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FF:11490-119E5

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Name:Mouse Neurons - substantia nigra, donor5
Species:Mouse (Mus musculus)
Library ID:CNhs12614,CNhs12923
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 numberRNASUB1
catalog numbercustom
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00004762
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12614 CAGE DRX008847 DRR009719
CNhs12923 CAGE DRX023599 DRR025994
Accession ID Mm9

Library idBAMCTSS
CNhs12614 DRZ001144 DRZ002529
CNhs12923 DRZ005246 DRZ006036
Accession ID Mm10

Library idBAMCTSS
CNhs12614 DRZ012494 DRZ013879
CNhs12923 DRZ009987 DRZ010651
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

CNhs12614

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.694
10 0
100 0
1000 --0.0355
1001 --0.0305
1002 --0.032
1003 --0.0249
1004 0
1005 0
1006 0.687
1007 --0.114
1008 0
1009 --0.19
101 --0.174
1010 0
1011 0.304
1012 0
1013 0.355
1014 0.0653
1015 0.0246
1016 --0.0127
1017 0
1018 0
1019 0
102 0
1020 0.387
1021 0
1022 0.2
1023 0
1024 0
1025 --0.0611
1026 0
1027 0.533
1028 0
1029 --0.176
103 --0.0665
1030 0
1031 --0.27
1032 0.465
1033 0
1034 0
1035 0
1036 --0.184
1037 0
1038 --0.105
1039 0.183
104 0
1040 --0.278
1041 0



CNhs12923



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: CNhs12614

Jaspar motif P-value
MA0002.2 0.00537
MA0003.1 0.435
MA0004.1 0.487
MA0006.1 0.161
MA0007.1 0.292
MA0009.1 0.846
MA0014.1 0.867
MA0017.1 8.3748e-7
MA0018.2 0.00835
MA0019.1 0.497
MA0024.1 0.0109
MA0025.1 0.00112
MA0027.1 0.0768
MA0028.1 0.118
MA0029.1 0.778
MA0030.1 0.585
MA0031.1 0.249
MA0035.2 0.0213
MA0038.1 0.877
MA0039.2 0.0142
MA0040.1 0.294
MA0041.1 0.0966
MA0042.1 0.29
MA0043.1 0.0835
MA0046.1 1.477e-10
MA0047.2 3.39584e-4
MA0048.1 0.0298
MA0050.1 7.6571e-6
MA0051.1 9.39236e-5
MA0052.1 0.612
MA0055.1 0.00803
MA0057.1 0.354
MA0058.1 0.593
MA0059.1 0.325
MA0060.1 0.624
MA0061.1 0.0137
MA0062.2 0.00217
MA0065.2 1.74653e-5
MA0066.1 0.0807
MA0067.1 0.368
MA0068.1 0.531
MA0069.1 0.0499
MA0070.1 0.404
MA0071.1 0.21
MA0072.1 0.215
MA0073.1 0.891
MA0074.1 0.168
MA0076.1 0.306
MA0077.1 0.386
MA0078.1 0.891
MA0079.2 0.41
MA0080.2 2.24086e-10
MA0081.1 0.164
MA0083.1 4.15671e-4
MA0084.1 0.273
MA0087.1 0.132
MA0088.1 0.336
MA0090.1 0.228
MA0091.1 0.121
MA0092.1 0.136
MA0093.1 0.539
MA0099.2 8.06354e-4
MA0100.1 0.317
MA0101.1 0.00305
MA0102.2 0.524
MA0103.1 0.233
MA0104.2 0.976
MA0105.1 0.0111
MA0106.1 0.055
MA0107.1 0.00368
MA0108.2 0.00166
MA0111.1 0.749
MA0112.2 0.002
MA0113.1 0.329
MA0114.1 4.33709e-6
MA0115.1 1.02712e-4
MA0116.1 0.167
MA0117.1 0.884
MA0119.1 0.0709
MA0122.1 0.713
MA0124.1 0.419
MA0125.1 0.0356
MA0131.1 0.546
MA0135.1 0.371
MA0136.1 5.3253e-12
MA0137.2 0.102
MA0138.2 1.6088e-4
MA0139.1 0.719
MA0140.1 2.10689e-4
MA0141.1 0.0683
MA0142.1 0.0275
MA0143.1 0.543
MA0144.1 0.0309
MA0145.1 0.0914
MA0146.1 0.0391
MA0147.1 0.869
MA0148.1 0.0012
MA0149.1 0.465
MA0150.1 0.238
MA0152.1 0.162
MA0153.1 4.75483e-10
MA0154.1 0.0566
MA0155.1 0.658
MA0156.1 2.72807e-9
MA0157.1 0.409
MA0159.1 0.04
MA0160.1 0.0485
MA0162.1 0.374
MA0163.1 0.0066
MA0164.1 0.831
MA0258.1 0.0376
MA0259.1 0.895


library id: CNhs12923This sample isn't target for the analysis



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: CNhs12614

Novel motif P-value
1 0.253
10 0.0705
100 0.44
101 0.837
102 0.659
103 0.278
104 0.771
105 0.489
106 0.0163
107 0.0631
108 0.564
109 0.0261
11 0.186
110 0.0556
111 0.541
112 0.0237
113 0.539
114 0.623
115 0.749
116 0.433
117 0.00284
118 0.578
119 0.176
12 0.945
120 0.895
121 0.136
122 0.722
123 0.00123
124 0.0775
125 0.0952
126 0.0445
127 0.224
128 0.0362
129 0.235
13 3.01285e-8
130 0.0778
131 0.583
132 0.655
133 0.791
134 0.222
135 0.3
136 0.265
137 0.373
138 0.732
139 0.508
14 0.688
140 0.2
141 0.832
142 0.552
143 0.662
144 0.602
145 1.35458e-4
146 0.261
147 0.189
148 0.905
149 0.93
15 0.247
150 0.0655
151 0.977
152 0.113
153 0.552
154 0.727
155 0.417
156 0.0641
157 0.0858
158 0.0748
159 0.0871
160 0.343
161 0.26
162 0.675
163 0.663
164 0.0329
165 0.275
166 0.396
167 0.378
168 0.97
169 0.00231
17 0.0595
18 0.729
19 0.0852
2 0.64
20 0.0233
21 0.267
22 0.134
23 0.469
24 0.0839
25 0.82
26 1.77003e-9
27 0.3
28 0.72
29 0.0182
3 0.127
30 0.824
31 0.56
32 0.907
33 0.159
34 0.847
35 0.463
36 0.52
37 0.0329
38 0.379
39 0.243
4 0.303
40 0.245
41 0.653
42 0.207
43 0.0991
44 0.857
45 0.636
46 0.0558
47 0.521
48 0.354
49 0.169
5 0.156
50 0.18
51 0.829
52 0.272
53 0.433
54 0.785
55 0.746
56 0.562
57 0.663
58 0.366
59 0.268
6 0.869
60 0.0213
61 0.048
62 0.24
63 0.141
64 0.769
65 0.301
66 0.837
67 0.749
68 0.961
69 0.693
7 0.0144
70 0.312
71 0.00249
72 0.608
73 0.0432
74 0.985
75 0.0607
76 0.43
77 0.468
78 3.77131e-4
79 0.054
8 0.135
80 0.982
81 0.659
82 0.368
83 0.128
84 0.894
85 0.14
86 0.14
87 0.97
88 0.451
89 0.709
9 0.306
90 0.227
91 0.0848
92 0.648
93 0.0175
94 0.779
95 0.0503
96 0.262
97 0.86
98 0.588
99 0.544


library id: CNhs12923This sample isn't target for the analysis



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: CNhs12614
library id: CNhs12923


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)
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)