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FF:1830-49C7

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Name:mouse fibroblast cell line: CRL-1658 NIH/3T3
Species:Mouse (Mus musculus)
Library ID:CNhs11093
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNIH/Swiss
tissuewhole body
dev stageembryo
sexunknown_sex_type
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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  SAMD00005849
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11093 CAGE DRX008760 DRR009632
Accession ID Mm9

Library idBAMCTSS
CNhs11093 DRZ001057 DRZ002442
Accession ID Mm10

Library idBAMCTSS
CNhs11093 DRZ012407 DRZ013792
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11093

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0659
1001 -0.0195
1002 0.0797
1003 0.291
1004 0
1005 0
1006 -0.143
1007 -0.0134
1008 0
1009 0.349
101 0.177
1010 0
1011 -0.175
1012 0
1013 -0.102
1014 -0.0851
1015 0.183
1016 0.0736
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0172
1022 -0.124
1023 0
1024 -0.307
1025 0
1026 0
1027 -0.048
1028 0
1029 -0.148
103 0.215
1030 0
1031 0.242
1032 -0.111
1033 -0.0752
1034 0
1035 0
1036 -0.0597
1037 0
1038 -0.23
1039 -0.0742
104 0
1040 0.411
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: CNhs11093
Jaspar motif P-value
MA0002.2 0.631
MA0003.1 0.75
MA0004.1 0.115
MA0006.1 0.547
MA0007.1 0.64
MA0009.1 0.665
MA0014.1 0.709
MA0017.1 0.0104
MA0018.2 0.707
MA0019.1 0.417
MA0024.1 0.0112
MA0025.1 0.454
MA0027.1 0.195
MA0028.1 0.00199
MA0029.1 0.374
MA0030.1 0.0511
MA0031.1 0.171
MA0035.2 9.98939e-4
MA0038.1 0.276
MA0039.2 0.11
MA0040.1 0.178
MA0041.1 0.57
MA0042.1 0.712
MA0043.1 0.143
MA0046.1 1.17976e-8
MA0047.2 0.0658
MA0048.1 4.58889e-5
MA0050.1 0.456
MA0051.1 0.946
MA0052.1 2.38173e-4
MA0055.1 2.66278e-4
MA0057.1 0.742
MA0058.1 0.052
MA0059.1 0.0198
MA0060.1 0.682
MA0061.1 0.561
MA0062.2 0.012
MA0065.2 0.308
MA0066.1 0.74
MA0067.1 0.72
MA0068.1 0.304
MA0069.1 0.606
MA0070.1 0.14
MA0071.1 0.986
MA0072.1 0.888
MA0073.1 0.346
MA0074.1 0.783
MA0076.1 0.022
MA0077.1 0.148
MA0078.1 0.0186
MA0079.2 0.284
MA0080.2 0.00342
MA0081.1 0.418
MA0083.1 0.537
MA0084.1 0.588
MA0087.1 0.996
MA0088.1 0.073
MA0090.1 0.0375
MA0091.1 0.468
MA0092.1 0.69
MA0093.1 0.17
MA0099.2 2.72436e-9
MA0100.1 0.0101
MA0101.1 0.102
MA0102.2 0.417
MA0103.1 3.19984e-4
MA0104.2 0.051
MA0105.1 0.644
MA0106.1 0.00728
MA0107.1 0.408
MA0108.2 1.44633e-7
MA0111.1 0.537
MA0112.2 0.602
MA0113.1 0.844
MA0114.1 0.0475
MA0115.1 0.298
MA0116.1 0.387
MA0117.1 0.895
MA0119.1 0.494
MA0122.1 0.902
MA0124.1 0.689
MA0125.1 0.00793
MA0131.1 0.192
MA0135.1 0.696
MA0136.1 0.419
MA0137.2 0.578
MA0138.2 5.07383e-4
MA0139.1 0.12
MA0140.1 0.00101
MA0141.1 0.608
MA0142.1 0.416
MA0143.1 0.516
MA0144.1 0.587
MA0145.1 0.275
MA0146.1 0.0084
MA0147.1 0.0567
MA0148.1 0.194
MA0149.1 0.392
MA0150.1 0.0157
MA0152.1 0.97
MA0153.1 5.01577e-8
MA0154.1 0.298
MA0155.1 0.634
MA0156.1 0.29
MA0157.1 0.777
MA0159.1 0.478
MA0160.1 0.673
MA0162.1 0.467
MA0163.1 0.0502
MA0164.1 0.241
MA0258.1 0.79
MA0259.1 0.0544



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: CNhs11093
Novel motif P-value
1 0.561
10 0.176
100 0.716
101 0.0799
102 0.783
103 0.422
104 0.711
105 0.539
106 0.475
107 0.119
108 0.792
109 0.202
11 0.186
110 0.0311
111 0.321
112 0.668
113 0.335
114 0.609
115 0.726
116 0.0642
117 9.28766e-4
118 0.747
119 0.353
12 0.943
120 0.448
121 0.477
122 0.182
123 0.329
124 0.0235
125 0.187
126 0.423
127 0.333
128 0.358
129 0.436
13 0.474
130 0.339
131 0.196
132 0.31
133 0.13
134 0.705
135 0.429
136 0.933
137 0.746
138 0.713
139 0.0322
14 0.397
140 0.921
141 0.872
142 0.74
143 0.012
144 0.649
145 0.118
146 0.125
147 0.88
148 0.55
149 0.481
15 0.702
150 0.0601
151 0.96
152 0.104
153 0.951
154 0.571
155 0.171
156 0.793
157 0.499
158 0.548
159 0.0285
160 0.916
161 0.527
162 0.983
163 0.668
164 0.00139
165 0.362
166 0.489
167 0.944
168 0.639
169 0.0487
17 0.78
18 0.0261
19 0.645
2 0.106
20 0.0185
21 0.0221
22 0.748
23 0.269
24 0.258
25 0.969
26 0.0375
27 0.288
28 0.427
29 0.0286
3 0.656
30 0.272
31 0.68
32 0.639
33 0.91
34 0.22
35 0.41
36 0.937
37 0.027
38 0.856
39 0.607
4 0.399
40 0.048
41 0.264
42 0.36
43 0.915
44 0.474
45 0.253
46 0.723
47 0.875
48 0.792
49 0.601
5 0.736
50 0.956
51 0.735
52 0.45
53 0.278
54 0.304
55 0.5
56 0.488
57 0.205
58 0.394
59 0.531
6 0.685
60 0.816
61 0.464
62 0.87
63 0.627
64 0.928
65 0.83
66 0.417
67 0.824
68 0.161
69 0.388
7 0.975
70 0.138
71 0.066
72 0.967
73 0.0113
74 0.41
75 0.033
76 0.0506
77 0.699
78 0.0919
79 0.113
8 0.109
80 0.0418
81 0.879
82 0.715
83 0.436
84 0.36
85 0.934
86 0.272
87 0.292
88 0.373
89 0.215
9 0.694
90 0.0443
91 0.444
92 0.741
93 0.0848
94 0.394
95 0.0118
96 0.781
97 0.584
98 0.705
99 0.422



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: CNhs11093


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
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)
0011287 (mouse fibroblast cell line: CRL-1658 NIH/3T3 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


NA