316
25 0.121
26 0.308
27 0.878
28 0.28
29 0.024
3 0.233
30 0.107
31 0.694
32 0.236
33 0.0803
34 0.404
35 0.0489
36 0.0415
37 0.151
38 0.517
39 0.436
4 0.937
40 0.447
41 0.299
42 0.219
43 0.516
44 0.692
45 0.435
46 0.404
47 0.521
48 0.286
49 0.2
5 0.0394
50 0.563
51 0.82
52 0.0625
53 0.727
54 0.663
55 0.546
56 0.872
57 0.567
58 0.262
59 0.639
6 0.578
60 0.943
61 0.151
62 0.0642
63 0.76
64 0.863
65 0.472
66 0.239
67 0.624
68 0.996
69 0.853
7 0.384
70 0.00883
71 0.089
72 0.567
73 0.239
74 0.83
75 0.00524
76 0.0124
77 0.101
78 0.119
79 0.691
8 0.475
80 0.147
81 0.902
82 0.163
83 0.0439
84 0.591
85 0.939
86 0.188
87 0.925
88 0.434
89 0.767
9 0.958
90 0.0368
91 0.937
92 0.469
93 0.174
94 0.292
95 0.139
96 0.233
97 0.556
98 0.428
99 0.117



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs13217


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)
Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji



link to source data

data

CL: Cell type
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)
0011450 (CD4-positiveCD25-CD44- naive conventional T cells- (C57BL_6J) sample)

Ancestor terms (development)
Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship

Analyst: Hideya Kawaji

link to source data

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)