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FF:11807-124D7

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Name:neurospheres - parasympathetic neuron derived, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs13084
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 numberpara1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005929
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13084 CAGE DRX008865 DRR009737
Accession ID Mm9

Library idBAMCTSS
CNhs13084 DRZ001162 DRZ002547
Accession ID Mm10

Library idBAMCTSS
CNhs13084 DRZ012512 DRZ013897
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

CNhs13084

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0356
1002 --0.0986
1003 --0.102
1004 0
1005 --0.0389
1006 --0.09
1007 --0.0036
1008 0
1009 --0.0572
101 0.0203
1010 0
1011 --0.0145
1012 0
1013 --0.066
1014 0
1015 0.133
1016 0.447
1017 0
1018 0
1019 0
102 0
1020 0.386
1021 0.0931
1022 --0.284
1023 0
1024 0
1025 --0.0611
1026 0
1027 0.341
1028 0.0931
1029 --0.0217
103 --0.0754
1030 0
1031 0.377
1032 --0.052
1033 0.17
1034 0
1035 0
1036 0.0254
1037 0
1038 0
1039 --0.293
104 0
1040 0.148
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: CNhs13084

Jaspar motif P-value
MA0002.2 0.00104
MA0003.1 0.00807
MA0004.1 0.619
MA0006.1 0.387
MA0007.1 0.852
MA0009.1 0.0336
MA0014.1 0.669
MA0017.1 3.63867e-5
MA0018.2 0.00971
MA0019.1 0.974
MA0024.1 0.00149
MA0025.1 0.747
MA0027.1 0.732
MA0028.1 0.114
MA0029.1 0.279
MA0030.1 0.794
MA0031.1 0.312
MA0035.2 0.00228
MA0038.1 0.307
MA0039.2 0.296
MA0040.1 0.978
MA0041.1 0.0809
MA0042.1 0.658
MA0043.1 0.163
MA0046.1 3.34815e-18
MA0047.2 0.00213
MA0048.1 0.809
MA0050.1 0.0183
MA0051.1 0.0273
MA0052.1 0.00363
MA0055.1 0.663
MA0057.1 0.19
MA0058.1 0.281
MA0059.1 0.554
MA0060.1 1.72033e-6
MA0061.1 0.0368
MA0062.2 0.14
MA0065.2 2.3043e-5
MA0066.1 0.216
MA0067.1 0.489
MA0068.1 0.41
MA0069.1 0.508
MA0070.1 0.115
MA0071.1 0.263
MA0072.1 0.286
MA0073.1 0.986
MA0074.1 0.973
MA0076.1 0.0555
MA0077.1 0.00516
MA0078.1 0.074
MA0079.2 0.276
MA0080.2 5.49205e-7
MA0081.1 0.975
MA0083.1 0.0915
MA0084.1 0.8
MA0087.1 0.517
MA0088.1 0.725
MA0090.1 0.568
MA0091.1 0.691
MA0092.1 0.627
MA0093.1 0.506
MA0099.2 0.459
MA0100.1 0.28
MA0101.1 0.329
MA0102.2 0.297
MA0103.1 2.28132e-4
MA0104.2 0.859
MA0105.1 1.94939e-5
MA0106.1 0.0925
MA0107.1 0.0978
MA0108.2 7.21559e-4
MA0111.1 0.973
MA0112.2 4.46611e-5
MA0113.1 0.551
MA0114.1 7.84356e-5
MA0115.1 0.113
MA0116.1 2.45625e-4
MA0117.1 0.654
MA0119.1 0.0595
MA0122.1 0.731
MA0124.1 0.585
MA0125.1 0.21
MA0131.1 0.341
MA0135.1 0.778
MA0136.1 0.00196
MA0137.2 0.381
MA0138.2 0.00616
MA0139.1 0.0249
MA0140.1 0.00132
MA0141.1 0.0218
MA0142.1 0.147
MA0143.1 0.06
MA0144.1 0.857
MA0145.1 0.0893
MA0146.1 0.893
MA0147.1 0.843
MA0148.1 0.0128
MA0149.1 0.295
MA0150.1 0.218
MA0152.1 0.89
MA0153.1 7.31059e-13
MA0154.1 0.00169
MA0155.1 0.577
MA0156.1 0.0305
MA0157.1 0.122
MA0159.1 0.397
MA0160.1 0.121
MA0162.1 0.318
MA0163.1 0.00589
MA0164.1 0.886
MA0258.1 0.0268
MA0259.1 0.992



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: CNhs13084

Novel motif P-value
1 0.145
10 0.136
100 0.821
101 0.768
102 0.914
103 0.0815
104 0.884
105 0.0573
106 0.0117
107 0.0325
108 0.918
109 0.104
11 0.116
110 0.3
111 0.0101
112 0.0399
113 0.453
114 0.035
115 0.456
116 0.711
117 0.664
118 0.623
119 0.0621
12 0.479
120 0.696
121 0.252
122 0.44
123 0.678
124 0.578
125 0.644
126 0.253
127 0.462
128 0.00834
129 0.0928
13 0.155
130 0.679
131 0.547
132 0.145
133 0.464
134 0.819
135 0.47
136 0.653
137 0.361
138 0.254
139 0.0688
14 0.39
140 0.00292
141 0.0818
142 0.937
143 0.668
144 0.805
145 0.357
146 0.424
147 0.854
148 0.585
149 0.272
15 0.126
150 0.518
151 0.374
152 0.0973
153 0.583
154 0.616
155 0.863
156 0.368
157 0.512
158 0.736
159 0.366
160 0.181
161 0.602
162 0.909
163 0.823
164 0.139
165 0.258
166 0.478
167 0.549
168 0.704
169 0.0238
17 0.0686
18 0.728
19 0.0814
2 0.326
20 0.997
21 0.36
22 0.563
23 0.345
24 0.415
25 0.347
26 0.0502
27 0.26
28 0.437
29 0.931
3 0.101
30 0.519
31 0.69
32 0.0779
33 0.471
34 0.357
35 0.602
36 0.689
37 0.126
38 0.366
39 0.437
4 0.877
40 0.428
41 0.987
42 0.282
43 0.197
44 0.309
45 0.33
46 0.197
47 0.169
48 0.206
49 0.135
5 0.209
50 0.81
51 0.51
52 0.211
53 0.323
54 0.461
55 0.983
56 0.557
57 0.484
58 0.0617
59 0.0381
6 0.855
60 0.0898
61 0.645
62 0.0211
63 0.15
64 0.395
65 0.23
66 0.431
67 0.792
68 0.505
69 0.734
7 0.126
70 0.0172
71 0.193
72 0.421
73 0.288
74 0.172
75 0.338
76 0.963
77 0.229
78 0.132
79 0.327
8 0.146
80 0.717
81 0.474
82 0.0198
83 0.125
84 0.735
85 0.0673
86 0.372
87 0.35
88 0.512
89 0.0307
9 0.357
90 0.742
91 0.288
92 0.0436
93 0.53
94 0.264
95 0.294
96 0.252
97 0.622
98 0.168
99 0.186



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: CNhs13084


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)
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)
0000011 (parasympathetic 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)
0011143 (mouse neurospheres - parasympathetic 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)