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FF:11816-124E7

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Name:CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool1 (C57BL_6J)
Species:Mouse (Mus musculus)
Library ID:CNhs13219
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 numberB6TsPI-2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005993
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13219 CAGE DRX008791 DRR009663
Accession ID Mm9

Library idBAMCTSS
CNhs13219 DRZ001088 DRZ002473
Accession ID Mm10

Library idBAMCTSS
CNhs13219 DRZ012438 DRZ013823
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

CNhs13219

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0355
1001 -0.0631
1002 -0.116
1003 -0.15
1004 0
1005 -0.0747
1006 -0.436
1007 -0.223
1008 0
1009 -0.19
101 0.676
1010 0
1011 0.153
1012 0.00667
1013 -0.323
1014 -0.0279
1015 0.167
1016 -0.594
1017 0
1018 0.0572
1019 0
102 0.906
1020 0.108
1021 0.266
1022 -0.281
1023 0.153
1024 -0.14
1025 -0.0611
1026 0
1027 -0.048
1028 0
1029 -0.111
103 -0.0887
1030 0
1031 -1.09
1032 -0.655
1033 0.949
1034 0
1035 0
1036 0.618
1037 0
1038 -0.162
1039 -0.441
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: CNhs13219
Jaspar motif P-value
MA0002.2 0.0167
MA0003.1 0.103
MA0004.1 0.018
MA0006.1 0.154
MA0007.1 0.568
MA0009.1 0.555
MA0014.1 0.867
MA0017.1 0.19
MA0018.2 2.45043e-9
MA0019.1 0.825
MA0024.1 0.943
MA0025.1 0.297
MA0027.1 0.487
MA0028.1 0.00133
MA0029.1 0.765
MA0030.1 0.961
MA0031.1 0.28
MA0035.2 0.601
MA0038.1 0.0152
MA0039.2 0.106
MA0040.1 0.862
MA0041.1 0.0164
MA0042.1 0.176
MA0043.1 7.94709e-4
MA0046.1 1.01137e-11
MA0047.2 0.771
MA0048.1 0.192
MA0050.1 2.12062e-5
MA0051.1 0.00243
MA0052.1 0.953
MA0055.1 0.0937
MA0057.1 0.921
MA0058.1 0.00447
MA0059.1 1.28302e-4
MA0060.1 0.00203
MA0061.1 7.00791e-11
MA0062.2 1.51164e-11
MA0065.2 0.427
MA0066.1 0.582
MA0067.1 5.32808e-4
MA0068.1 5.19127e-5
MA0069.1 0.424
MA0070.1 0.845
MA0071.1 0.603
MA0072.1 0.0893
MA0073.1 0.515
MA0074.1 0.558
MA0076.1 0.00126
MA0077.1 0.543
MA0078.1 0.518
MA0079.2 0.263
MA0080.2 6.67227e-10
MA0081.1 0.0017
MA0083.1 0.873
MA0084.1 0.468
MA0087.1 0.873
MA0088.1 0.175
MA0090.1 0.0329
MA0091.1 0.766
MA0092.1 0.111
MA0093.1 0.0187
MA0099.2 1.79377e-6
MA0100.1 0.298
MA0101.1 5.73466e-16
MA0102.2 0.583
MA0103.1 0.644
MA0104.2 1.06591e-4
MA0105.1 1.43349e-6
MA0106.1 0.658
MA0107.1 5.90608e-16
MA0108.2 0.601
MA0111.1 0.449
MA0112.2 0.609
MA0113.1 0.885
MA0114.1 0.00737
MA0115.1 0.175
MA0116.1 0.937
MA0117.1 0.0252
MA0119.1 0.0407
MA0122.1 0.539
MA0124.1 0.954
MA0125.1 0.0857
MA0131.1 0.372
MA0135.1 0.765
MA0136.1 2.503e-18
MA0137.2 0.00456
MA0138.2 4.47061e-4
MA0139.1 0.267
MA0140.1 0.857
MA0141.1 0.705
MA0142.1 0.579
MA0143.1 0.156
MA0144.1 0.199
MA0145.1 0.028
MA0146.1 0.913
MA0147.1 6.24597e-6
MA0148.1 0.595
MA0149.1 0.227
MA0150.1 0.0344
MA0152.1 0.0561
MA0153.1 2.30202e-6
MA0154.1 0.862
MA0155.1 0.295
MA0156.1 2.29709e-15
MA0157.1 0.182
MA0159.1 0.854
MA0160.1 0.945
MA0162.1 0.0203
MA0163.1 0.531
MA0164.1 0.0365
MA0258.1 0.567
MA0259.1 0.0168



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: CNhs13219
Novel motif P-value
1 0.851
10 0.194
100 0.472
101 0.474
102 0.377
103 0.289
104 0.64
105 0.455
106 0.196
107 0.892
108 0.683
109 0.873
11 0.637
110 0.355
111 0.141
112 0.277
113 0.824
114 0.858
115 0.735
116 0.536
117 3.10959e-4
118 0.468
119 0.878
12 0.396
120 0.137
121 0.308
122 0.78
123 0.544
124 0.259
125 0.514
126 0.416
127 0.488
128 0.115
129 0.64
13 0.109
130 0.647
131 0.242
132 0.469
133 0.125
134 0.448
135 0.173
136 0.761
137 0.776
138 0.953
139 0.189
14 0.084
140 0.413
141 0.967
142 0.486
143 0.0152
144 0.425
145 0.173
146 0.832
147 0.596
148 0.138
149 0.13
15 0.457
150 0.836
151 0.966
152 0.544
153 0.456
154 0.143
155 0.291
156 0.698
157 0.885
158 0.0151
159 0.535
160 0.171
161 0.237
162 0.117
163 0.749
164 0.0464
165 0.546
166 0.199
167 0.0674
168 0.557
169 0.277
17 0.856
18 0.252
19 0.0213
2 0.00797
20 0.00313
21 0.203
22 0.402
23 0.758
24 0.529
25 0.362
26 0.403
27 0.109
28 0.505
29 0.183
3 0.922
30 0.0986
31 0.479
32 0.0892
33 0.214
34 0.255
35 0.263
36 0.147
37 0.321
38 0.635
39 0.626
4 0.808
40 0.984
41 0.164
42 0.728
43 0.811
44 0.72
45 0.296
46 0.793
47 0.714
48 0.742
49 0.519
5 0.293
50 0.63
51 0.778
52 0.497
53 0.638
54 0.736
55 0.982
56 0.708
57 0.807
58 0.645
59 0.421
6 0.875
60 0.52
61 0.188
62 0.253
63 0.706
64 0.651
65 0.859
66 0.727
67 0.705
68 0.196
69 0.591
7 0.695
70 0.0152
71 0.174
72 0.806
73 0.432
74 0.735
75 0.0231
76 0.0247
77 0.0235
78 0.0322
79 0.858
8 0.856
80 0.42
81 0.827
82 0.9
83 0.169
84 0.242
85 0.513
86 0.17
87 0.604
88 0.552
89 0.433
9 0.842
90 0.376
91 0.616
92 0.515
93 0.146
94 0.422
95 0.534
96 0.426
97 0.556
98 0.758
99 0.0348



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: CNhs13219


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)
0000350 (experimentally modified sample)
0000359 (2 hr sample)
0000409 (T cell expansion sample)
0011448 (CD4-positiveCD25-CD44- naive conventional T cells stimulated with PMA an ionomycin- 02hr- (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)