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FF:11770-123I6

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Name:Mouse Neurons - substantia nigra, donor6
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesubstantia nigra
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companySciencell/3H
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNASUB2
catalog numbercustom
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs12643

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.712
10 0
100 0
1000 0
1001 0.0932
1002 0
1003 0.118
1004 0
1005 0
1006 0.566
1007 --0.0812
1008 0
1009 --0.128
101 --0.138
1010 0
1011 0.311
1012 0.164
1013 0.186
1014 0.152
1015 --0.0629
1016 --0.056
1017 0
1018 0
1019 0
102 0
1020 0.574
1021 0.0131
1022 0.0688
1023 0
1024 0
1025 6.239854e-4
1026 0
1027 0.427
1028 0
1029 --0.013
103 --0.0709
1030 0
1031 --0.374
1032 0.52
1033 0.0406
1034 0
1035 0
1036 --0.183
1037 0
1038 --0.04
1039 0.134
104 0
1040 --0.258
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: CNhs12643

Jaspar motif P-value
MA0002.2 9.93509e-4
MA0003.1 0.328
MA0004.1 0.523
MA0006.1 0.185
MA0007.1 0.36
MA0009.1 0.912
MA0014.1 0.774
MA0017.1 4.82693e-7
MA0018.2 0.0315
MA0019.1 0.521
MA0024.1 0.0599
MA0025.1 0.00715
MA0027.1 0.0473
MA0028.1 0.0628
MA0029.1 1
MA0030.1 0.943
MA0031.1 0.189
MA0035.2 0.00967
MA0038.1 0.831
MA0039.2 0.0151
MA0040.1 0.25
MA0041.1 0.0938
MA0042.1 0.248
MA0043.1 0.189
MA0046.1 6.41334e-11
MA0047.2 6.07714e-4
MA0048.1 0.0442
MA0050.1 7.23053e-5
MA0051.1 7.21684e-4
MA0052.1 0.131
MA0055.1 0.0136
MA0057.1 0.278
MA0058.1 0.556
MA0059.1 0.263
MA0060.1 0.604
MA0061.1 0.0246
MA0062.2 3.65343e-4
MA0065.2 7.15793e-6
MA0066.1 0.0469
MA0067.1 0.348
MA0068.1 0.654
MA0069.1 0.108
MA0070.1 0.499
MA0071.1 0.088
MA0072.1 0.294
MA0073.1 0.926
MA0074.1 0.135
MA0076.1 0.151
MA0077.1 0.278
MA0078.1 0.802
MA0079.2 0.362
MA0080.2 1.06297e-10
MA0081.1 0.114
MA0083.1 0.00183
MA0084.1 0.568
MA0087.1 0.102
MA0088.1 0.272
MA0090.1 0.141
MA0091.1 0.137
MA0092.1 0.131
MA0093.1 0.592
MA0099.2 5.54619e-4
MA0100.1 0.232
MA0101.1 0.0103
MA0102.2 0.636
MA0103.1 0.183
MA0104.2 0.855
MA0105.1 0.00752
MA0106.1 0.0675
MA0107.1 0.0228
MA0108.2 0.00125
MA0111.1 0.95
MA0112.2 5.79976e-4
MA0113.1 0.254
MA0114.1 5.57156e-6
MA0115.1 9.06248e-5
MA0116.1 0.0911
MA0117.1 0.926
MA0119.1 0.109
MA0122.1 0.805
MA0124.1 0.602
MA0125.1 0.0357
MA0131.1 0.651
MA0135.1 0.856
MA0136.1 9.89907e-14
MA0137.2 0.0805
MA0138.2 9.90491e-4
MA0139.1 0.586
MA0140.1 1.25481e-4
MA0141.1 0.0119
MA0142.1 0.404
MA0143.1 0.879
MA0144.1 0.0545
MA0145.1 0.0874
MA0146.1 0.0367
MA0147.1 0.734
MA0148.1 5.12605e-4
MA0149.1 0.323
MA0150.1 0.14
MA0152.1 0.132
MA0153.1 3.81474e-12
MA0154.1 0.0467
MA0155.1 0.526
MA0156.1 5.23522e-10
MA0157.1 0.157
MA0159.1 0.00777
MA0160.1 0.0166
MA0162.1 0.241
MA0163.1 0.00347
MA0164.1 0.888
MA0258.1 0.0152
MA0259.1 0.835



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: CNhs12643

Novel motif P-value
1 0.206
10 0.0606
100 0.337
101 0.991
102 0.915
103 0.115
104 0.882
105 0.358
106 0.0466
107 0.108
108 0.499
109 0.0124
11 0.0896
110 0.0472
111 0.331
112 0.0093
113 0.664
114 0.521
115 0.675
116 0.435
117 0.00299
118 0.59
119 0.194
12 0.903
120 0.945
121 0.18
122 0.886
123 3.88617e-4
124 0.132
125 0.155
126 0.0504
127 0.46
128 0.0355
129 0.222
13 8.80261e-8
130 0.115
131 0.471
132 0.491
133 0.599
134 0.135
135 0.369
136 0.183
137 0.481
138 0.873
139 0.505
14 0.936
140 0.171
141 0.752
142 0.641
143 0.323
144 0.634
145 2.94738e-4
146 0.23
147 0.161
148 0.964
149 0.703
15 0.206
150 0.0773
151 0.881
152 0.111
153 0.618
154 0.652
155 0.343
156 0.419
157 0.101
158 0.0954
159 0.717
160 0.289
161 0.176
162 0.638
163 0.801
164 0.0308
165 0.276
166 0.513
167 0.545
168 0.533
169 0.00218
17 0.0594
18 0.813
19 0.0846
2 0.707
20 0.0475
21 0.229
22 0.139
23 0.567
24 0.069
25 0.748
26 2.3136e-8
27 0.47
28 0.721
29 0.0382
3 0.0909
30 0.833
31 0.659
32 0.821
33 0.111
34 0.728
35 0.714
36 0.2
37 0.0371
38 0.368
39 0.431
4 0.261
40 0.11
41 0.431
42 0.186
43 0.123
44 0.982
45 0.665
46 0.0444
47 0.379
48 0.25
49 0.173
5 0.191
50 0.247
51 0.739
52 0.319
53 0.641
54 0.856
55 0.907
56 0.503
57 0.625
58 0.291
59 0.179
6 0.975
60 0.0308
61 0.0548
62 0.178
63 0.152
64 0.67
65 0.333
66 0.708
67 0.817
68 0.845
69 0.586
7 0.0136
70 0.178
71 0.00293
72 0.486
73 0.0521
74 0.956
75 0.0487
76 0.422
77 0.529
78 0.00122
79 0.0224
8 0.0819
80 0.965
81 0.708
82 0.264
83 0.0658
84 0.865
85 0.163
86 0.153
87 0.282
88 0.516
89 0.619
9 0.345
90 0.202
91 0.108
92 0.413
93 0.0143
94 0.65
95 0.0633
96 0.208
97 0.889
98 0.601
99 0.491



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: CNhs12643


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000117 (CNS neuron (sensu Vertebrata))
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000337 (neuroblast (sensu Vertebrata))
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000125 (neural nucleus)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001891 (midbrain)
0001893 (telencephalon)
0002020 (gray matter)
0002038 (substantia nigra)
0002050 (embryonic structure)
0002298 (brainstem)
0002308 (nucleus of brain)
0002346 (neurectoderm)
0002420 (basal ganglion)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0002950 (regional part of midbrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003528 (brain grey matter)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006331 (brainstem nucleus)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

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