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FF:11646-122D8

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Name:Mouse Neurons - striatal, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12111
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
tissuecorpus striatum
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMNS1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005045
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12111 CAGE DRX008845 DRR009717
Accession ID Mm9

Library idBAMCTSS
CNhs12111 DRZ001142 DRZ002527
Accession ID Mm10

Library idBAMCTSS
CNhs12111 DRZ012492 DRZ013877
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

CNhs12111

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.398
10 0
100 0.409
1000 -0.0355
1001 -0.0445
1002 -0.00676
1003 -0.0711
1004 0
1005 -0.0459
1006 0.34
1007 -0.177
1008 0
1009 -0.19
101 -0.155
1010 0
1011 0.152
1012 0
1013 -0.0888
1014 0
1015 0.421
1016 0.164
1017 0
1018 0
1019 0
102 0
1020 0.489
1021 0
1022 -0.124
1023 0
1024 -0.152
1025 0
1026 0
1027 0.319
1028 0
1029 -0.115
103 -0.0829
1030 0
1031 -0.393
1032 -0.0325
1033 0
1034 0
1035 0
1036 -0.115
1037 0
1038 0.0553
1039 -0.323
104 0
1040 -0.254
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: CNhs12111
Jaspar motif P-value
MA0002.2 0.0037
MA0003.1 0.172
MA0004.1 0.645
MA0006.1 0.0787
MA0007.1 0.152
MA0009.1 0.977
MA0014.1 0.407
MA0017.1 3.31809e-5
MA0018.2 0.0193
MA0019.1 0.325
MA0024.1 0.921
MA0025.1 0.213
MA0027.1 0.537
MA0028.1 0.528
MA0029.1 0.811
MA0030.1 0.264
MA0031.1 0.0315
MA0035.2 0.0801
MA0038.1 0.293
MA0039.2 0.00892
MA0040.1 0.471
MA0041.1 0.375
MA0042.1 0.84
MA0043.1 0.132
MA0046.1 6.08913e-9
MA0047.2 5.49351e-4
MA0048.1 0.469
MA0050.1 1.83841e-10
MA0051.1 1.86929e-5
MA0052.1 0.0149
MA0055.1 0.34
MA0057.1 0.102
MA0058.1 0.578
MA0059.1 0.458
MA0060.1 0.00366
MA0061.1 0.0491
MA0062.2 0.0977
MA0065.2 2.65608e-5
MA0066.1 0.233
MA0067.1 0.785
MA0068.1 0.924
MA0069.1 0.127
MA0070.1 0.944
MA0071.1 0.175
MA0072.1 0.126
MA0073.1 0.738
MA0074.1 0.323
MA0076.1 0.91
MA0077.1 0.0128
MA0078.1 0.0511
MA0079.2 0.925
MA0080.2 2.44692e-10
MA0081.1 0.285
MA0083.1 0.00325
MA0084.1 0.8
MA0087.1 0.263
MA0088.1 0.249
MA0090.1 0.00837
MA0091.1 0.171
MA0092.1 0.185
MA0093.1 0.643
MA0099.2 9.15911e-5
MA0100.1 0.965
MA0101.1 0.0285
MA0102.2 0.958
MA0103.1 0.126
MA0104.2 0.572
MA0105.1 0.0698
MA0106.1 0.126
MA0107.1 0.0313
MA0108.2 0.0856
MA0111.1 0.902
MA0112.2 1.52331e-4
MA0113.1 0.245
MA0114.1 7.73243e-5
MA0115.1 0.0168
MA0116.1 0.087
MA0117.1 0.774
MA0119.1 0.04
MA0122.1 0.506
MA0124.1 0.945
MA0125.1 0.0821
MA0131.1 0.889
MA0135.1 0.219
MA0136.1 2.3536e-8
MA0137.2 0.00421
MA0138.2 0.289
MA0139.1 0.27
MA0140.1 0.00353
MA0141.1 0.00534
MA0142.1 0.0168
MA0143.1 0.00625
MA0144.1 0.0101
MA0145.1 0.0374
MA0146.1 0.0399
MA0147.1 0.63
MA0148.1 2.10993e-6
MA0149.1 0.0759
MA0150.1 0.04
MA0152.1 0.107
MA0153.1 1.66945e-8
MA0154.1 0.0174
MA0155.1 0.765
MA0156.1 2.29417e-6
MA0157.1 0.0354
MA0159.1 0.00503
MA0160.1 0.0483
MA0162.1 0.308
MA0163.1 0.00814
MA0164.1 0.94
MA0258.1 0.0138
MA0259.1 0.512



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: CNhs12111
Novel motif P-value
1 0.166
10 0.132
100 0.708
101 0.899
102 0.728
103 0.0713
104 0.829
105 0.188
106 0.00624
107 0.0326
108 0.476
109 0.00171
11 0.0877
110 0.0973
111 0.153
112 0.0136
113 0.952
114 0.275
115 0.995
116 0.436
117 0.0554
118 0.531
119 0.0993
12 0.604
120 0.904
121 0.286
122 0.885
123 0.0999
124 0.959
125 0.452
126 0.133
127 0.129
128 0.038
129 0.224
13 1.45978e-6
130 0.254
131 0.695
132 0.97
133 0.283
134 0.478
135 0.72
136 0.0537
137 0.199
138 0.74
139 0.163
14 0.63
140 0.192
141 0.252
142 0.0635
143 0.528
144 0.902
145 0.0216
146 0.353
147 0.708
148 0.421
149 0.16
15 0.252
150 0.126
151 0.412
152 0.0381
153 0.527
154 0.712
155 0.51
156 0.00393
157 0.0673
158 0.211
159 0.218
160 0.281
161 0.249
162 0.807
163 0.251
164 0.0224
165 0.0445
166 0.972
167 0.805
168 0.763
169 0.00462
17 0.0228
18 0.586
19 0.0501
2 0.842
20 0.492
21 0.558
22 0.0849
23 0.28
24 0.0353
25 0.705
26 3.20157e-4
27 0.796
28 0.317
29 0.156
3 0.0806
30 0.584
31 0.921
32 0.373
33 0.174
34 0.415
35 0.386
36 0.495
37 0.00882
38 0.303
39 0.132
4 0.529
40 0.188
41 0.845
42 0.238
43 0.142
44 0.737
45 0.427
46 0.16
47 0.209
48 0.114
49 0.17
5 0.17
50 0.219
51 0.55
52 0.0882
53 0.676
54 0.642
55 0.915
56 0.366
57 0.724
58 0.266
59 0.0688
6 0.527
60 0.0112
61 0.164
62 0.155
63 0.0821
64 0.902
65 0.259
66 0.843
67 0.903
68 0.626
69 0.517
7 0.0189
70 0.0145
71 0.0179
72 0.335
73 0.0208
74 0.581
75 0.148
76 0.699
77 0.265
78 0.0148
79 0.591
8 0.204
80 0.817
81 0.543
82 0.117
83 0.0586
84 0.97
85 0.0625
86 0.272
87 0.072
88 0.285
89 0.246
9 0.35
90 0.155
91 0.32
92 0.345
93 0.0119
94 0.944
95 0.0229
96 0.32
97 0.8
98 0.793
99 0.237



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: CNhs12111


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)
0002613 (striatum neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0000369 (corpus striatum)
0002435 (striatum)
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)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
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)
0000209 (mouse striatal neuron 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)