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FF:11809-124D9

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Name:neurospheres - parasympathetic neuron derived, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs13086
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 numberpara3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005235
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13086 CAGE DRX008867 DRR009739
Accession ID Mm9

Library idBAMCTSS
CNhs13086 DRZ001164 DRZ002549
Accession ID Mm10

Library idBAMCTSS
CNhs13086 DRZ012514 DRZ013899
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

CNhs13086

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -0.0749
1002 -0.116
1003 -0.118
1004 0
1005 -0.101
1006 -0.0376
1007 0.121
1008 0
1009 0.00729
101 -0.0159
1010 0
1011 -0.108
1012 0
1013 -0.123
1014 -0.0851
1015 0.213
1016 0.442
1017 0
1018 0
1019 0
102 0
1020 0.431
1021 0.198
1022 -0.14
1023 0
1024 -0.0313
1025 -0.0525
1026 0
1027 0.267
1028 0
1029 -0.115
103 -0.0848
1030 0
1031 0.383
1032 0.0944
1033 0.148
1034 0
1035 0
1036 -0.0746
1037 0
1038 0.0604
1039 -0.17
104 0
1040 0.103
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: CNhs13086
Jaspar motif P-value
MA0002.2 0.00263
MA0003.1 0.053
MA0004.1 0.982
MA0006.1 0.347
MA0007.1 0.617
MA0009.1 0.0363
MA0014.1 0.761
MA0017.1 7.01846e-4
MA0018.2 6.51267e-5
MA0019.1 0.944
MA0024.1 0.0374
MA0025.1 0.634
MA0027.1 0.961
MA0028.1 0.611
MA0029.1 0.572
MA0030.1 0.608
MA0031.1 0.579
MA0035.2 0.006
MA0038.1 0.441
MA0039.2 0.386
MA0040.1 0.943
MA0041.1 0.124
MA0042.1 0.509
MA0043.1 0.0101
MA0046.1 1.03915e-6
MA0047.2 0.0452
MA0048.1 0.883
MA0050.1 0.00316
MA0051.1 0.00936
MA0052.1 0.0712
MA0055.1 0.75
MA0057.1 0.263
MA0058.1 0.737
MA0059.1 0.172
MA0060.1 3.74419e-4
MA0061.1 0.0486
MA0062.2 0.767
MA0065.2 2.67924e-4
MA0066.1 0.213
MA0067.1 0.257
MA0068.1 0.338
MA0069.1 0.448
MA0070.1 0.0269
MA0071.1 0.279
MA0072.1 0.6
MA0073.1 0.941
MA0074.1 0.625
MA0076.1 0.244
MA0077.1 0.0264
MA0078.1 0.059
MA0079.2 0.244
MA0080.2 1.4951e-7
MA0081.1 0.747
MA0083.1 0.4
MA0084.1 0.72
MA0087.1 0.579
MA0088.1 0.837
MA0090.1 0.728
MA0091.1 0.911
MA0092.1 0.749
MA0093.1 0.936
MA0099.2 0.351
MA0100.1 0.554
MA0101.1 0.326
MA0102.2 0.759
MA0103.1 3.05695e-4
MA0104.2 0.834
MA0105.1 3.2462e-5
MA0106.1 0.671
MA0107.1 0.136
MA0108.2 0.116
MA0111.1 0.985
MA0112.2 4.1254e-5
MA0113.1 0.443
MA0114.1 4.37954e-4
MA0115.1 0.27
MA0116.1 7.7378e-4
MA0117.1 0.831
MA0119.1 0.11
MA0122.1 0.866
MA0124.1 0.877
MA0125.1 0.0803
MA0131.1 0.587
MA0135.1 0.332
MA0136.1 3.39243e-5
MA0137.2 0.467
MA0138.2 0.0827
MA0139.1 0.0245
MA0140.1 0.00695
MA0141.1 0.00632
MA0142.1 0.19
MA0143.1 0.0316
MA0144.1 0.667
MA0145.1 0.123
MA0146.1 0.641
MA0147.1 0.608
MA0148.1 0.0558
MA0149.1 0.741
MA0150.1 0.276
MA0152.1 0.796
MA0153.1 4.01314e-5
MA0154.1 0.00529
MA0155.1 0.554
MA0156.1 0.00762
MA0157.1 0.0657
MA0159.1 0.193
MA0160.1 0.158
MA0162.1 0.172
MA0163.1 0.00127
MA0164.1 0.886
MA0258.1 0.0292
MA0259.1 0.992



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: CNhs13086
Novel motif P-value
1 0.103
10 0.0603
100 0.911
101 0.709
102 0.836
103 0.0161
104 0.859
105 0.307
106 0.0392
107 0.114
108 0.744
109 0.0254
11 0.0643
110 0.149
111 0.00398
112 0.0567
113 0.647
114 0.0424
115 0.324
116 0.484
117 0.239
118 0.522
119 0.0343
12 0.704
120 0.437
121 0.177
122 0.328
123 0.617
124 0.774
125 0.907
126 0.35
127 0.5
128 0.0701
129 0.0866
13 0.0306
130 0.65
131 0.975
132 0.378
133 0.673
134 0.598
135 0.585
136 0.793
137 0.415
138 0.71
139 0.17
14 0.536
140 0.0402
141 0.112
142 0.589
143 0.867
144 0.645
145 0.233
146 0.582
147 0.753
148 0.536
149 0.118
15 0.0851
150 0.489
151 0.441
152 0.127
153 0.605
154 0.711
155 0.716
156 0.00188
157 0.254
158 0.676
159 0.0549
160 0.164
161 0.412
162 0.898
163 0.404
164 0.118
165 0.173
166 0.642
167 0.892
168 0.716
169 0.0131
17 0.0401
18 0.745
19 0.117
2 0.506
20 0.828
21 0.489
22 0.416
23 0.325
24 0.257
25 0.365
26 0.0447
27 0.245
28 0.582
29 0.274
3 0.0723
30 0.763
31 0.854
32 0.104
33 0.382
34 0.495
35 0.551
36 0.196
37 0.0706
38 0.253
39 0.457
4 0.739
40 0.341
41 0.912
42 0.246
43 0.173
44 0.11
45 0.521
46 0.158
47 0.118
48 0.161
49 0.164
5 0.174
50 0.739
51 0.465
52 0.319
53 0.489
54 0.545
55 0.554
56 0.517
57 0.251
58 0.0951
59 0.0461
6 0.799
60 0.12
61 0.329
62 0.0275
63 0.164
64 0.368
65 0.141
66 0.352
67 0.957
68 0.484
69 0.915
7 0.103
70 0.00924
71 0.0751
72 0.474
73 0.153
74 0.177
75 0.118
76 0.96
77 0.213
78 0.0536
79 0.108
8 0.097
80 0.703
81 0.451
82 0.0313
83 0.236
84 0.901
85 0.0246
86 0.345
87 0.408
88 0.519
89 0.0625
9 0.509
90 0.183
91 0.222
92 0.0568
93 0.292
94 0.218
95 0.124
96 0.33
97 0.939
98 0.163
99 0.157



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: CNhs13086


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)
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)