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FF:11805-124D5

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Name:neurospheres - sympathetic neuron derived, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs13082
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationHideki Enomoto (RIKEN CDB)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numbersym2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005733
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13082 CAGE DRX008869 DRR009741
Accession ID Mm9

Library idBAMCTSS
CNhs13082 DRZ001166 DRZ002551
Accession ID Mm10

Library idBAMCTSS
CNhs13082 DRZ012516 DRZ013901
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

CNhs13082

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.111
10 0
100 0.05
1000 0
1001 --0.0356
1002 --0.0941
1003 --0.0467
1004 0
1005 0
1006 0
1007 --0.0275
1008 0
1009 0.0833
101 --0.00347
1010 0
1011 0
1012 0
1013 0.0653
1014 --0.0851
1015 0.145
1016 0.397
1017 0
1018 0
1019 0
102 0
1020 0.391
1021 0.111
1022 --0.124
1023 0
1024 --0.14
1025 --0.0611
1026 0
1027 0.44
1028 0
1029 --0.0363
103 0
1030 0
1031 0.514
1032 0.0262
1033 0.0743
1034 0
1035 0
1036 --0.0419
1037 0
1038 0.0367
1039 --0.162
104 0
1040 0.319
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: CNhs13082

Jaspar motif P-value
MA0002.2 3.22114e-6
MA0003.1 0.0103
MA0004.1 0.971
MA0006.1 0.446
MA0007.1 0.361
MA0009.1 0.0625
MA0014.1 0.894
MA0017.1 3.38682e-6
MA0018.2 0.0341
MA0019.1 0.359
MA0024.1 0.0423
MA0025.1 0.265
MA0027.1 0.711
MA0028.1 0.915
MA0029.1 0.48
MA0030.1 0.342
MA0031.1 0.0107
MA0035.2 2.83557e-4
MA0038.1 0.263
MA0039.2 0.101
MA0040.1 0.51
MA0041.1 0.487
MA0042.1 0.42
MA0043.1 0.326
MA0046.1 2.8135e-14
MA0047.2 6.4813e-5
MA0048.1 0.725
MA0050.1 0.00896
MA0051.1 0.00442
MA0052.1 3.13642e-6
MA0055.1 0.473
MA0057.1 0.123
MA0058.1 0.594
MA0059.1 0.425
MA0060.1 0.00459
MA0061.1 0.0514
MA0062.2 0.262
MA0065.2 1.93051e-6
MA0066.1 0.239
MA0067.1 0.61
MA0068.1 0.23
MA0069.1 0.527
MA0070.1 0.0173
MA0071.1 0.281
MA0072.1 0.269
MA0073.1 0.887
MA0074.1 0.642
MA0076.1 0.843
MA0077.1 0.0768
MA0078.1 0.359
MA0079.2 0.49
MA0080.2 3.66839e-9
MA0081.1 0.392
MA0083.1 0.829
MA0084.1 0.457
MA0087.1 0.771
MA0088.1 0.844
MA0090.1 0.673
MA0091.1 0.712
MA0092.1 0.978
MA0093.1 0.889
MA0099.2 0.226
MA0100.1 0.84
MA0101.1 0.135
MA0102.2 0.568
MA0103.1 7.5403e-4
MA0104.2 0.758
MA0105.1 5.24016e-4
MA0106.1 0.0478
MA0107.1 0.059
MA0108.2 0.00835
MA0111.1 0.871
MA0112.2 4.14692e-5
MA0113.1 0.102
MA0114.1 1.39601e-5
MA0115.1 0.00505
MA0116.1 0.0024
MA0117.1 0.658
MA0119.1 0.0895
MA0122.1 0.756
MA0124.1 0.233
MA0125.1 0.186
MA0131.1 0.533
MA0135.1 0.144
MA0136.1 1.13197e-7
MA0137.2 0.718
MA0138.2 0.179
MA0139.1 0.0934
MA0140.1 5.77652e-5
MA0141.1 0.00195
MA0142.1 0.0596
MA0143.1 0.284
MA0144.1 0.354
MA0145.1 0.0591
MA0146.1 0.413
MA0147.1 0.522
MA0148.1 5.31719e-4
MA0149.1 0.683
MA0150.1 0.0656
MA0152.1 0.439
MA0153.1 1.09888e-14
MA0154.1 0.00326
MA0155.1 0.477
MA0156.1 4.22661e-5
MA0157.1 0.0116
MA0159.1 0.133
MA0160.1 0.0229
MA0162.1 0.316
MA0163.1 0.00414
MA0164.1 0.702
MA0258.1 0.00796
MA0259.1 0.889



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: CNhs13082

Novel motif P-value
1 0.153
10 0.0757
100 0.954
101 0.869
102 0.941
103 0.202
104 0.657
105 0.0739
106 0.0382
107 0.0614
108 0.997
109 0.0375
11 0.132
110 0.13
111 0.0171
112 0.0246
113 0.503
114 0.0822
115 0.629
116 0.487
117 0.359
118 0.697
119 0.0371
12 0.663
120 0.607
121 0.119
122 0.354
123 0.469
124 0.398
125 0.733
126 0.205
127 0.219
128 0.0242
129 0.372
13 0.0134
130 0.975
131 0.72
132 0.315
133 0.517
134 0.953
135 0.726
136 0.69
137 0.319
138 0.938
139 0.165
14 0.444
140 0.152
141 0.275
142 0.663
143 0.93
144 0.912
145 0.333
146 0.374
147 0.653
148 0.424
149 0.118
15 0.0736
150 0.461
151 0.338
152 0.113
153 0.85
154 0.944
155 0.636
156 1.2857e-11
157 0.253
158 0.32
159 0.23
160 0.106
161 0.321
162 0.9
163 0.683
164 0.0939
165 0.173
166 0.857
167 0.395
168 0.706
169 0.00729
17 0.0854
18 0.864
19 0.194
2 0.554
20 0.775
21 0.363
22 0.288
23 0.289
24 0.0691
25 0.342
26 0.0213
27 0.228
28 0.417
29 0.389
3 0.123
30 0.641
31 0.797
32 0.199
33 0.268
34 0.406
35 0.885
36 0.643
37 0.0721
38 0.225
39 0.572
4 0.524
40 0.414
41 0.165
42 0.288
43 0.25
44 0.226
45 0.351
46 0.251
47 0.19
48 0.113
49 0.158
5 0.23
50 0.711
51 0.558
52 0.337
53 0.382
54 0.692
55 0.661
56 0.644
57 0.784
58 0.104
59 0.0313
6 0.58
60 0.0743
61 0.324
62 0.0373
63 0.115
64 0.399
65 0.108
66 0.676
67 0.598
68 0.67
69 0.976
7 0.0404
70 0.00599
71 0.111
72 0.203
73 0.224
74 0.97
75 0.15
76 0.83
77 0.185
78 0.0661
79 0.167
8 0.098
80 0.328
81 0.67
82 0.0158
83 0.0773
84 0.295
85 0.149
86 0.326
87 0.985
88 0.568
89 0.069
9 0.453
90 0.465
91 0.333
92 0.223
93 0.317
94 0.389
95 0.131
96 0.544
97 0.77
98 0.0988
99 0.299



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: CNhs13082


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)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000107 (autonomic neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000013 (sympathetic nervous system)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0011144 (mouse neurospheres - sympathetic neuron derived 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:0000031 (neuroblast)
CL:0000221 (ectodermal cell)