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FF:11854-124I9

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Name:Mouse CD4+ T Cells, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespleen
dev stageNA
sexNA
ageNA
cell typet cell, CD4+
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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.
Analyst:NA

link to dataset.
data

CNhs13509

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0749
1002 --0.116
1003 --0.123
1004 0
1005 0.116
1006 --0.148
1007 0.032
1008 0
1009 --0.19
101 0.139
1010 0
1011 0.129
1012 0.186
1013 --0.188
1014 --0.0874
1015 --0.0376
1016 --0.594
1017 0
1018 0
1019 0
102 0.729
1020 0
1021 0
1022 --0.315
1023 0
1024 --0.0899
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 -1.148
1032 --0.655
1033 0.427
1034 0
1035 0
1036 0.433
1037 0
1038 0.0211
1039 --0.223
104 0
1040 --0.216
1041 0



Repeat families with enriched expression in this sampleSummary: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
no result for this sample


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


JASPAR motifsSummary: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: CNhs13509

Jaspar motif P-value
MA0002.2 3.97871e-5
MA0003.1 0.264
MA0004.1 0.0952
MA0006.1 0.434
MA0007.1 0.648
MA0009.1 0.71
MA0014.1 0.793
MA0017.1 0.357
MA0018.2 4.81796e-8
MA0019.1 0.79
MA0024.1 0.774
MA0025.1 0.644
MA0027.1 0.808
MA0028.1 2.303e-4
MA0029.1 0.506
MA0030.1 0.122
MA0031.1 2.07317e-4
MA0035.2 0.809
MA0038.1 7.6594e-4
MA0039.2 0.191
MA0040.1 0.164
MA0041.1 0.387
MA0042.1 0.511
MA0043.1 0.0193
MA0046.1 9.60373e-11
MA0047.2 0.0705
MA0048.1 0.504
MA0050.1 3.66975e-8
MA0051.1 1.93679e-5
MA0052.1 0.0857
MA0055.1 0.411
MA0057.1 0.911
MA0058.1 0.0525
MA0059.1 0.0967
MA0060.1 0.00865
MA0061.1 1.79873e-6
MA0062.2 1.82661e-18
MA0065.2 0.487
MA0066.1 0.21
MA0067.1 0.00178
MA0068.1 0.0105
MA0069.1 0.862
MA0070.1 0.87
MA0071.1 0.667
MA0072.1 0.0321
MA0073.1 0.772
MA0074.1 0.659
MA0076.1 1.01233e-5
MA0077.1 0.224
MA0078.1 0.541
MA0079.2 0.0862
MA0080.2 1.16003e-13
MA0081.1 0.00354
MA0083.1 0.245
MA0084.1 0.823
MA0087.1 0.871
MA0088.1 0.536
MA0090.1 0.0235
MA0091.1 0.987
MA0092.1 0.59
MA0093.1 0.118
MA0099.2 0.692
MA0100.1 0.111
MA0101.1 4.06577e-8
MA0102.2 0.863
MA0103.1 0.106
MA0104.2 0.123
MA0105.1 3.5427e-5
MA0106.1 0.821
MA0107.1 7.94176e-8
MA0108.2 0.0245
MA0111.1 0.354
MA0112.2 0.81
MA0113.1 0.587
MA0114.1 0.0194
MA0115.1 0.358
MA0116.1 0.481
MA0117.1 0.104
MA0119.1 0.11
MA0122.1 0.414
MA0124.1 0.516
MA0125.1 0.12
MA0131.1 0.537
MA0135.1 0.832
MA0136.1 7.22525e-25
MA0137.2 0.013
MA0138.2 0.00272
MA0139.1 0.567
MA0140.1 0.508
MA0141.1 0.488
MA0142.1 0.259
MA0143.1 0.35
MA0144.1 0.0904
MA0145.1 0.127
MA0146.1 0.549
MA0147.1 0.0656
MA0148.1 0.18
MA0149.1 0.0738
MA0150.1 0.669
MA0152.1 0.628
MA0153.1 2.54423e-6
MA0154.1 0.785
MA0155.1 0.351
MA0156.1 7.58134e-25
MA0157.1 4.2973e-4
MA0159.1 0.467
MA0160.1 0.913
MA0162.1 0.365
MA0163.1 0.162
MA0164.1 0.31
MA0258.1 0.182
MA0259.1 0.211



FANTOM5 phase1 novel unique motifsSummary: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: CNhs13509

Novel motif P-value
1 0.467
10 0.0592
100 0.526
101 0.995
102 0.475
103 0.486
104 0.998
105 0.569
106 0.559
107 0.487
108 0.754
109 0.504
11 0.415
110 0.292
111 0.328
112 0.177
113 0.444
114 0.3
115 0.608
116 0.57
117 2.97036e-4
118 0.211
119 0.656
12 0.239
120 0.0611
121 0.337
122 0.97
123 0.66
124 0.465
125 0.561
126 0.456
127 0.784
128 0.246
129 0.332
13 0.143
130 0.71
131 0.267
132 0.828
133 0.55
134 0.592
135 0.878
136 0.546
137 0.336
138 0.267
139 0.321
14 0.603
140 0.528
141 0.324
142 0.263
143 2.52455e-4
144 0.507
145 0.199
146 0.784
147 0.469
148 0.178
149 0.176
15 0.185
150 0.881
151 0.288
152 0.379
153 0.47
154 0.166
155 0.0504
156 0.0661
157 0.833
158 0.0143
159 0.805
160 0.354
161 0.185
162 0.277
163 0.32
164 0.0919
165 0.819
166 0.487
167 0.0943
168 0.337
169 0.625
17 0.855
18 0.224
19 0.0776
2 0.018
20 0.0211
21 0.0869
22 0.615
23 0.995
24 0.552
25 0.198
26 0.363
27 0.658
28 0.384
29 0.0651
3 0.522
30 0.119
31 0.597
32 0.146
33 0.0987
34 0.353
35 0.0339
36 0.0899
37 0.232
38 0.618
39 0.365
4 0.7
40 0.504
41 0.149
42 0.281
43 0.713
44 0.683
45 0.27
46 0.506
47 0.862
48 0.431
49 0.207
5 0.119
50 0.469
51 0.69
52 0.184
53 0.607
54 0.639
55 0.896
56 0.993
57 0.688
58 0.321
59 0.565
6 0.661
60 0.854
61 0.209
62 0.0923
63 0.995
64 0.993
65 0.407
66 0.451
67 0.698
68 0.439
69 0.737
7 0.555
70 0.0234
71 0.192
72 0.954
73 0.322
74 0.713
75 0.00795
76 0.0271
77 0.0257
78 0.0404
79 0.954
8 0.71
80 0.163
81 0.992
82 0.495
83 0.0946
84 0.925
85 0.847
86 0.158
87 0.542
88 0.37
89 0.664
9 0.923
90 0.102
91 0.718
92 0.643
93 0.111
94 0.282
95 0.367
96 0.41
97 0.459
98 0.467
99 0.0285



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs13509


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), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000624 (CD4-positive, alpha-beta T cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000789 (alpha-beta T cell)
0000790 (immature alpha-beta T cell)
0000791 (mature alpha-beta T cell)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002419 (mature T cell)
0002420 (immature T cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

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

link to source data
data

NA