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FF:11804-124D4

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Name:neurospheres - sympathetic neuron derived, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs13081
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 numbersym1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005758
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13081 CAGE DRX008868 DRR009740
Accession ID Mm9

Library idBAMCTSS
CNhs13081 DRZ001165 DRZ002550
Accession ID Mm10

Library idBAMCTSS
CNhs13081 DRZ012515 DRZ013900
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs13081

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -0.0262
1002 -0.0708
1003 -0.0671
1004 0
1005 -0.0389
1006 -0.143
1007 -0.00185
1008 0
1009 0.2
101 -0.0182
1010 0
1011 -0.108
1012 0
1013 0.0497
1014 -0.0851
1015 0.248
1016 0.271
1017 0
1018 0
1019 0
102 0
1020 0.258
1021 0.0989
1022 -0.196
1023 0
1024 -0.14
1025 -0.0611
1026 0
1027 0.536
1028 0
1029 0.0747
103 -0.0317
1030 0
1031 0.449
1032 0.074
1033 0.148
1034 0
1035 0
1036 0.162
1037 0
1038 0.0602
1039 -0.181
104 0
1040 0.137
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: CNhs13081
Jaspar motif P-value
MA0002.2 7.62982e-6
MA0003.1 0.00575
MA0004.1 0.616
MA0006.1 0.376
MA0007.1 0.55
MA0009.1 0.0988
MA0014.1 0.916
MA0017.1 9.75597e-5
MA0018.2 0.00783
MA0019.1 0.543
MA0024.1 4.75145e-4
MA0025.1 0.328
MA0027.1 0.346
MA0028.1 0.617
MA0029.1 0.199
MA0030.1 0.664
MA0031.1 0.199
MA0035.2 6.07397e-4
MA0038.1 0.0825
MA0039.2 0.118
MA0040.1 0.514
MA0041.1 0.415
MA0042.1 0.83
MA0043.1 0.204
MA0046.1 1.26522e-12
MA0047.2 0.00365
MA0048.1 0.773
MA0050.1 0.00783
MA0051.1 0.00694
MA0052.1 1.76075e-4
MA0055.1 0.982
MA0057.1 0.135
MA0058.1 0.27
MA0059.1 0.565
MA0060.1 2.03227e-6
MA0061.1 0.0757
MA0062.2 0.842
MA0065.2 5.04823e-6
MA0066.1 0.22
MA0067.1 0.783
MA0068.1 0.166
MA0069.1 0.651
MA0070.1 0.0436
MA0071.1 0.226
MA0072.1 0.168
MA0073.1 0.959
MA0074.1 0.684
MA0076.1 0.367
MA0077.1 0.0335
MA0078.1 0.202
MA0079.2 0.582
MA0080.2 7.48407e-9
MA0081.1 0.641
MA0083.1 0.636
MA0084.1 0.704
MA0087.1 0.743
MA0088.1 0.73
MA0090.1 0.479
MA0091.1 0.33
MA0092.1 0.993
MA0093.1 0.532
MA0099.2 0.406
MA0100.1 0.451
MA0101.1 0.321
MA0102.2 0.724
MA0103.1 4.26651e-4
MA0104.2 0.973
MA0105.1 3.93693e-4
MA0106.1 0.0617
MA0107.1 0.158
MA0108.2 0.0142
MA0111.1 0.928
MA0112.2 1.3078e-5
MA0113.1 0.19
MA0114.1 6.60723e-5
MA0115.1 0.0103
MA0116.1 0.00121
MA0117.1 0.805
MA0119.1 0.13
MA0122.1 0.539
MA0124.1 0.616
MA0125.1 0.152
MA0131.1 0.599
MA0135.1 0.0695
MA0136.1 1.58515e-5
MA0137.2 0.717
MA0138.2 0.0491
MA0139.1 0.058
MA0140.1 2.43632e-5
MA0141.1 0.00413
MA0142.1 0.199
MA0143.1 0.157
MA0144.1 0.299
MA0145.1 0.0281
MA0146.1 0.461
MA0147.1 0.642
MA0148.1 0.0142
MA0149.1 0.506
MA0150.1 0.18
MA0152.1 0.534
MA0153.1 8.10987e-12
MA0154.1 0.00556
MA0155.1 0.437
MA0156.1 0.00472
MA0157.1 0.0868
MA0159.1 0.307
MA0160.1 0.0834
MA0162.1 0.298
MA0163.1 0.0083
MA0164.1 0.782
MA0258.1 0.01
MA0259.1 0.823



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: CNhs13081
Novel motif P-value
1 0.117
10 0.114
100 0.986
101 0.853
102 0.956
103 0.137
104 0.977
105 0.0687
106 0.0247
107 0.0485
108 0.973
109 0.0515
11 0.142
110 0.212
111 0.00828
112 0.0362
113 0.372
114 0.0256
115 0.338
116 0.537
117 0.627
118 0.464
119 0.046
12 0.484
120 0.951
121 0.241
122 0.371
123 0.451
124 0.722
125 0.68
126 0.373
127 0.189
128 0.0274
129 0.167
13 0.0525
130 0.498
131 0.795
132 0.351
133 0.979
134 0.945
135 0.773
136 0.954
137 0.419
138 0.703
139 0.0786
14 0.371
140 0.0134
141 0.108
142 0.893
143 0.996
144 0.999
145 0.511
146 0.606
147 0.82
148 0.645
149 0.19
15 0.106
150 0.381
151 0.297
152 0.18
153 0.986
154 0.922
155 0.885
156 6.70479e-8
157 0.351
158 0.522
159 0.11
160 0.0967
161 0.293
162 0.627
163 0.817
164 0.172
165 0.254
166 0.826
167 0.483
168 0.812
169 0.0187
17 0.0984
18 0.972
19 0.258
2 0.527
20 0.795
21 0.28
22 0.278
23 0.234
24 0.22
25 0.398
26 0.0686
27 0.291
28 0.355
29 0.776
3 0.134
30 0.529
31 0.817
32 0.0804
33 0.423
34 0.293
35 0.968
36 0.611
37 0.0927
38 0.212
39 0.399
4 0.667
40 0.515
41 0.669
42 0.33
43 0.224
44 0.165
45 0.299
46 0.244
47 0.237
48 0.138
49 0.131
5 0.21
50 0.629
51 0.518
52 0.285
53 0.309
54 0.584
55 0.97
56 0.66
57 0.826
58 0.0794
59 0.0608
6 0.68
60 0.0803
61 0.438
62 0.0408
63 0.112
64 0.457
65 0.149
66 0.538
67 0.916
68 0.525
69 0.998
7 0.0787
70 0.00414
71 0.25
72 0.284
73 0.35
74 0.967
75 0.227
76 0.786
77 0.226
78 0.108
79 0.349
8 0.14
80 0.546
81 0.545
82 0.026
83 0.241
84 0.472
85 0.129
86 0.424
87 0.44
88 0.865
89 0.013
9 0.481
90 0.942
91 0.354
92 0.166
93 0.336
94 0.519
95 0.217
96 0.327
97 0.465
98 0.11
99 0.311



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: CNhs13081


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)
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)