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FF:19-21D8

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Name:corpus striatum, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10487
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecorpus striatum
dev stageadult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00004779
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10487 CAGE DRX008945 DRR009819
Accession ID Mm9

Library idBAMCTSS
CNhs10487 DRZ001244 DRZ002627
Accession ID Mm10

Library idBAMCTSS
CNhs10487 DRZ012594 DRZ013977
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

CNhs10487

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.749
10 0
100 0
1000 0
1001 0.0819
1002 --0.0941
1003 0.103
1004 0
1005 0.125
1006 0.631
1007 0.0436
1008 0
1009 --0.0572
101 --0.057
1010 0
1011 0.948
1012 0.452
1013 0.179
1014 --0.0851
1015 --0.0207
1016 0.00992
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 0.058
1023 0
1024 0.0737
1025 0
1026 0
1027 0.193
1028 0
1029 0.0488
103 --0.0861
1030 0
1031 --0.338
1032 0.203
1033 0
1034 0
1035 0
1036 --0.223
1037 0
1038 --0.059
1039 0.103
104 0
1040 --0.216
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



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: CNhs10487

Jaspar motif P-value
MA0002.2 0.0105
MA0003.1 0.342
MA0004.1 0.59
MA0006.1 0.126
MA0007.1 0.45
MA0009.1 0.885
MA0014.1 0.641
MA0017.1 7.89366e-7
MA0018.2 0.00334
MA0019.1 0.475
MA0024.1 0.0232
MA0025.1 3.19862e-4
MA0027.1 0.0613
MA0028.1 0.044
MA0029.1 0.992
MA0030.1 0.773
MA0031.1 0.21
MA0035.2 0.0268
MA0038.1 0.398
MA0039.2 0.0264
MA0040.1 0.308
MA0041.1 0.0252
MA0042.1 0.225
MA0043.1 0.0214
MA0046.1 1.55268e-9
MA0047.2 5.29828e-4
MA0048.1 0.0238
MA0050.1 0.00191
MA0051.1 0.0399
MA0052.1 0.998
MA0055.1 0.00297
MA0057.1 0.479
MA0058.1 0.476
MA0059.1 0.148
MA0060.1 0.534
MA0061.1 0.0486
MA0062.2 6.40671e-4
MA0065.2 5.59256e-6
MA0066.1 0.0376
MA0067.1 0.522
MA0068.1 0.302
MA0069.1 0.0721
MA0070.1 0.363
MA0071.1 0.0349
MA0072.1 0.363
MA0073.1 0.905
MA0074.1 0.112
MA0076.1 0.103
MA0077.1 0.648
MA0078.1 0.935
MA0079.2 0.342
MA0080.2 6.93201e-10
MA0081.1 0.343
MA0083.1 0.0269
MA0084.1 0.852
MA0087.1 0.257
MA0088.1 0.337
MA0090.1 0.197
MA0091.1 0.148
MA0092.1 0.193
MA0093.1 0.643
MA0099.2 0.00857
MA0100.1 0.259
MA0101.1 0.0202
MA0102.2 0.426
MA0103.1 0.234
MA0104.2 0.909
MA0105.1 0.0173
MA0106.1 0.0477
MA0107.1 0.0598
MA0108.2 9.73762e-4
MA0111.1 0.762
MA0112.2 0.00132
MA0113.1 0.563
MA0114.1 7.01942e-6
MA0115.1 1.40044e-4
MA0116.1 0.0776
MA0117.1 0.928
MA0119.1 0.156
MA0122.1 0.545
MA0124.1 0.364
MA0125.1 0.0328
MA0131.1 0.516
MA0135.1 0.27
MA0136.1 5.5405e-13
MA0137.2 0.132
MA0138.2 4.66998e-5
MA0139.1 0.604
MA0140.1 1.88748e-4
MA0141.1 0.00151
MA0142.1 0.0973
MA0143.1 0.933
MA0144.1 0.0966
MA0145.1 0.191
MA0146.1 0.0176
MA0147.1 0.765
MA0148.1 0.00155
MA0149.1 0.132
MA0150.1 0.182
MA0152.1 0.256
MA0153.1 5.71264e-9
MA0154.1 0.079
MA0155.1 0.503
MA0156.1 2.19603e-8
MA0157.1 0.0919
MA0159.1 0.00248
MA0160.1 0.00441
MA0162.1 0.132
MA0163.1 0.00224
MA0164.1 0.933
MA0258.1 0.0366
MA0259.1 0.841



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: CNhs10487

Novel motif P-value
1 0.209
10 0.048
100 0.304
101 0.485
102 0.947
103 0.106
104 0.97
105 0.794
106 0.102
107 0.264
108 0.576
109 0.00919
11 0.0755
110 0.0612
111 0.196
112 0.00875
113 0.302
114 0.501
115 0.688
116 0.185
117 0.00351
118 0.472
119 0.372
12 0.967
120 0.908
121 0.866
122 0.675
123 4.6079e-4
124 0.0139
125 0.158
126 0.029
127 0.251
128 0.0664
129 0.749
13 6.68914e-8
130 0.149
131 0.66
132 0.491
133 0.687
134 0.0849
135 0.197
136 0.0284
137 0.658
138 0.649
139 0.45
14 0.877
140 0.0952
141 0.822
142 0.71
143 0.429
144 0.795
145 5.11567e-4
146 0.317
147 0.249
148 0.946
149 0.735
15 0.282
150 0.0334
151 0.987
152 0.0859
153 0.875
154 1
155 0.215
156 0.00884
157 0.199
158 0.507
159 0.555
160 0.169
161 0.108
162 0.507
163 0.518
164 0.0532
165 0.106
166 0.822
167 0.779
168 0.433
169 0.0038
17 0.0463
18 0.849
19 0.0855
2 0.665
20 0.0202
21 0.181
22 0.137
23 0.973
24 0.0546
25 0.81
26 4.76458e-8
27 0.417
28 0.766
29 0.0262
3 0.0658
30 0.696
31 0.783
32 0.643
33 0.164
34 0.829
35 0.756
36 0.194
37 0.024
38 0.651
39 0.289
4 0.224
40 0.105
41 0.66
42 0.216
43 0.142
44 0.655
45 0.771
46 0.144
47 0.478
48 0.363
49 0.196
5 0.234
50 0.195
51 0.798
52 0.345
53 0.327
54 0.998
55 0.76
56 0.537
57 0.73
58 0.445
59 0.126
6 0.877
60 0.0549
61 0.0383
62 0.358
63 0.21
64 0.735
65 0.584
66 0.742
67 0.905
68 0.976
69 0.39
7 0.0235
70 0.142
71 0.00469
72 0.46
73 0.0217
74 0.845
75 0.0444
76 0.324
77 0.314
78 0.00111
79 0.768
8 0.0623
80 0.196
81 0.657
82 0.27
83 0.159
84 0.992
85 0.319
86 0.211
87 0.12
88 0.482
89 0.908
9 0.545
90 0.163
91 0.101
92 0.212
93 0.433
94 0.841
95 0.0198
96 0.388
97 0.928
98 0.769
99 0.456



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: CNhs10487


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000955 (brain)
0000369 (corpus striatum)
0002435 (striatum)
0000479 (tissue)
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)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011288 (mouse corpus striatum- adult 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

UBERON:0010082 (future corpus striatum)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)