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FF:17-12C2

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Name:medulla oblongata, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10477
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
tissuemedulla oblongata
dev stageadult
sexmale
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  SAMD00005853
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10477 CAGE DRX009046 DRR009920
Accession ID Mm9

Library idBAMCTSS
CNhs10477 DRZ001345 DRZ002728
Accession ID Mm10

Library idBAMCTSS
CNhs10477 DRZ012695 DRZ014078
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

CNhs10477

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.728
10 0
100 0
1000 0.0138
1001 0.0534
1002 0
1003 0.0884
1004 0
1005 0.0863
1006 0.61
1007 -0.0594
1008 0
1009 -0.0691
101 -0.0826
1010 0
1011 0.423
1012 0.0647
1013 0.295
1014 -0.0299
1015 -0.135
1016 -0.153
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0505
1023 0
1024 0.203
1025 0.0598
1026 0
1027 0.443
1028 0
1029 -0.00378
103 -0.0813
1030 0
1031 -0.304
1032 0.457
1033 -0.0105
1034 0
1035 0
1036 -0.279
1037 0
1038 -0.112
1039 0.181
104 0
1040 -0.151
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: CNhs10477
Jaspar motif P-value
MA0002.2 0.00138
MA0003.1 0.4
MA0004.1 0.412
MA0006.1 0.26
MA0007.1 0.287
MA0009.1 0.796
MA0014.1 0.941
MA0017.1 2.88822e-6
MA0018.2 0.00566
MA0019.1 0.65
MA0024.1 0.0398
MA0025.1 6.74289e-4
MA0027.1 0.199
MA0028.1 0.122
MA0029.1 0.684
MA0030.1 0.637
MA0031.1 0.496
MA0035.2 0.0216
MA0038.1 0.247
MA0039.2 0.0887
MA0040.1 0.671
MA0041.1 0.0358
MA0042.1 0.183
MA0043.1 0.0332
MA0046.1 1.98885e-10
MA0047.2 0.00105
MA0048.1 0.0189
MA0050.1 5.37196e-4
MA0051.1 0.0036
MA0052.1 0.419
MA0055.1 0.00491
MA0057.1 0.312
MA0058.1 0.498
MA0059.1 0.126
MA0060.1 0.629
MA0061.1 0.017
MA0062.2 0.0042
MA0065.2 1.86399e-6
MA0066.1 0.0225
MA0067.1 0.371
MA0068.1 0.998
MA0069.1 0.0438
MA0070.1 0.178
MA0071.1 0.19
MA0072.1 0.733
MA0073.1 0.85
MA0074.1 0.0998
MA0076.1 0.277
MA0077.1 0.24
MA0078.1 0.621
MA0079.2 0.216
MA0080.2 2.69538e-9
MA0081.1 0.269
MA0083.1 0.0224
MA0084.1 0.451
MA0087.1 0.081
MA0088.1 0.421
MA0090.1 0.0908
MA0091.1 0.15
MA0092.1 0.142
MA0093.1 0.487
MA0099.2 0.012
MA0100.1 0.136
MA0101.1 0.0103
MA0102.2 0.532
MA0103.1 0.123
MA0104.2 0.656
MA0105.1 0.00157
MA0106.1 0.0417
MA0107.1 0.0197
MA0108.2 1.26154e-4
MA0111.1 0.769
MA0112.2 0.00123
MA0113.1 0.395
MA0114.1 4.04951e-6
MA0115.1 2.31787e-5
MA0116.1 0.0599
MA0117.1 0.922
MA0119.1 0.181
MA0122.1 0.958
MA0124.1 0.437
MA0125.1 0.0176
MA0131.1 0.728
MA0135.1 0.123
MA0136.1 4.20794e-10
MA0137.2 0.546
MA0138.2 2.71959e-5
MA0139.1 0.703
MA0140.1 1.43397e-5
MA0141.1 0.025
MA0142.1 0.222
MA0143.1 0.695
MA0144.1 0.144
MA0145.1 0.25
MA0146.1 0.0495
MA0147.1 0.467
MA0148.1 0.00137
MA0149.1 0.169
MA0150.1 0.405
MA0152.1 0.24
MA0153.1 7.75729e-11
MA0154.1 0.0352
MA0155.1 0.423
MA0156.1 1.01848e-6
MA0157.1 0.299
MA0159.1 0.0051
MA0160.1 0.0342
MA0162.1 0.288
MA0163.1 6.03178e-4
MA0164.1 0.94
MA0258.1 0.0166
MA0259.1 0.698



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: CNhs10477
Novel motif P-value
1 0.259
10 0.0434
100 0.254
101 0.859
102 0.996
103 0.0897
104 0.999
105 0.644
106 0.0355
107 0.146
108 0.54
109 0.0262
11 0.138
110 0.0339
111 0.232
112 0.0129
113 0.451
114 0.516
115 0.915
116 0.274
117 0.00243
118 0.197
119 0.255
12 0.762
120 0.891
121 0.683
122 0.746
123 2.19989e-4
124 0.0206
125 0.123
126 0.0246
127 0.186
128 0.0529
129 0.356
13 1.87954e-7
130 0.179
131 0.571
132 0.723
133 0.678
134 0.214
135 0.0713
136 0.294
137 0.713
138 0.695
139 0.251
14 0.634
140 0.101
141 0.95
142 0.572
143 0.314
144 0.982
145 8.44091e-5
146 0.498
147 0.363
148 0.935
149 0.848
15 0.198
150 0.0691
151 0.94
152 0.166
153 0.845
154 0.719
155 0.416
156 0.00972
157 0.27
158 0.297
159 0.67
160 0.237
161 0.327
162 0.773
163 0.612
164 0.0329
165 0.544
166 0.446
167 0.922
168 0.782
169 0.00432
17 0.0895
18 0.927
19 0.185
2 0.589
20 0.0127
21 0.189
22 0.225
23 0.831
24 0.115
25 0.786
26 5.54404e-10
27 0.283
28 0.853
29 0.0272
3 0.098
30 0.799
31 0.715
32 0.65
33 0.201
34 0.908
35 0.952
36 0.168
37 0.0703
38 0.527
39 0.403
4 0.22
40 0.154
41 0.535
42 0.238
43 0.132
44 0.504
45 0.777
46 0.034
47 0.634
48 0.418
49 0.137
5 0.193
50 0.298
51 0.757
52 0.4
53 0.27
54 0.966
55 0.807
56 0.64
57 0.475
58 0.342
59 0.169
6 0.981
60 0.0461
61 0.0735
62 0.229
63 0.197
64 0.741
65 0.427
66 0.802
67 0.857
68 0.31
69 0.655
7 0.0184
70 0.1
71 0.00221
72 0.633
73 0.0748
74 0.805
75 0.0558
76 0.198
77 0.563
78 0.0022
79 0.213
8 0.0476
80 0.976
81 0.542
82 0.372
83 0.401
84 0.874
85 0.299
86 0.149
87 0.746
88 0.61
89 0.712
9 0.538
90 0.103
91 0.0778
92 0.387
93 0.129
94 0.585
95 0.107
96 0.515
97 0.92
98 0.702
99 0.61



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: CNhs10477


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)
0007023 (adult organism)
0000955 (brain)
0001896 (medulla oblongata)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0002298 (brainstem)
0002028 (hindbrain)
0005290 (myelencephalon)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011284 (mouse medulla oblongata- adult 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


UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)