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FF:692-21D1

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Name:whole body, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs10515
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 stage6 days neonate
sexmixture
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  SAMD00005097
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10515 CAGE DRX009153 DRR010027
Accession ID Mm9

Library idBAMCTSS
CNhs10515 DRZ001452 DRZ002835
Accession ID Mm10

Library idBAMCTSS
CNhs10515 DRZ012802 DRZ014185
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

CNhs10515

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0866
10 0
100 0
1000 0.52
1001 0.0833
1002 --0.00349
1003 0.176
1004 0
1005 0.147
1006 0.422
1007 --0.0287
1008 0
1009 0.238
101 --0.0672
1010 0
1011 0.0512
1012 0
1013 --0.0387
1014 0.187
1015 --0.0837
1016 0.122
1017 0
1018 0.159
1019 0
102 0
1020 0
1021 0.0373
1022 0.562
1023 0
1024 0.316
1025 0
1026 0
1027 0.223
1028 0
1029 --0.0123
103 0.862
1030 0
1031 0.262
1032 0.17
1033 --0.0665
1034 0
1035 0.0866
1036 --0.0433
1037 0.0866
1038 0.122
1039 0.0972
104 0
1040 0.214
1041 0.275



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: CNhs10515

Jaspar motif P-value
MA0002.2 0.186
MA0003.1 0.0188
MA0004.1 0.122
MA0006.1 0.138
MA0007.1 0.487
MA0009.1 0.436
MA0014.1 0.832
MA0017.1 0.0851
MA0018.2 0.00365
MA0019.1 0.725
MA0024.1 0.116
MA0025.1 0.872
MA0027.1 0.205
MA0028.1 1.74082e-6
MA0029.1 0.53
MA0030.1 0.274
MA0031.1 0.991
MA0035.2 0.835
MA0038.1 0.726
MA0039.2 0.0738
MA0040.1 0.0801
MA0041.1 0.405
MA0042.1 0.449
MA0043.1 0.0153
MA0046.1 0.0278
MA0047.2 0.491
MA0048.1 0.00188
MA0050.1 0.029
MA0051.1 0.092
MA0052.1 3.84795e-39
MA0055.1 4.9752e-5
MA0057.1 0.26
MA0058.1 0.0682
MA0059.1 0.0159
MA0060.1 0.0806
MA0061.1 0.941
MA0062.2 4.2411e-11
MA0065.2 0.134
MA0066.1 0.868
MA0067.1 0.177
MA0068.1 0.502
MA0069.1 0.498
MA0070.1 0.724
MA0071.1 0.3
MA0072.1 0.499
MA0073.1 0.921
MA0074.1 0.885
MA0076.1 1.69328e-7
MA0077.1 0.883
MA0078.1 0.131
MA0079.2 0.00434
MA0080.2 0.00908
MA0081.1 0.363
MA0083.1 1.14204e-8
MA0084.1 0.861
MA0087.1 0.758
MA0088.1 0.53
MA0090.1 0.161
MA0091.1 0.661
MA0092.1 0.104
MA0093.1 0.123
MA0099.2 0.00904
MA0100.1 0.0167
MA0101.1 0.216
MA0102.2 0.765
MA0103.1 0.261
MA0104.2 0.0329
MA0105.1 0.785
MA0106.1 0.535
MA0107.1 0.472
MA0108.2 3.32065e-73
MA0111.1 0.861
MA0112.2 0.0173
MA0113.1 0.321
MA0114.1 0.193
MA0115.1 0.0135
MA0116.1 0.301
MA0117.1 0.716
MA0119.1 0.358
MA0122.1 0.183
MA0124.1 0.619
MA0125.1 0.00263
MA0131.1 0.183
MA0135.1 0.106
MA0136.1 9.65978e-7
MA0137.2 0.00597
MA0138.2 1.25411e-4
MA0139.1 0.573
MA0140.1 0.0772
MA0141.1 0.955
MA0142.1 0.0579
MA0143.1 0.176
MA0144.1 0.457
MA0145.1 0.0186
MA0146.1 0.564
MA0147.1 0.0327
MA0148.1 0.966
MA0149.1 0.0337
MA0150.1 0.993
MA0152.1 0.78
MA0153.1 6.4136e-4
MA0154.1 0.0481
MA0155.1 0.118
MA0156.1 1.96907e-7
MA0157.1 0.645
MA0159.1 0.66
MA0160.1 0.97
MA0162.1 0.364
MA0163.1 0.376
MA0164.1 0.0685
MA0258.1 0.252
MA0259.1 0.0728



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: CNhs10515

Novel motif P-value
1 0.951
10 0.293
100 0.726
101 0.0592
102 0.932
103 0.404
104 0.357
105 0.199
106 0.046
107 0.0301
108 0.324
109 0.451
11 0.858
110 0.979
111 0.275
112 0.581
113 0.539
114 0.775
115 0.659
116 0.0306
117 0.0932
118 0.479
119 0.558
12 0.206
120 0.567
121 0.925
122 0.612
123 0.141
124 0.748
125 0.85
126 0.43
127 0.276
128 0.211
129 0.784
13 0.81
130 0.811
131 0.175
132 0.858
133 0.333
134 0.725
135 0.368
136 0.468
137 0.397
138 0.813
139 0.955
14 0.223
140 0.947
141 0.295
142 0.462
143 0.878
144 0.0522
145 0.726
146 0.292
147 0.981
148 0.827
149 0.288
15 0.168
150 0.65
151 0.429
152 0.021
153 0.552
154 0.458
155 0.214
156 0.35
157 0.115
158 0.0927
159 0.251
160 0.149
161 0.144
162 0.86
163 0.865
164 0.177
165 0.882
166 0.462
167 0.00367
168 0.037
169 0.0243
17 0.302
18 0.5
19 0.105
2 0.0107
20 0.0112
21 0.738
22 0.285
23 0.251
24 0.956
25 0.951
26 0.938
27 0.546
28 0.819
29 0.137
3 0.875
30 0.122
31 0.555
32 0.0095
33 0.36
34 0.102
35 0.194
36 0.0789
37 0.373
38 0.908
39 0.293
4 0.871
40 0.656
41 0.519
42 0.928
43 0.628
44 0.747
45 0.145
46 0.678
47 0.774
48 0.969
49 0.684
5 0.699
50 0.34
51 0.55
52 0.101
53 0.173
54 0.299
55 0.57
56 0.378
57 0.797
58 0.701
59 0.00531
6 0.997
60 0.148
61 0.551
62 0.657
63 0.299
64 0.884
65 0.478
66 0.796
67 0.422
68 0.207
69 0.0792
7 0.666
70 0.934
71 0.72
72 0.794
73 0.201
74 0.524
75 0.367
76 0.00497
77 0.121
78 0.152
79 0.348
8 0.81
80 0.463
81 0.371
82 0.325
83 0.765
84 0.202
85 0.0907
86 0.661
87 0.084
88 0.608
89 0.167
9 0.17
90 0.0174
91 0.421
92 0.439
93 0.0246
94 0.85
95 0.689
96 0.941
97 0.932
98 0.864
99 0.184



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: CNhs10515


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)
0000312 (mouse neonate N6 sample)
0011405 (mouse whole body- neonate N06 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)