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FF:1396-42A3

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Name:medulla oblongata, neonate N30
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuemedulla oblongata
dev stage30 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
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

CNhs11200

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.718
10 0
100 0
1000 0.0343
1001 0.1
1002 --0.0161
1003 0.0268
1004 0.0241
1005 0.00926
1006 0.6
1007 --0.0214
1008 0
1009 --0.152
101 --0.0749
1010 0
1011 0.287
1012 0.131
1013 0.328
1014 --0.037
1015 --0.184
1016 --0.0983
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0857
1023 0
1024 0.17
1025 0
1026 0
1027 0.464
1028 0
1029 0.0527
103 --0.0799
1030 0
1031 --0.317
1032 0.46
1033 --0.0142
1034 0
1035 0.0481
1036 --0.233
1037 0
1038 --0.0942
1039 0.116
104 0
1040 --0.168
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: CNhs11200

Jaspar motif P-value
MA0002.2 2.7993e-4
MA0003.1 0.291
MA0004.1 0.437
MA0006.1 0.259
MA0007.1 0.379
MA0009.1 0.879
MA0014.1 0.854
MA0017.1 2.63946e-6
MA0018.2 0.00504
MA0019.1 0.447
MA0024.1 0.0638
MA0025.1 0.00179
MA0027.1 0.224
MA0028.1 0.125
MA0029.1 0.911
MA0030.1 0.604
MA0031.1 0.417
MA0035.2 0.0179
MA0038.1 0.206
MA0039.2 0.0762
MA0040.1 0.485
MA0041.1 0.0489
MA0042.1 0.151
MA0043.1 0.0282
MA0046.1 2.47318e-12
MA0047.2 1.63525e-4
MA0048.1 0.0365
MA0050.1 3.79163e-5
MA0051.1 5.45499e-4
MA0052.1 0.357
MA0055.1 0.0162
MA0057.1 0.234
MA0058.1 0.536
MA0059.1 0.131
MA0060.1 0.281
MA0061.1 0.0172
MA0062.2 0.00506
MA0065.2 1.58615e-6
MA0066.1 0.022
MA0067.1 0.246
MA0068.1 0.938
MA0069.1 0.0581
MA0070.1 0.341
MA0071.1 0.181
MA0072.1 0.918
MA0073.1 0.826
MA0074.1 0.109
MA0076.1 0.308
MA0077.1 0.159
MA0078.1 0.747
MA0079.2 0.262
MA0080.2 1.25764e-9
MA0081.1 0.208
MA0083.1 0.014
MA0084.1 0.657
MA0087.1 0.0642
MA0088.1 0.358
MA0090.1 0.0844
MA0091.1 0.157
MA0092.1 0.227
MA0093.1 0.525
MA0099.2 0.0105
MA0100.1 0.19
MA0101.1 0.0123
MA0102.2 0.461
MA0103.1 0.104
MA0104.2 0.632
MA0105.1 0.0012
MA0106.1 0.0618
MA0107.1 0.024
MA0108.2 9.57768e-4
MA0111.1 0.815
MA0112.2 8.70092e-4
MA0113.1 0.497
MA0114.1 6.48243e-6
MA0115.1 5.76756e-5
MA0116.1 0.0382
MA0117.1 0.982
MA0119.1 0.127
MA0122.1 0.98
MA0124.1 0.476
MA0125.1 0.00717
MA0131.1 0.802
MA0135.1 0.368
MA0136.1 3.77549e-11
MA0137.2 0.305
MA0138.2 1.48988e-4
MA0139.1 0.521
MA0140.1 1.58628e-5
MA0141.1 0.0204
MA0142.1 0.434
MA0143.1 0.74
MA0144.1 0.0795
MA0145.1 0.217
MA0146.1 0.0528
MA0147.1 0.435
MA0148.1 5.51366e-4
MA0149.1 0.237
MA0150.1 0.255
MA0152.1 0.259
MA0153.1 1.92247e-12
MA0154.1 0.0235
MA0155.1 0.454
MA0156.1 5.23882e-7
MA0157.1 0.287
MA0159.1 0.00324
MA0160.1 0.0279
MA0162.1 0.265
MA0163.1 5.39927e-4
MA0164.1 0.895
MA0258.1 0.015
MA0259.1 0.679



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: CNhs11200

Novel motif P-value
1 0.276
10 0.0529
100 0.357
101 0.752
102 0.914
103 0.0717
104 0.948
105 0.581
106 0.0306
107 0.126
108 0.591
109 0.0181
11 0.121
110 0.0394
111 0.2
112 0.00867
113 0.526
114 0.459
115 0.782
116 0.25
117 0.00379
118 0.255
119 0.215
12 0.786
120 0.646
121 0.606
122 0.812
123 4.86989e-4
124 0.0428
125 0.215
126 0.0274
127 0.209
128 0.0282
129 0.298
13 6.21618e-7
130 0.182
131 0.507
132 0.67
133 0.537
134 0.204
135 0.14
136 0.27
137 0.627
138 0.853
139 0.261
14 0.741
140 0.0969
141 0.74
142 0.527
143 0.326
144 0.937
145 1.6809e-4
146 0.406
147 0.364
148 0.88
149 0.988
15 0.164
150 0.0792
151 0.984
152 0.156
153 0.852
154 0.789
155 0.475
156 0.00763
157 0.283
158 0.326
159 0.617
160 0.183
161 0.243
162 0.864
163 0.471
164 0.028
165 0.517
166 0.454
167 0.774
168 0.496
169 0.00356
17 0.0884
18 0.935
19 0.164
2 0.78
20 0.0271
21 0.178
22 0.207
23 0.7
24 0.098
25 0.718
26 3.73002e-10
27 0.45
28 0.846
29 0.0272
3 0.0935
30 0.906
31 0.758
32 0.533
33 0.179
34 0.818
35 0.884
36 0.163
37 0.066
38 0.49
39 0.415
4 0.237
40 0.153
41 0.442
42 0.217
43 0.126
44 0.494
45 0.716
46 0.0249
47 0.495
48 0.338
49 0.167
5 0.19
50 0.294
51 0.724
52 0.384
53 0.354
54 0.924
55 0.949
56 0.539
57 0.473
58 0.284
59 0.098
6 0.88
60 0.0383
61 0.0785
62 0.157
63 0.168
64 0.622
65 0.358
66 0.818
67 0.845
68 0.514
69 0.606
7 0.018
70 0.0922
71 0.00258
72 0.586
73 0.0826
74 0.906
75 0.0589
76 0.256
77 0.498
78 0.00266
79 0.167
8 0.0519
80 0.861
81 0.576
82 0.305
83 0.3
84 0.586
85 0.239
86 0.134
87 0.652
88 0.596
89 0.511
9 0.495
90 0.208
91 0.0585
92 0.279
93 0.14
94 0.779
95 0.12
96 0.479
97 0.893
98 0.452
99 0.465



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: CNhs11200


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011465 (mouse medulla oblongata- neonate N30 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)
FF:0000294 (mouse embryonic day 11 sample)