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FF:12338-130I7

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Name:ST2 (Mesenchymal stem cells) cells, medium change (without induction)
Species:Mouse (Mus musculus)
Library ID:CNhs11939
Sample type:time courses
Genomic View: UCSC
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  SAMD00005927
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11939 CAGE DRX008905 DRR009779
Accession ID Mm9

Library idBAMCTSS
CNhs11939 DRZ001204 DRZ002587
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11939

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.247
1001 0.0155
1002 --0.116
1003 0.228
1004 0
1005 0
1006 --0.0916
1007 0.00293
1008 0
1009 0.746
101 0.0347
1010 0
1011 --0.229
1012 0
1013 0.0165
1014 --0.0874
1015 0.0378
1016 0.141
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.124
1023 0
1024 --0.307
1025 --0.0611
1026 0
1027 --0.00273
1028 0.127
1029 --0.151
103 0.404
1030 0
1031 --0.195
1032 --0.115
1033 0.0157
1034 0
1035 0
1036 0.106
1037 0
1038 0.112
1039 --0.0843
104 0
1040 0.396
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: CNhs11939

Jaspar motif P-value
MA0002.2 0.136
MA0003.1 0.644
MA0004.1 0.282
MA0006.1 0.394
MA0007.1 0.853
MA0009.1 0.588
MA0014.1 0.32
MA0017.1 0.0165
MA0018.2 0.685
MA0019.1 0.52
MA0024.1 0.0412
MA0025.1 0.253
MA0027.1 0.454
MA0028.1 4.99891e-5
MA0029.1 0.61
MA0030.1 0.783
MA0031.1 0.636
MA0035.2 0.00121
MA0038.1 0.468
MA0039.2 0.289
MA0040.1 0.258
MA0041.1 0.664
MA0042.1 0.347
MA0043.1 0.36
MA0046.1 1.46058e-6
MA0047.2 0.709
MA0048.1 4.64156e-4
MA0050.1 0.216
MA0051.1 0.23
MA0052.1 8.49384e-4
MA0055.1 3.88065e-4
MA0057.1 0.135
MA0058.1 0.0621
MA0059.1 0.829
MA0060.1 0.834
MA0061.1 0.309
MA0062.2 3.48067e-6
MA0065.2 0.669
MA0066.1 0.44
MA0067.1 0.608
MA0068.1 0.362
MA0069.1 0.659
MA0070.1 0.152
MA0071.1 0.907
MA0072.1 0.899
MA0073.1 0.547
MA0074.1 0.745
MA0076.1 1.18221e-4
MA0077.1 0.401
MA0078.1 0.262
MA0079.2 0.641
MA0080.2 0.32
MA0081.1 0.983
MA0083.1 3.11196e-4
MA0084.1 0.552
MA0087.1 0.902
MA0088.1 1.1465e-4
MA0090.1 0.0179
MA0091.1 0.795
MA0092.1 0.352
MA0093.1 0.257
MA0099.2 1.73472e-7
MA0100.1 0.0798
MA0101.1 0.232
MA0102.2 0.471
MA0103.1 2.43676e-7
MA0104.2 0.629
MA0105.1 0.259
MA0106.1 1.71478e-4
MA0107.1 0.701
MA0108.2 0.00448
MA0111.1 0.149
MA0112.2 0.062
MA0113.1 0.772
MA0114.1 0.314
MA0115.1 0.22
MA0116.1 0.108
MA0117.1 0.294
MA0119.1 0.394
MA0122.1 0.699
MA0124.1 0.28
MA0125.1 0.0191
MA0131.1 0.603
MA0135.1 0.0407
MA0136.1 0.445
MA0137.2 0.00396
MA0138.2 1.00494e-4
MA0139.1 0.848
MA0140.1 9.79602e-5
MA0141.1 0.975
MA0142.1 0.0175
MA0143.1 0.857
MA0144.1 0.024
MA0145.1 0.235
MA0146.1 5.4912e-4
MA0147.1 0.473
MA0148.1 0.683
MA0149.1 0.198
MA0150.1 0.107
MA0152.1 0.0397
MA0153.1 4.8865e-6
MA0154.1 0.372
MA0155.1 0.761
MA0156.1 0.179
MA0157.1 0.738
MA0159.1 0.931
MA0160.1 0.781
MA0162.1 0.118
MA0163.1 0.666
MA0164.1 0.556
MA0258.1 0.751
MA0259.1 0.413



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: CNhs11939

Novel motif P-value
1 0.301
10 0.0391
100 0.788
101 0.276
102 0.0974
103 0.569
104 0.962
105 0.802
106 0.904
107 0.373
108 0.523
109 0.0698
11 0.167
110 0.0373
111 0.791
112 0.947
113 0.139
114 0.911
115 0.89
116 0.344
117 4.42548e-4
118 0.907
119 0.2
12 0.652
120 0.232
121 0.41
122 0.32
123 0.19
124 0.213
125 0.578
126 0.549
127 0.0773
128 0.228
129 0.818
13 0.0129
130 0.612
131 0.598
132 0.227
133 0.152
134 0.901
135 0.298
136 0.293
137 0.97
138 0.595
139 0.0109
14 0.428
140 0.983
141 0.725
142 0.801
143 0.206
144 0.153
145 0.266
146 0.361
147 0.516
148 0.892
149 0.0859
15 0.537
150 0.0368
151 0.942
152 0.0821
153 0.91
154 0.403
155 0.186
156 1.19319e-28
157 0.771
158 0.543
159 0.148
160 0.931
161 0.793
162 0.814
163 0.723
164 0.00481
165 0.529
166 0.82
167 0.111
168 0.265
169 0.00175
17 0.55
18 0.497
19 0.393
2 0.539
20 0.0564
21 0.0503
22 0.204
23 0.288
24 0.712
25 0.978
26 0.232
27 0.376
28 0.909
29 0.0182
3 0.261
30 0.471
31 0.282
32 0.563
33 0.277
34 0.765
35 0.138
36 0.302
37 0.0132
38 0.917
39 0.724
4 0.552
40 0.917
41 0.312
42 0.505
43 0.835
44 0.222
45 0.855
46 0.545
47 0.231
48 0.356
49 0.412
5 0.433
50 0.575
51 0.844
52 0.735
53 0.608
54 0.313
55 0.779
56 0.57
57 0.409
58 0.826
59 0.445
6 0.844
60 0.445
61 0.922
62 0.555
63 0.742
64 0.666
65 0.844
66 0.477
67 0.278
68 0.251
69 0.863
7 0.247
70 0.0477
71 0.00954
72 0.785
73 0.0094
74 0.813
75 0.0975
76 0.485
77 0.344
78 0.0108
79 0.713
8 0.639
80 0.0124
81 0.887
82 0.512
83 0.767
84 0.794
85 0.996
86 0.791
87 0.0191
88 0.384
89 0.262
9 0.67
90 0.0552
91 0.943
92 0.544
93 0.245
94 0.751
95 0.0121
96 0.749
97 0.384
98 0.248
99 0.746



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: CNhs11939


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)