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FF:11808-124D8

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Name:neurospheres - parasympathetic neuron derived, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
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 numberpara2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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

CNhs13085

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.00311
10 0
100 0
1000 --0.0279
1001 0.00433
1002 --0.101
1003 --0.0687
1004 0
1005 --0.0666
1006 --0.074
1007 0.0353
1008 0
1009 --0.0399
101 0.0119
1010 0
1011 --0.012
1012 0
1013 --0.118
1014 0
1015 0.205
1016 0.456
1017 0
1018 0
1019 0
102 0
1020 0.277
1021 0.16
1022 --0.177
1023 0
1024 0
1025 --0.0611
1026 0
1027 0.444
1028 0
1029 --0.0228
103 --0.0787
1030 0
1031 0.385
1032 0.117
1033 0.0874
1034 0
1035 0
1036 --0.0061
1037 0
1038 0.0344
1039 --0.29
104 0
1040 0.159
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
no result for this sample


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: CNhs13085

Jaspar motif P-value
MA0002.2 0.00206
MA0003.1 0.00358
MA0004.1 0.854
MA0006.1 0.275
MA0007.1 0.816
MA0009.1 0.0397
MA0014.1 0.805
MA0017.1 3.58791e-5
MA0018.2 9.13955e-4
MA0019.1 0.878
MA0024.1 0.0254
MA0025.1 0.504
MA0027.1 0.664
MA0028.1 0.24
MA0029.1 0.286
MA0030.1 0.915
MA0031.1 0.185
MA0035.2 2.70397e-4
MA0038.1 0.375
MA0039.2 0.268
MA0040.1 0.662
MA0041.1 0.0545
MA0042.1 0.798
MA0043.1 0.0398
MA0046.1 1.11785e-17
MA0047.2 0.00352
MA0048.1 0.742
MA0050.1 0.00303
MA0051.1 0.00394
MA0052.1 0.00294
MA0055.1 0.842
MA0057.1 0.154
MA0058.1 0.527
MA0059.1 0.357
MA0060.1 0.0011
MA0061.1 0.0448
MA0062.2 0.46
MA0065.2 4.18308e-5
MA0066.1 0.596
MA0067.1 0.272
MA0068.1 0.533
MA0069.1 0.401
MA0070.1 0.0195
MA0071.1 0.156
MA0072.1 0.459
MA0073.1 0.988
MA0074.1 0.642
MA0076.1 0.124
MA0077.1 0.0307
MA0078.1 0.157
MA0079.2 0.295
MA0080.2 4.9489e-8
MA0081.1 0.737
MA0083.1 0.0994
MA0084.1 0.92
MA0087.1 0.53
MA0088.1 0.661
MA0090.1 0.994
MA0091.1 0.841
MA0092.1 0.72
MA0093.1 0.745
MA0099.2 0.347
MA0100.1 0.472
MA0101.1 0.26
MA0102.2 0.874
MA0103.1 2.26963e-4
MA0104.2 0.963
MA0105.1 4.96889e-5
MA0106.1 0.13
MA0107.1 0.0952
MA0108.2 0.0129
MA0111.1 0.8
MA0112.2 9.57361e-5
MA0113.1 0.286
MA0114.1 7.00781e-5
MA0115.1 0.143
MA0116.1 9.73195e-4
MA0117.1 0.739
MA0119.1 0.0971
MA0122.1 0.9
MA0124.1 0.664
MA0125.1 0.181
MA0131.1 0.337
MA0135.1 0.556
MA0136.1 4.24004e-5
MA0137.2 0.465
MA0138.2 0.0115
MA0139.1 0.021
MA0140.1 3.79431e-4
MA0141.1 0.00653
MA0142.1 0.0966
MA0143.1 0.123
MA0144.1 0.697
MA0145.1 0.11
MA0146.1 0.669
MA0147.1 0.786
MA0148.1 0.00448
MA0149.1 0.417
MA0150.1 0.187
MA0152.1 0.915
MA0153.1 2.60193e-11
MA0154.1 0.00487
MA0155.1 0.668
MA0156.1 0.00559
MA0157.1 0.0253
MA0159.1 0.363
MA0160.1 0.0689
MA0162.1 0.185
MA0163.1 0.0131
MA0164.1 0.5
MA0258.1 0.023
MA0259.1 0.723



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: CNhs13085

Novel motif P-value
1 0.158
10 0.151
100 0.715
101 0.785
102 0.746
103 0.0886
104 0.986
105 0.104
106 0.0183
107 0.0904
108 0.79
109 0.0748
11 0.0918
110 0.302
111 0.019
112 0.0488
113 0.377
114 0.0423
115 0.378
116 0.545
117 0.528
118 0.57
119 0.0508
12 0.512
120 0.44
121 0.0841
122 0.603
123 0.829
124 0.732
125 0.704
126 0.309
127 0.427
128 0.0247
129 0.0796
13 0.1
130 0.609
131 0.425
132 0.374
133 0.281
134 0.736
135 0.316
136 0.752
137 0.372
138 0.376
139 0.163
14 0.402
140 0.0315
141 0.168
142 0.52
143 0.903
144 0.54
145 0.391
146 0.544
147 0.884
148 0.707
149 0.152
15 0.0991
150 0.617
151 0.334
152 0.0941
153 0.69
154 0.682
155 0.787
156 1.43764e-4
157 0.275
158 0.811
159 0.329
160 0.112
161 0.78
162 0.925
163 0.311
164 0.137
165 0.134
166 0.759
167 0.567
168 0.96
169 0.00958
17 0.0597
18 0.644
19 0.111
2 0.429
20 0.988
21 0.365
22 0.447
23 0.313
24 0.435
25 0.323
26 0.0563
27 0.234
28 0.591
29 0.676
3 0.119
30 0.59
31 0.757
32 0.105
33 0.371
34 0.365
35 0.534
36 0.614
37 0.146
38 0.27
39 0.353
4 0.738
40 0.415
41 0.739
42 0.296
43 0.249
44 0.349
45 0.391
46 0.219
47 0.164
48 0.2
49 0.182
5 0.233
50 0.831
51 0.49
52 0.224
53 0.342
54 0.555
55 0.568
56 0.618
57 0.417
58 0.0723
59 0.0282
6 0.998
60 0.0858
61 0.435
62 0.032
63 0.211
64 0.477
65 0.178
66 0.52
67 0.718
68 0.629
69 0.808
7 0.102
70 0.0304
71 0.147
72 0.462
73 0.212
74 0.222
75 0.236
76 0.839
77 0.258
78 0.0883
79 0.277
8 0.103
80 0.387
81 0.614
82 0.0306
83 0.161
84 0.506
85 0.0794
86 0.341
87 0.587
88 0.498
89 0.0603
9 0.375
90 0.73
91 0.227
92 0.0696
93 0.494
94 0.194
95 0.249
96 0.277
97 0.802
98 0.0835
99 0.109



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: CNhs13085


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)
0000003 (native cell)
0000540 (neuron)
0000055 (non-terminally differentiated cell)
0000047 (neuronal stem cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000034 (stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002319 (neural cell)
0000221 (ectodermal cell)
0000393 (electrically responsive cell)
0000031 (neuroblast)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000107 (autonomic neuron)
0000133 (neurectodermal cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000479 (tissue)
0000073 (regional part of nervous system)
0002410 (autonomic nervous system)
0004121 (ectoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0005291 (embryonic tissue)
0006598 (presumptive structure)
0002532 (epiblast (generic))
0001017 (central nervous system)
0000010 (peripheral nervous system)
0000011 (parasympathetic nervous system)
0001016 (nervous system)
0000924 (ectoderm)
0006601 (presumptive ectoderm)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA