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FF:11489-119E4

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Name:Mouse Neurons - substantia nigra, donor4
Species:Mouse (Mus musculus)
Library ID:CNhs12612,CNhs12821
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
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 numberRNASUB3
catalog numbercustom
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005603
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12612 CAGE DRX008846 DRR009718
CNhs12821 CAGE DRX023598 DRR025993
Accession ID Mm9

Library idBAMCTSS
CNhs12612 DRZ001143 DRZ002528
CNhs12821 DRZ005245 DRZ006035
Accession ID Mm10

Library idBAMCTSS
CNhs12612 DRZ012493 DRZ013878
CNhs12821 DRZ009986 DRZ010650
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

CNhs12612

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.695
10 0
100 0
1000 0
1001 0.0169
1002 -0.0474
1003 0.0735
1004 0
1005 0.0412
1006 0.66
1007 -0.19
1008 0
1009 -0.067
101 -0.216
1010 0
1011 0.281
1012 0
1013 0.111
1014 0
1015 -0.0301
1016 0.00142
1017 0
1018 0
1019 0
102 0
1020 0.546
1021 0.12
1022 0.148
1023 0
1024 0
1025 0
1026 0
1027 0.42
1028 0
1029 -0.148
103 -0.0736
1030 0
1031 -0.378
1032 0.531
1033 0.0626
1034 0
1035 0
1036 -0.0759
1037 0
1038 -0.0327
1039 0.18
104 0
1040 -0.369
1041 0


CNhs12821



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: CNhs12612
Jaspar motif P-value
MA0002.2 0.0127
MA0003.1 0.488
MA0004.1 0.445
MA0006.1 0.193
MA0007.1 0.312
MA0009.1 0.933
MA0014.1 0.824
MA0017.1 3.12378e-6
MA0018.2 0.00288
MA0019.1 0.793
MA0024.1 0.0233
MA0025.1 5.68038e-4
MA0027.1 0.0694
MA0028.1 0.129
MA0029.1 0.851
MA0030.1 0.872
MA0031.1 0.342
MA0035.2 0.0721
MA0038.1 0.916
MA0039.2 0.0514
MA0040.1 0.627
MA0041.1 0.144
MA0042.1 0.309
MA0043.1 0.034
MA0046.1 3.72067e-6
MA0047.2 9.84777e-4
MA0048.1 0.0262
MA0050.1 3.33456e-6
MA0051.1 1.16883e-4
MA0052.1 0.98
MA0055.1 0.0187
MA0057.1 0.396
MA0058.1 0.51
MA0059.1 0.206
MA0060.1 0.797
MA0061.1 0.0143
MA0062.2 0.00355
MA0065.2 2.71854e-5
MA0066.1 0.1
MA0067.1 0.243
MA0068.1 0.983
MA0069.1 0.13
MA0070.1 0.21
MA0071.1 0.402
MA0072.1 0.933
MA0073.1 0.865
MA0074.1 0.242
MA0076.1 0.365
MA0077.1 0.13
MA0078.1 0.94
MA0079.2 0.162
MA0080.2 6.18274e-10
MA0081.1 0.169
MA0083.1 0.00205
MA0084.1 0.423
MA0087.1 0.18
MA0088.1 0.368
MA0090.1 0.0511
MA0091.1 0.226
MA0092.1 0.206
MA0093.1 0.499
MA0099.2 0.0238
MA0100.1 0.0826
MA0101.1 0.00917
MA0102.2 0.458
MA0103.1 0.397
MA0104.2 0.925
MA0105.1 0.00246
MA0106.1 0.0531
MA0107.1 0.0143
MA0108.2 0.00713
MA0111.1 0.971
MA0112.2 0.00161
MA0113.1 0.389
MA0114.1 4.03739e-6
MA0115.1 7.14526e-4
MA0116.1 0.101
MA0117.1 0.854
MA0119.1 0.183
MA0122.1 0.785
MA0124.1 0.633
MA0125.1 0.033
MA0131.1 0.512
MA0135.1 0.0723
MA0136.1 2.59924e-11
MA0137.2 0.0779
MA0138.2 5.07395e-5
MA0139.1 0.77
MA0140.1 7.6329e-5
MA0141.1 0.239
MA0142.1 0.556
MA0143.1 0.854
MA0144.1 0.0351
MA0145.1 0.17
MA0146.1 0.0913
MA0147.1 0.805
MA0148.1 0.00148
MA0149.1 0.408
MA0150.1 0.272
MA0152.1 0.0313
MA0153.1 1.78499e-7
MA0154.1 0.0484
MA0155.1 0.602
MA0156.1 4.04048e-9
MA0157.1 0.229
MA0159.1 0.0297
MA0160.1 0.135
MA0162.1 0.279
MA0163.1 0.00229
MA0164.1 0.854
MA0258.1 0.0499
MA0259.1 0.786

library id: CNhs12821This sample isn't target for the analysis



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: CNhs12612
Novel motif P-value
1 0.273
10 0.0355
100 0.316
101 0.986
102 0.791
103 0.088
104 0.85
105 0.462
106 0.0316
107 0.0762
108 0.312
109 0.0332
11 0.23
110 0.0424
111 0.478
112 0.0121
113 0.6
114 0.836
115 0.88
116 0.638
117 0.00296
118 0.355
119 0.186
12 0.94
120 0.808
121 0.472
122 0.742
123 4.28563e-4
124 0.0815
125 0.188
126 0.065
127 0.503
128 0.016
129 0.231
13 3.41613e-8
130 0.0973
131 0.528
132 0.594
133 0.764
134 0.21
135 0.237
136 0.716
137 0.564
138 0.566
139 0.347
14 0.756
140 0.136
141 0.764
142 0.32
143 0.447
144 0.642
145 7.47928e-5
146 0.433
147 0.241
148 0.761
149 0.718
15 0.175
150 0.0629
151 0.971
152 0.164
153 0.417
154 0.54
155 0.721
156 0.0164
157 0.241
158 0.0887
159 0.178
160 0.216
161 0.652
162 0.739
163 0.762
164 0.0249
165 0.319
166 0.29
167 0.95
168 0.554
169 0.00247
17 0.103
18 0.588
19 0.106
2 0.45
20 0.0156
21 0.322
22 0.211
23 0.651
24 0.112
25 0.875
26 2.269e-10
27 0.192
28 0.864
29 0.0493
3 0.107
30 0.708
31 0.541
32 0.814
33 0.136
34 0.968
35 0.693
36 0.163
37 0.0588
38 0.483
39 0.37
4 0.366
40 0.16
41 0.639
42 0.208
43 0.104
44 0.825
45 0.775
46 0.0248
47 0.615
48 0.433
49 0.137
5 0.166
50 0.298
51 0.651
52 0.299
53 0.488
54 0.951
55 0.97
56 0.659
57 0.539
58 0.309
59 0.289
6 0.748
60 0.0359
61 0.0607
62 0.23
63 0.22
64 0.995
65 0.578
66 0.942
67 0.979
68 0.974
69 0.809
7 0.00931
70 0.269
71 0.00139
72 0.667
73 0.0919
74 0.732
75 0.0618
76 0.286
77 0.775
78 0.00322
79 0.112
8 0.0838
80 0.943
81 0.737
82 0.414
83 0.359
84 0.642
85 0.251
86 0.105
87 0.47
88 0.718
89 0.778
9 0.355
90 0.144
91 0.0842
92 0.468
93 0.0597
94 0.449
95 0.139
96 0.415
97 0.979
98 0.725
99 0.527

library id: CNhs12821This sample isn't target for the analysis



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: CNhs12612
library id: CNhs12821


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)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002038 (substantia nigra)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009663 (telencephalic nucleus)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0009661 (midbrain nucleus)
0000125 (neural nucleus)
0002950 (regional part of midbrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0002308 (nucleus of brain)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0001891 (midbrain)
0010011 (collection of basal ganglia)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000208 (mouse neuron of the substantia nigra 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:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)