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FF:11643-122D5

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Name:Mouse Neurons - dorsal spinal cord, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12618
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespinal cord
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNADOR3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  DRS008726
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12618 CAGE DRX008836 DRR009708
Accession ID Mm9

Library idBAMCTSS
CNhs12618 DRZ001133 DRZ002518
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

CNhs12618

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.535
10 0
100 0.0867
1000 0
1001 --0.0668
1002 0.00807
1003 0.00203
1004 0
1005 0.0491
1006 0.605
1007 --0.25
1008 0
1009 --0.103
101 --0.244
1010 0
1011 0.298
1012 0
1013 0.25
1014 -6.860561e-4
1015 0.263
1016 0.12
1017 0
1018 0
1019 0
102 0
1020 0.588
1021 0.0867
1022 0
1023 0
1024 0.0514
1025 0.06
1026 0.0572
1027 0.406
1028 0
1029 --0.176
103 0.0635
1030 0
1031 --0.127
1032 0.408
1033 0
1034 0
1035 0
1036 --0.179
1037 0
1038 --0.0644
1039 0.0535
104 0
1040 --0.256
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: CNhs12618

Jaspar motif P-value
MA0002.2 0.00558
MA0003.1 0.583
MA0004.1 0.449
MA0006.1 0.228
MA0007.1 0.221
MA0009.1 0.893
MA0014.1 0.556
MA0017.1 2.34405e-6
MA0018.2 0.046
MA0019.1 0.972
MA0024.1 0.61
MA0025.1 0.757
MA0027.1 0.616
MA0028.1 0.0369
MA0029.1 0.916
MA0030.1 0.473
MA0031.1 0.0895
MA0035.2 0.0673
MA0038.1 0.405
MA0039.2 0.169
MA0040.1 0.54
MA0041.1 0.204
MA0042.1 0.535
MA0043.1 0.285
MA0046.1 4.18402e-7
MA0047.2 2.70993e-4
MA0048.1 0.0435
MA0050.1 1.47572e-6
MA0051.1 7.46617e-5
MA0052.1 0.475
MA0055.1 0.0295
MA0057.1 0.474
MA0058.1 0.517
MA0059.1 0.204
MA0060.1 0.0843
MA0061.1 0.0608
MA0062.2 2.36859e-4
MA0065.2 9.72105e-5
MA0066.1 0.0605
MA0067.1 0.891
MA0068.1 0.619
MA0069.1 0.0573
MA0070.1 0.239
MA0071.1 0.156
MA0072.1 0.127
MA0073.1 0.9
MA0074.1 0.235
MA0076.1 0.0936
MA0077.1 0.0655
MA0078.1 0.825
MA0079.2 0.117
MA0080.2 2.39885e-9
MA0081.1 0.29
MA0083.1 0.14
MA0084.1 0.268
MA0087.1 0.306
MA0088.1 0.178
MA0090.1 0.0913
MA0091.1 0.303
MA0092.1 0.254
MA0093.1 0.494
MA0099.2 0.00463
MA0100.1 0.0823
MA0101.1 0.0321
MA0102.2 0.48
MA0103.1 0.152
MA0104.2 0.925
MA0105.1 0.0216
MA0106.1 0.0526
MA0107.1 0.0538
MA0108.2 0.672
MA0111.1 0.997
MA0112.2 4.12756e-4
MA0113.1 0.231
MA0114.1 1.13147e-5
MA0115.1 1.29803e-4
MA0116.1 0.102
MA0117.1 0.467
MA0119.1 0.197
MA0122.1 0.849
MA0124.1 0.562
MA0125.1 0.172
MA0131.1 0.555
MA0135.1 0.0302
MA0136.1 4.85043e-11
MA0137.2 0.00728
MA0138.2 0.0107
MA0139.1 0.552
MA0140.1 2.16179e-4
MA0141.1 0.0598
MA0142.1 0.792
MA0143.1 0.796
MA0144.1 0.0209
MA0145.1 0.114
MA0146.1 0.0459
MA0147.1 0.79
MA0148.1 4.88007e-5
MA0149.1 0.145
MA0150.1 0.016
MA0152.1 0.0304
MA0153.1 9.59236e-7
MA0154.1 0.0389
MA0155.1 0.92
MA0156.1 2.07301e-8
MA0157.1 0.0679
MA0159.1 0.00238
MA0160.1 0.0385
MA0162.1 0.315
MA0163.1 0.00238
MA0164.1 0.885
MA0258.1 0.021
MA0259.1 0.824



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: CNhs12618

Novel motif P-value
1 0.114
10 0.0371
100 0.489
101 0.751
102 0.873
103 0.0766
104 0.601
105 0.64
106 0.0757
107 0.156
108 0.319
109 0.0159
11 0.105
110 0.0277
111 0.0414
112 0.00146
113 0.764
114 0.147
115 0.981
116 0.949
117 0.00221
118 0.219
119 0.141
12 0.936
120 0.677
121 0.179
122 0.773
123 0.00923
124 0.131
125 0.389
126 0.0545
127 0.121
128 0.0772
129 0.329
13 1.34149e-6
130 0.355
131 0.817
132 0.584
133 0.737
134 0.278
135 0.154
136 0.429
137 0.34
138 0.894
139 0.266
14 0.968
140 0.0385
141 0.391
142 0.046
143 0.528
144 0.977
145 0.00106
146 0.589
147 0.558
148 0.627
149 0.942
15 0.0989
150 0.0831
151 0.705
152 0.163
153 0.309
154 0.488
155 0.993
156 0.00501
157 0.154
158 0.0273
159 0.0568
160 0.244
161 0.223
162 0.728
163 0.431
164 0.00537
165 0.303
166 0.743
167 0.61
168 0.706
169 0.00222
17 0.0729
18 0.968
19 0.14
2 0.441
20 0.0305
21 0.488
22 0.214
23 0.587
24 0.13
25 0.727
26 4.35304e-8
27 0.378
28 0.497
29 0.0242
3 0.0586
30 0.606
31 0.754
32 0.969
33 0.14
34 0.683
35 0.874
36 0.439
37 0.0267
38 0.484
39 0.438
4 0.49
40 0.593
41 0.568
42 0.144
43 0.12
44 0.937
45 0.87
46 0.0289
47 0.305
48 0.188
49 0.104
5 0.0848
50 0.394
51 0.738
52 0.646
53 0.641
54 0.924
55 0.93
56 0.578
57 0.501
58 0.27
59 0.316
6 0.86
60 0.0547
61 0.0584
62 0.149
63 0.211
64 0.808
65 0.398
66 0.822
67 0.784
68 0.69
69 0.849
7 0.014
70 0.0583
71 0.00537
72 0.619
73 0.0348
74 0.33
75 0.038
76 0.278
77 0.638
78 0.00736
79 0.566
8 0.0771
80 0.715
81 0.736
82 0.306
83 0.51
84 0.82
85 0.183
86 0.107
87 0.764
88 0.142
89 0.508
9 0.53
90 0.0478
91 0.253
92 0.413
93 0.0333
94 0.326
95 0.0882
96 0.167
97 0.96
98 0.695
99 0.778



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: CNhs12618


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002611 (neuron of the dorsal spinal cord)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002240 (spinal cord)
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)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0001948 (regional part of spinal cord)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002256 (dorsal horn of spinal cord)
0001016 (nervous system)
0001137 (dorsum)
0002315 (gray matter of spinal cord)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000206 (mouse neuron of the dorsal spinal cord 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

CL:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)