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FF:12460-132E3

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Name:ST2 (Mesenchymal stem cells) cells, medium change (without induction)
Species:Mouse (Mus musculus)
Library ID:CNhs13275
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
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineST2
companyNA
collaborationYasushi Okazaki (Saitama medical college)
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  SAMD00005712
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13275 CAGE DRX008906 DRR009780
Accession ID Mm9

Library idBAMCTSS
CNhs13275 DRZ001205 DRZ002588
Accession ID Mm10

Library idBAMCTSS
CNhs13275 DRZ012555 DRZ013938
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs13275

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.236
1001 -0.0631
1002 -0.0655
1003 0.173
1004 0
1005 0
1006 -0.142
1007 -0.0401
1008 0
1009 0.653
101 -0.024
1010 0
1011 -0.237
1012 0
1013 0.0697
1014 -0.0851
1015 0.171
1016 0.113
1017 0
1018 0
1019 0
102 0
1020 0.1
1021 0.182
1022 -0.124
1023 0
1024 -0.307
1025 0
1026 0
1027 -0.048
1028 0.1
1029 -0.176
103 0.45
1030 0
1031 -0.446
1032 -0.167
1033 0.1
1034 0
1035 0
1036 0.179
1037 0
1038 0.0302
1039 -0.0646
104 0
1040 0.31
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: CNhs13275
Jaspar motif P-value
MA0002.2 0.187
MA0003.1 0.713
MA0004.1 0.432
MA0006.1 0.567
MA0007.1 0.698
MA0009.1 0.779
MA0014.1 0.242
MA0017.1 0.482
MA0018.2 0.1
MA0019.1 0.885
MA0024.1 0.288
MA0025.1 0.763
MA0027.1 0.35
MA0028.1 0.00164
MA0029.1 0.52
MA0030.1 0.267
MA0031.1 0.376
MA0035.2 0.00311
MA0038.1 0.737
MA0039.2 0.924
MA0040.1 0.263
MA0041.1 0.706
MA0042.1 0.236
MA0043.1 0.672
MA0046.1 6.82727e-8
MA0047.2 0.24
MA0048.1 8.77558e-4
MA0050.1 0.752
MA0051.1 0.992
MA0052.1 2.9933e-4
MA0055.1 6.42822e-5
MA0057.1 0.204
MA0058.1 0.155
MA0059.1 0.165
MA0060.1 0.0236
MA0061.1 0.264
MA0062.2 4.92563e-4
MA0065.2 0.109
MA0066.1 0.242
MA0067.1 0.997
MA0068.1 0.749
MA0069.1 0.522
MA0070.1 0.17
MA0071.1 0.55
MA0072.1 0.879
MA0073.1 0.576
MA0074.1 0.897
MA0076.1 0.00316
MA0077.1 0.521
MA0078.1 0.17
MA0079.2 0.0834
MA0080.2 0.0674
MA0081.1 0.482
MA0083.1 0.00283
MA0084.1 0.458
MA0087.1 0.75
MA0088.1 0.00398
MA0090.1 0.101
MA0091.1 0.412
MA0092.1 0.204
MA0093.1 0.431
MA0099.2 5.68978e-5
MA0100.1 0.149
MA0101.1 0.456
MA0102.2 0.401
MA0103.1 1.92649e-4
MA0104.2 0.988
MA0105.1 0.0171
MA0106.1 0.00156
MA0107.1 0.892
MA0108.2 0.0194
MA0111.1 0.335
MA0112.2 0.00476
MA0113.1 0.983
MA0114.1 0.938
MA0115.1 0.461
MA0116.1 0.0288
MA0117.1 0.556
MA0119.1 0.307
MA0122.1 0.68
MA0124.1 0.454
MA0125.1 0.00295
MA0131.1 0.576
MA0135.1 0.0307
MA0136.1 0.92
MA0137.2 0.0518
MA0138.2 0.00141
MA0139.1 0.479
MA0140.1 2.04701e-4
MA0141.1 0.166
MA0142.1 0.178
MA0143.1 0.783
MA0144.1 0.0887
MA0145.1 0.379
MA0146.1 0.0113
MA0147.1 0.88
MA0148.1 0.553
MA0149.1 0.0481
MA0150.1 0.231
MA0152.1 0.04
MA0153.1 2.50664e-5
MA0154.1 0.212
MA0155.1 0.952
MA0156.1 0.999
MA0157.1 0.774
MA0159.1 0.266
MA0160.1 0.673
MA0162.1 0.0601
MA0163.1 0.0184
MA0164.1 0.335
MA0258.1 0.232
MA0259.1 0.346



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: CNhs13275
Novel motif P-value
1 0.206
10 0.0123
100 0.63
101 0.235
102 0.188
103 0.0729
104 0.708
105 0.886
106 0.542
107 0.74
108 0.543
109 0.0248
11 0.0774
110 0.0194
111 0.501
112 0.427
113 0.118
114 0.444
115 0.689
116 0.0351
117 8.12752e-4
118 0.843
119 0.242
12 0.66
120 0.211
121 0.778
122 0.147
123 0.312
124 0.145
125 0.195
126 0.34
127 0.137
128 0.657
129 0.701
13 0.00555
130 0.779
131 0.527
132 0.35
133 0.163
134 0.516
135 0.188
136 0.563
137 0.538
138 0.81
139 0.349
14 0.503
140 0.922
141 0.797
142 0.814
143 0.0897
144 0.159
145 0.102
146 0.443
147 0.907
148 0.543
149 0.199
15 0.864
150 0.0358
151 0.973
152 0.126
153 0.921
154 0.411
155 0.206
156 4.29054e-38
157 0.823
158 0.415
159 0.124
160 0.595
161 0.376
162 0.901
163 0.598
164 0.00508
165 0.962
166 0.764
167 0.301
168 0.411
169 0.00264
17 0.15
18 0.228
19 0.316
2 0.421
20 0.0373
21 0.0336
22 0.32
23 0.129
24 0.706
25 0.868
26 0.0228
27 0.39
28 0.691
29 0.00394
3 0.0826
30 0.451
31 0.625
32 0.344
33 0.17
34 0.657
35 0.683
36 0.0261
37 0.0118
38 0.715
39 0.489
4 0.757
40 0.36
41 0.4
42 0.366
43 0.514
44 0.176
45 0.574
46 0.341
47 0.138
48 0.265
49 0.869
5 0.185
50 0.72
51 0.935
52 0.689
53 0.379
54 0.57
55 0.378
56 0.773
57 0.107
58 0.902
59 0.242
6 0.933
60 0.358
61 0.627
62 0.399
63 0.549
64 0.584
65 0.925
66 0.636
67 0.966
68 0.691
69 0.487
7 0.315
70 0.00285
71 0.00104
72 0.954
73 0.0189
74 0.735
75 0.0383
76 0.204
77 0.38
78 0.025
79 0.732
8 0.0824
80 0.0473
81 0.698
82 0.518
83 0.502
84 0.927
85 0.653
86 0.572
87 0.0823
88 0.711
89 0.783
9 0.959
90 0.0226
91 0.337
92 0.678
93 0.205
94 0.835
95 0.0439
96 0.415
97 0.661
98 0.402
99 0.748



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: CNhs13275


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)

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

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000404 (mouse mesenchymal stem cell line: ST2 sample)
0000333 (medium change sample)
0000357 (0 hr sample)
0000488 (mouse ST2 Mesenchymal stem cells, cells 0hr after medium change , without induction 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)