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FF:12582-133I8

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Name:ST2 (Mesenchymal stem cells) cells, medium change (without induction)
Species:Mouse (Mus musculus)
Library ID:CNhs13324
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  SAMD00005351
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13324 CAGE DRX008907 DRR009781
Accession ID Mm9

Library idBAMCTSS
CNhs13324 DRZ001206 DRZ002589
Accession ID Mm10

Library idBAMCTSS
CNhs13324 DRZ012556 DRZ013939
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

CNhs13324

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.131
1001 0.0161
1002 --0.116
1003 0.0794
1004 0
1005 0
1006 --0.09
1007 --0.0484
1008 0
1009 0.733
101 --0.0667
1010 0
1011 --0.166
1012 0
1013 0.0443
1014 --0.0874
1015 0.221
1016 0.0754
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.232
1022 --0.124
1023 0
1024 --0.307
1025 --0.0611
1026 0
1027 0
1028 0
1029 --0.176
103 0.442
1030 0
1031 --0.395
1032 --0.0522
1033 --0.0322
1034 0
1035 0
1036 0.131
1037 0
1038 0.0377
1039 --0.0317
104 0
1040 0.406
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: CNhs13324

Jaspar motif P-value
MA0002.2 0.114
MA0003.1 0.649
MA0004.1 0.312
MA0006.1 0.529
MA0007.1 0.476
MA0009.1 0.578
MA0014.1 0.208
MA0017.1 0.366
MA0018.2 0.166
MA0019.1 0.911
MA0024.1 0.279
MA0025.1 0.914
MA0027.1 0.176
MA0028.1 0.00629
MA0029.1 0.554
MA0030.1 0.429
MA0031.1 0.29
MA0035.2 0.0248
MA0038.1 0.9
MA0039.2 0.976
MA0040.1 0.528
MA0041.1 0.78
MA0042.1 0.518
MA0043.1 0.669
MA0046.1 4.96545e-7
MA0047.2 0.527
MA0048.1 3.55386e-4
MA0050.1 0.814
MA0051.1 0.962
MA0052.1 0.00207
MA0055.1 2.43341e-4
MA0057.1 0.166
MA0058.1 0.11
MA0059.1 0.193
MA0060.1 0.0172
MA0061.1 0.389
MA0062.2 0.0017
MA0065.2 0.103
MA0066.1 0.199
MA0067.1 0.856
MA0068.1 0.258
MA0069.1 0.605
MA0070.1 0.239
MA0071.1 0.568
MA0072.1 0.739
MA0073.1 0.645
MA0074.1 0.706
MA0076.1 0.0213
MA0077.1 0.642
MA0078.1 0.237
MA0079.2 0.195
MA0080.2 0.0467
MA0081.1 0.339
MA0083.1 0.00175
MA0084.1 0.641
MA0087.1 0.704
MA0088.1 0.00632
MA0090.1 0.0941
MA0091.1 0.456
MA0092.1 0.142
MA0093.1 0.299
MA0099.2 2.01487e-4
MA0100.1 0.079
MA0101.1 0.505
MA0102.2 0.402
MA0103.1 6.11348e-5
MA0104.2 0.947
MA0105.1 0.0484
MA0106.1 0.00511
MA0107.1 0.865
MA0108.2 0.0796
MA0111.1 0.407
MA0112.2 0.00486
MA0113.1 0.865
MA0114.1 0.923
MA0115.1 0.585
MA0116.1 0.0286
MA0117.1 0.498
MA0119.1 0.282
MA0122.1 0.782
MA0124.1 0.562
MA0125.1 0.00334
MA0131.1 0.429
MA0135.1 0.0593
MA0136.1 0.649
MA0137.2 0.114
MA0138.2 9.49313e-4
MA0139.1 0.796
MA0140.1 0.00154
MA0141.1 0.142
MA0142.1 0.106
MA0143.1 0.79
MA0144.1 0.107
MA0145.1 0.423
MA0146.1 0.00247
MA0147.1 0.88
MA0148.1 0.729
MA0149.1 0.0686
MA0150.1 0.195
MA0152.1 0.0544
MA0153.1 8.5661e-5
MA0154.1 0.155
MA0155.1 0.935
MA0156.1 0.557
MA0157.1 0.775
MA0159.1 0.32
MA0160.1 0.558
MA0162.1 0.0538
MA0163.1 0.0433
MA0164.1 0.626
MA0258.1 0.177
MA0259.1 0.264



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: CNhs13324

Novel motif P-value
1 0.172
10 0.0068
100 0.929
101 0.472
102 0.289
103 0.141
104 0.906
105 0.621
106 0.633
107 0.743
108 0.345
109 0.0205
11 0.0997
110 0.0288
111 0.352
112 0.898
113 0.0812
114 0.356
115 0.703
116 0.0283
117 5.35328e-4
118 0.895
119 0.271
12 0.933
120 0.152
121 0.822
122 0.207
123 0.328
124 0.24
125 0.194
126 0.276
127 0.0548
128 0.775
129 0.59
13 0.00876
130 0.524
131 0.563
132 0.476
133 0.141
134 0.624
135 0.343
136 0.575
137 0.671
138 0.545
139 0.218
14 0.472
140 0.546
141 0.613
142 0.958
143 0.0409
144 0.205
145 0.117
146 0.352
147 0.983
148 0.644
149 0.265
15 0.849
150 0.0309
151 0.996
152 0.118
153 0.762
154 0.48
155 0.151
156 7.1938e-60
157 0.863
158 0.717
159 0.395
160 0.486
161 0.613
162 0.893
163 0.976
164 0.00209
165 0.809
166 0.67
167 0.171
168 0.456
169 0.00131
17 0.16
18 0.267
19 0.304
2 0.39
20 0.0461
21 0.0836
22 0.247
23 0.171
24 0.98
25 0.95
26 0.0399
27 0.441
28 0.644
29 0.00227
3 0.0778
30 0.491
31 0.772
32 0.395
33 0.328
34 0.788
35 0.356
36 0.0898
37 0.0151
38 0.574
39 0.366
4 0.588
40 0.473
41 0.16
42 0.287
43 0.425
44 0.201
45 0.649
46 0.307
47 0.166
48 0.269
49 0.9
5 0.0618
50 0.614
51 0.885
52 0.851
53 0.534
54 0.546
55 0.63
56 0.812
57 0.235
58 0.835
59 0.163
6 0.649
60 0.342
61 0.678
62 0.449
63 0.51
64 0.511
65 0.852
66 0.58
67 0.728
68 0.682
69 0.938
7 0.278
70 0.00256
71 8.21729e-4
72 0.918
73 0.0188
74 0.971
75 0.0465
76 0.175
77 0.226
78 0.048
79 0.756
8 0.0764
80 0.00944
81 0.7
82 0.2
83 0.589
84 0.662
85 0.561
86 0.659
87 0.178
88 0.675
89 0.869
9 0.867
90 0.0378
91 0.413
92 0.673
93 0.291
94 0.687
95 0.0189
96 0.411
97 0.689
98 0.309
99 0.853



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: CNhs13324


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)
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)