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FF:657-19C2

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Name:whole body, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs10525
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
strainC57BL/6J
tissuewhole body
dev stage0 day neonate
sexfemale
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  SAMD00004943
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10525 CAGE DRX009151 DRR010025
Accession ID Mm9

Library idBAMCTSS
CNhs10525 DRZ001450 DRZ002833
Accession ID Mm10

Library idBAMCTSS
CNhs10525 DRZ012800 DRZ014183
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

CNhs10525

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.129
10 0
100 0.0845
1000 0.206
1001 0.0695
1002 -0.00451
1003 0.0873
1004 0
1005 0.022
1006 0.237
1007 -0.00118
1008 0
1009 0.17
101 -0.016
1010 0
1011 0.0845
1012 0
1013 -0.0543
1014 0.23
1015 -0.0624
1016 0.222
1017 0.0845
1018 0.0845
1019 0
102 0
1020 0
1021 0
1022 0.406
1023 0
1024 0.311
1025 0.585
1026 0.126
1027 0.107
1028 0
1029 -0.0207
103 0.573
1030 0
1031 0.361
1032 0.0108
1033 0
1034 0.155
1035 0.0845
1036 -0.00681
1037 0
1038 0.0206
1039 0.0904
104 0
1040 0.252
1041 0.155



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: CNhs10525
Jaspar motif P-value
MA0002.2 0.679
MA0003.1 0.0265
MA0004.1 0.153
MA0006.1 0.215
MA0007.1 0.211
MA0009.1 0.519
MA0014.1 0.213
MA0017.1 0.13
MA0018.2 8.60808e-4
MA0019.1 0.763
MA0024.1 0.0282
MA0025.1 0.456
MA0027.1 0.206
MA0028.1 1.57843e-8
MA0029.1 0.292
MA0030.1 0.00827
MA0031.1 0.245
MA0035.2 0.0744
MA0038.1 0.144
MA0039.2 0.308
MA0040.1 0.212
MA0041.1 0.281
MA0042.1 0.415
MA0043.1 0.0142
MA0046.1 3.34964e-26
MA0047.2 0.0533
MA0048.1 0.00158
MA0050.1 0.0793
MA0051.1 0.0822
MA0052.1 2.60886e-19
MA0055.1 1.03463e-5
MA0057.1 0.488
MA0058.1 0.0293
MA0059.1 0.00348
MA0060.1 0.0795
MA0061.1 0.717
MA0062.2 3.43294e-14
MA0065.2 0.0915
MA0066.1 0.84
MA0067.1 0.191
MA0068.1 0.882
MA0069.1 0.431
MA0070.1 0.191
MA0071.1 0.287
MA0072.1 0.793
MA0073.1 0.924
MA0074.1 0.949
MA0076.1 1.35763e-9
MA0077.1 0.718
MA0078.1 0.0489
MA0079.2 0.0148
MA0080.2 4.95348e-5
MA0081.1 0.0389
MA0083.1 2.20393e-8
MA0084.1 0.887
MA0087.1 0.122
MA0088.1 0.0716
MA0090.1 0.0473
MA0091.1 0.353
MA0092.1 0.0727
MA0093.1 0.113
MA0099.2 0.116
MA0100.1 0.0155
MA0101.1 0.0903
MA0102.2 0.325
MA0103.1 0.541
MA0104.2 0.0379
MA0105.1 0.77
MA0106.1 0.308
MA0107.1 0.303
MA0108.2 2.33065e-57
MA0111.1 0.93
MA0112.2 0.334
MA0113.1 0.483
MA0114.1 0.0316
MA0115.1 0.817
MA0116.1 0.793
MA0117.1 0.562
MA0119.1 0.262
MA0122.1 0.571
MA0124.1 0.853
MA0125.1 0.00939
MA0131.1 0.193
MA0135.1 0.0196
MA0136.1 6.19661e-13
MA0137.2 0.00438
MA0138.2 7.81506e-7
MA0139.1 0.406
MA0140.1 0.136
MA0141.1 0.42
MA0142.1 0.447
MA0143.1 0.753
MA0144.1 0.356
MA0145.1 0.015
MA0146.1 0.609
MA0147.1 0.0255
MA0148.1 0.00893
MA0149.1 0.00875
MA0150.1 0.583
MA0152.1 0.99
MA0153.1 9.36347e-12
MA0154.1 0.156
MA0155.1 0.048
MA0156.1 3.20817e-11
MA0157.1 0.174
MA0159.1 0.244
MA0160.1 0.593
MA0162.1 0.712
MA0163.1 0.999
MA0164.1 0.297
MA0258.1 0.699
MA0259.1 0.0706



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: CNhs10525
Novel motif P-value
1 0.671
10 0.114
100 0.67
101 0.164
102 0.2
103 0.18
104 0.792
105 0.541
106 0.053
107 0.012
108 0.376
109 0.709
11 0.658
110 0.456
111 0.0454
112 0.614
113 0.469
114 0.895
115 0.813
116 0.103
117 0.0112
118 0.402
119 0.593
12 0.653
120 0.788
121 0.651
122 0.281
123 0.194
124 0.454
125 0.101
126 0.163
127 0.768
128 0.152
129 0.804
13 0.135
130 0.664
131 0.181
132 0.555
133 0.151
134 0.237
135 0.398
136 0.736
137 0.875
138 0.81
139 0.968
14 0.293
140 0.775
141 0.593
142 0.337
143 0.201
144 0.842
145 0.586
146 0.21
147 0.74
148 0.8
149 0.332
15 0.188
150 0.915
151 0.529
152 0.1
153 0.323
154 0.479
155 0.0855
156 0.856
157 0.0483
158 0.00651
159 0.0974
160 0.307
161 0.0632
162 0.222
163 0.692
164 0.123
165 0.781
166 0.166
167 0.0118
168 0.0031
169 0.172
17 0.489
18 0.549
19 0.257
2 0.0135
20 0.00823
21 0.185
22 0.519
23 0.133
24 0.292
25 0.642
26 0.691
27 0.309
28 0.962
29 0.0402
3 0.637
30 0.0996
31 0.473
32 0.0932
33 0.395
34 0.218
35 0.393
36 0.0684
37 0.821
38 0.972
39 0.669
4 0.658
40 0.473
41 0.359
42 0.696
43 0.634
44 0.652
45 0.135
46 0.867
47 0.979
48 0.782
49 0.855
5 0.94
50 0.522
51 0.649
52 0.0797
53 0.242
54 0.333
55 0.66
56 0.405
57 0.301
58 0.942
59 0.063
6 0.65
60 0.236
61 0.314
62 0.942
63 0.488
64 0.897
65 0.557
66 0.493
67 0.443
68 0.562
69 0.814
7 0.961
70 0.279
71 0.653
72 0.853
73 0.881
74 0.845
75 0.12
76 0.00774
77 0.146
78 0.519
79 0.925
8 0.743
80 0.554
81 0.332
82 0.622
83 0.885
84 0.181
85 0.261
86 0.629
87 0.351
88 0.308
89 0.302
9 0.294
90 0.0187
91 0.539
92 0.369
93 0.0464
94 0.432
95 0.237
96 0.878
97 0.7
98 0.836
99 0.133



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: CNhs10525


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)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011398 (mouse whole body- neonate N00 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


FF:0000294 (mouse embryonic day 11 sample)