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FF:12972-138H2

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Name:EBF KO HPCs induced to T cell
Species:Mouse (Mus musculus)
Library ID:CNhs11058
Sample type:time courses
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationTomokatsu Ikawa (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005018
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11058 CAGE DRX008899 DRR009771
Accession ID Mm9

Library idBAMCTSS
CNhs11058 DRZ001196 DRZ002581
Accession ID Mm10

Library idBAMCTSS
CNhs11058 DRZ012546 DRZ013931
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.
Analyst:NA

link to dataset.
data

CNhs11058

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 --0.129
1004 0
1005 0
1006 --0.143
1007 --0.0529
1008 0
1009 --0.171
101 0.166
1010 0
1011 0.00572
1012 0
1013 0.0747
1014 --0.0874
1015 0.0462
1016 --0.344
1017 0
1018 0
1019 0
102 0.0411
1020 0.0411
1021 0.0672
1022 --0.263
1023 0.113
1024 0.139
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.142
103 --0.0796
1030 0
1031 --0.973
1032 --0.387
1033 0.113
1034 0
1035 0
1036 0.278
1037 0
1038 --0.377
1039 --0.169
104 0
1040 --0.175
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



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: CNhs11058

Jaspar motif P-value
MA0002.2 1.79247e-8
MA0003.1 0.573
MA0004.1 0.0417
MA0006.1 0.972
MA0007.1 0.356
MA0009.1 0.767
MA0014.1 0.545
MA0017.1 0.538
MA0018.2 0.951
MA0019.1 0.893
MA0024.1 5.31246e-4
MA0025.1 0.296
MA0027.1 0.98
MA0028.1 4.02835e-7
MA0029.1 0.425
MA0030.1 0.0424
MA0031.1 0.865
MA0035.2 0.571
MA0038.1 0.0314
MA0039.2 0.501
MA0040.1 0.654
MA0041.1 0.0336
MA0042.1 0.25
MA0043.1 0.917
MA0046.1 7.73929e-14
MA0047.2 0.448
MA0048.1 0.134
MA0050.1 3.64008e-6
MA0051.1 0.00583
MA0052.1 0.404
MA0055.1 0.0828
MA0057.1 0.934
MA0058.1 0.0087
MA0059.1 1.91928e-4
MA0060.1 0.774
MA0061.1 0.0295
MA0062.2 5.37088e-16
MA0065.2 0.116
MA0066.1 0.0477
MA0067.1 0.621
MA0068.1 0.083
MA0069.1 0.687
MA0070.1 0.767
MA0071.1 0.41
MA0072.1 0.906
MA0073.1 0.933
MA0074.1 0.0977
MA0076.1 7.86076e-9
MA0077.1 0.374
MA0078.1 0.706
MA0079.2 0.0385
MA0080.2 1.83773e-12
MA0081.1 5.85268e-4
MA0083.1 1.48896e-4
MA0084.1 0.458
MA0087.1 0.917
MA0088.1 0.0476
MA0090.1 0.0239
MA0091.1 0.075
MA0092.1 0.352
MA0093.1 0.0343
MA0099.2 0.922
MA0100.1 0.00108
MA0101.1 0.0127
MA0102.2 0.834
MA0103.1 0.47
MA0104.2 0.00603
MA0105.1 1.06413e-4
MA0106.1 0.0946
MA0107.1 0.0577
MA0108.2 1.82599e-6
MA0111.1 0.498
MA0112.2 0.00677
MA0113.1 0.375
MA0114.1 0.768
MA0115.1 0.652
MA0116.1 6.10863e-4
MA0117.1 0.956
MA0119.1 0.879
MA0122.1 0.597
MA0124.1 0.577
MA0125.1 0.0856
MA0131.1 0.257
MA0135.1 0.0438
MA0136.1 7.84112e-27
MA0137.2 1.45639e-4
MA0138.2 7.02612e-4
MA0139.1 0.236
MA0140.1 0.186
MA0141.1 0.389
MA0142.1 0.513
MA0143.1 0.304
MA0144.1 0.073
MA0145.1 0.719
MA0146.1 0.0716
MA0147.1 0.0024
MA0148.1 0.449
MA0149.1 0.099
MA0150.1 0.283
MA0152.1 0.995
MA0153.1 1.35916e-6
MA0154.1 0.108
MA0155.1 0.995
MA0156.1 1.71039e-23
MA0157.1 0.988
MA0159.1 0.0236
MA0160.1 0.389
MA0162.1 0.258
MA0163.1 2.43779e-6
MA0164.1 0.822
MA0258.1 0.013
MA0259.1 0.327



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: CNhs11058

Novel motif P-value
1 0.246
10 0.0269
100 0.824
101 0.899
102 0.231
103 0.16
104 0.731
105 0.713
106 0.667
107 0.432
108 0.334
109 0.0912
11 0.0662
110 0.0573
111 0.0207
112 0.079
113 0.673
114 0.752
115 0.905
116 0.942
117 1.51689e-4
118 0.0574
119 0.67
12 0.574
120 0.374
121 0.131
122 0.667
123 0.57
124 0.802
125 0.303
126 0.242
127 0.581
128 0.273
129 0.416
13 0.0126
130 0.518
131 0.911
132 0.507
133 0.756
134 0.314
135 0.644
136 0.522
137 0.0605
138 0.616
139 0.297
14 0.589
140 0.837
141 0.913
142 0.498
143 0.0781
144 0.733
145 0.0391
146 0.696
147 0.531
148 0.208
149 0.489
15 0.00918
150 0.338
151 0.398
152 0.826
153 0.825
154 0.6
155 0.242
156 0.0542
157 0.659
158 0.301
159 0.359
160 0.818
161 0.115
162 0.331
163 0.329
164 0.0127
165 0.661
166 0.513
167 0.385
168 0.418
169 0.0214
17 0.816
18 0.277
19 0.776
2 0.0854
20 0.042
21 0.162
22 0.684
23 0.53
24 0.0686
25 0.155
26 0.0134
27 0.947
28 0.536
29 0.01
3 0.0439
30 0.134
31 0.721
32 0.815
33 0.34
34 0.729
35 0.155
36 0.0345
37 0.0676
38 0.346
39 0.552
4 0.805
40 0.184
41 0.209
42 0.168
43 0.411
44 0.152
45 0.597
46 0.235
47 0.228
48 0.114
49 0.195
5 0.104
50 0.638
51 0.93
52 0.349
53 0.457
54 0.637
55 0.267
56 0.792
57 0.218
58 0.213
59 0.803
6 0.417
60 0.718
61 0.107
62 0.102
63 0.67
64 0.423
65 0.511
66 0.744
67 0.809
68 0.87
69 0.548
7 0.217
70 0.0179
71 0.00885
72 0.427
73 0.0915
74 0.56
75 0.0058
76 0.0831
77 0.398
78 0.0807
79 0.832
8 0.0385
80 0.191
81 0.951
82 0.825
83 0.213
84 0.416
85 0.716
86 0.0533
87 0.167
88 0.401
89 0.606
9 0.917
90 0.0103
91 0.918
92 0.928
93 0.91
94 0.161
95 0.0285
96 0.173
97 0.555
98 0.496
99 0.329



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: CNhs11058


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)
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)
0000084 (T cell)
0000837 (hematopoietic multipotent progenitor cell)

FF: FANTOM5
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000357 (0 hr sample)
0000342 (T-cell induction sample)
0000729 (mouse EBF KO HPCs induced to T cell 0h 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)