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FF:24-13C9

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Name:spinal cord, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10505
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
tissuespinal cord
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  SAMD00005286
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10505 CAGE DRX009083 DRR009957
Accession ID Mm9

Library idBAMCTSS
CNhs10505 DRZ001382 DRZ002765
Accession ID Mm10

Library idBAMCTSS
CNhs10505 DRZ012732 DRZ014115
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

CNhs10505

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.726
10 0
100 0
1000 0.117
1001 0.179
1002 -0.00984
1003 0.171
1004 0
1005 0.035
1006 0.587
1007 -0.0769
1008 0
1009 -0.0676
101 -0.0779
1010 0
1011 0.403
1012 0.19
1013 0.292
1014 -0.0851
1015 -0.116
1016 -0.138
1017 0
1018 0
1019 0
102 0
1020 0
1021 -0.0487
1022 0.268
1023 0
1024 0.195
1025 0
1026 0.0644
1027 0.578
1028 0
1029 0.0932
103 -0.0736
1030 0
1031 -0.306
1032 0.438
1033 -0.0665
1034 0
1035 0.137
1036 -0.258
1037 0
1038 -0.0134
1039 0.113
104 0
1040 -0.142
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: CNhs10505
Jaspar motif P-value
MA0002.2 0.00197
MA0003.1 0.369
MA0004.1 0.408
MA0006.1 0.283
MA0007.1 0.234
MA0009.1 0.708
MA0014.1 0.911
MA0017.1 2.46035e-6
MA0018.2 0.0136
MA0019.1 0.811
MA0024.1 0.0672
MA0025.1 0.00143
MA0027.1 0.137
MA0028.1 0.0721
MA0029.1 0.984
MA0030.1 0.598
MA0031.1 0.472
MA0035.2 0.0193
MA0038.1 0.242
MA0039.2 0.078
MA0040.1 0.56
MA0041.1 0.0875
MA0042.1 0.29
MA0043.1 0.0664
MA0046.1 5.04426e-11
MA0047.2 1.60614e-4
MA0048.1 0.0273
MA0050.1 6.03212e-4
MA0051.1 0.0044
MA0052.1 0.608
MA0055.1 0.0066
MA0057.1 0.27
MA0058.1 0.501
MA0059.1 0.104
MA0060.1 0.348
MA0061.1 0.024
MA0062.2 0.00145
MA0065.2 3.1389e-6
MA0066.1 0.0189
MA0067.1 0.271
MA0068.1 0.457
MA0069.1 0.136
MA0070.1 0.207
MA0071.1 0.0906
MA0072.1 0.602
MA0073.1 0.821
MA0074.1 0.0612
MA0076.1 0.176
MA0077.1 0.17
MA0078.1 0.681
MA0079.2 0.198
MA0080.2 3.51035e-9
MA0081.1 0.268
MA0083.1 0.0685
MA0084.1 0.591
MA0087.1 0.0672
MA0088.1 0.359
MA0090.1 0.0774
MA0091.1 0.192
MA0092.1 0.168
MA0093.1 0.509
MA0099.2 0.0233
MA0100.1 0.124
MA0101.1 0.0113
MA0102.2 0.544
MA0103.1 0.102
MA0104.2 0.579
MA0105.1 0.00119
MA0106.1 0.0535
MA0107.1 0.0345
MA0108.2 0.0129
MA0111.1 0.875
MA0112.2 0.00175
MA0113.1 0.377
MA0114.1 3.86651e-6
MA0115.1 5.44215e-5
MA0116.1 0.0422
MA0117.1 0.897
MA0119.1 0.132
MA0122.1 0.873
MA0124.1 0.358
MA0125.1 0.028
MA0131.1 0.736
MA0135.1 0.247
MA0136.1 1.7104e-11
MA0137.2 0.534
MA0138.2 8.39219e-5
MA0139.1 0.553
MA0140.1 4.80814e-5
MA0141.1 0.00981
MA0142.1 0.375
MA0143.1 0.912
MA0144.1 0.153
MA0145.1 0.276
MA0146.1 0.0411
MA0147.1 0.394
MA0148.1 7.90758e-4
MA0149.1 0.162
MA0150.1 0.372
MA0152.1 0.264
MA0153.1 7.49996e-12
MA0154.1 0.035
MA0155.1 0.574
MA0156.1 5.03258e-7
MA0157.1 0.293
MA0159.1 0.00486
MA0160.1 0.0259
MA0162.1 0.285
MA0163.1 3.1194e-4
MA0164.1 0.862
MA0258.1 0.0272
MA0259.1 0.602



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: CNhs10505
Novel motif P-value
1 0.304
10 0.0421
100 0.271
101 0.913
102 0.9
103 0.111
104 0.983
105 0.632
106 0.0434
107 0.127
108 0.606
109 0.0142
11 0.119
110 0.0403
111 0.196
112 0.00771
113 0.462
114 0.492
115 0.683
116 0.266
117 0.00292
118 0.199
119 0.186
12 0.749
120 0.889
121 0.76
122 0.954
123 7.07387e-5
124 0.0229
125 0.0785
126 0.0232
127 0.386
128 0.0253
129 0.467
13 3.27406e-7
130 0.202
131 0.426
132 0.77
133 0.543
134 0.143
135 0.0674
136 0.138
137 0.781
138 0.988
139 0.432
14 0.585
140 0.113
141 0.879
142 0.424
143 0.244
144 0.798
145 8.32693e-5
146 0.502
147 0.498
148 0.998
149 0.749
15 0.166
150 0.0793
151 0.916
152 0.175
153 0.864
154 0.776
155 0.48
156 0.0343
157 0.344
158 0.33
159 0.739
160 0.188
161 0.213
162 0.742
163 0.624
164 0.0206
165 0.515
166 0.678
167 0.989
168 0.743
169 0.00583
17 0.106
18 0.913
19 0.226
2 0.604
20 0.0134
21 0.183
22 0.238
23 0.815
24 0.0672
25 0.813
26 5.29694e-11
27 0.316
28 0.831
29 0.0225
3 0.12
30 0.832
31 0.716
32 0.63
33 0.145
34 0.904
35 1
36 0.122
37 0.0684
38 0.476
39 0.503
4 0.263
40 0.138
41 0.46
42 0.235
43 0.15
44 0.506
45 0.804
46 0.0254
47 0.641
48 0.41
49 0.136
5 0.237
50 0.28
51 0.721
52 0.434
53 0.3
54 0.874
55 0.989
56 0.565
57 0.48
58 0.337
59 0.156
6 0.867
60 0.0508
61 0.0831
62 0.229
63 0.195
64 0.632
65 0.387
66 0.803
67 0.967
68 0.355
69 0.577
7 0.0239
70 0.0746
71 0.00224
72 0.667
73 0.0682
74 0.811
75 0.0437
76 0.204
77 0.571
78 0.00334
79 0.1
8 0.0599
80 0.664
81 0.494
82 0.403
83 0.528
84 0.837
85 0.225
86 0.145
87 0.502
88 0.63
89 0.489
9 0.584
90 0.0621
91 0.0457
92 0.309
93 0.167
94 0.454
95 0.0803
96 0.513
97 0.895
98 0.687
99 0.54



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: CNhs10505


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)
0002240 (spinal cord)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001137 (dorsum)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011305 (mouse spinal cord- 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:0006241 (future spinal cord)
UBERON:0003057 (chordal neural plate)
UBERON:0010316 (germ layer / neural crest)