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FF:630-43F1

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Name:corpus striatum, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11226
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 stage0 day neonate
sexmixture
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  SAMD00005145
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11226 CAGE DRX008946 DRR009820
Accession ID Mm9

Library idBAMCTSS
CNhs11226 DRZ001245 DRZ002628
Accession ID Mm10

Library idBAMCTSS
CNhs11226 DRZ012595 DRZ013978
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

CNhs11226

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.452
10 0
100 0.329
1000 0
1001 -0.0668
1002 0.101
1003 0.0216
1004 0
1005 0
1006 0.459
1007 0.0964
1008 0
1009 -0.2
101 0.00721
1010 0
1011 0.559
1012 0.329
1013 -0.0225
1014 -0.0851
1015 0.338
1016 0.183
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 -0.103
1023 0
1024 -0.0882
1025 -0.0611
1026 0
1027 0.479
1028 0
1029 0.078
103 -0.0887
1030 0
1031 -0.481
1032 -0.112
1033 0
1034 0
1035 0
1036 -0.131
1037 0
1038 0.124
1039 -0.178
104 0
1040 -0.268
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: CNhs11226
Jaspar motif P-value
MA0002.2 5.96898e-4
MA0003.1 0.161
MA0004.1 0.806
MA0006.1 0.0842
MA0007.1 0.251
MA0009.1 0.905
MA0014.1 0.458
MA0017.1 3.71339e-6
MA0018.2 0.00463
MA0019.1 0.164
MA0024.1 0.568
MA0025.1 0.363
MA0027.1 0.0939
MA0028.1 0.656
MA0029.1 0.565
MA0030.1 0.196
MA0031.1 0.0196
MA0035.2 0.0327
MA0038.1 0.0971
MA0039.2 0.0254
MA0040.1 0.157
MA0041.1 0.86
MA0042.1 0.612
MA0043.1 0.0218
MA0046.1 7.68877e-14
MA0047.2 2.30883e-6
MA0048.1 0.351
MA0050.1 3.39151e-6
MA0051.1 0.00202
MA0052.1 0.0133
MA0055.1 0.266
MA0057.1 0.127
MA0058.1 0.7
MA0059.1 0.538
MA0060.1 0.0133
MA0061.1 0.0794
MA0062.2 0.298
MA0065.2 9.13215e-6
MA0066.1 0.125
MA0067.1 0.548
MA0068.1 0.6
MA0069.1 0.119
MA0070.1 0.524
MA0071.1 0.134
MA0072.1 0.124
MA0073.1 0.664
MA0074.1 0.285
MA0076.1 0.709
MA0077.1 0.153
MA0078.1 0.289
MA0079.2 0.638
MA0080.2 4.96795e-11
MA0081.1 0.391
MA0083.1 5.77967e-4
MA0084.1 0.678
MA0087.1 0.906
MA0088.1 0.385
MA0090.1 0.0187
MA0091.1 0.248
MA0092.1 0.199
MA0093.1 0.824
MA0099.2 4.35813e-5
MA0100.1 0.996
MA0101.1 0.094
MA0102.2 0.677
MA0103.1 0.129
MA0104.2 0.498
MA0105.1 0.0764
MA0106.1 0.178
MA0107.1 0.117
MA0108.2 1.74017e-4
MA0111.1 0.926
MA0112.2 2.37158e-4
MA0113.1 0.317
MA0114.1 6.7228e-5
MA0115.1 0.0013
MA0116.1 0.0878
MA0117.1 0.953
MA0119.1 0.113
MA0122.1 0.92
MA0124.1 0.903
MA0125.1 0.133
MA0131.1 0.774
MA0135.1 0.553
MA0136.1 3.11382e-9
MA0137.2 0.145
MA0138.2 0.304
MA0139.1 0.377
MA0140.1 5.94122e-4
MA0141.1 0.00174
MA0142.1 0.039
MA0143.1 0.112
MA0144.1 0.0702
MA0145.1 0.036
MA0146.1 0.0409
MA0147.1 0.609
MA0148.1 2.55932e-6
MA0149.1 0.056
MA0150.1 0.0489
MA0152.1 0.388
MA0153.1 2.9665e-12
MA0154.1 0.0258
MA0155.1 0.556
MA0156.1 3.23932e-5
MA0157.1 0.00864
MA0159.1 6.49223e-4
MA0160.1 0.0132
MA0162.1 0.2
MA0163.1 0.00403
MA0164.1 0.902
MA0258.1 0.00881
MA0259.1 0.406



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: CNhs11226
Novel motif P-value
1 0.181
10 0.149
100 0.733
101 0.941
102 0.941
103 0.128
104 0.972
105 0.167
106 0.00628
107 0.0338
108 0.826
109 0.00511
11 0.0764
110 0.0794
111 0.128
112 0.00433
113 0.774
114 0.231
115 0.723
116 0.383
117 0.0732
118 0.582
119 0.189
12 0.702
120 0.859
121 0.422
122 0.979
123 0.305
124 0.476
125 0.648
126 0.141
127 0.0865
128 0.015
129 0.0803
13 2.89775e-5
130 0.801
131 0.361
132 0.843
133 0.584
134 0.228
135 0.985
136 0.0622
137 0.548
138 0.913
139 0.21
14 0.606
140 0.224
141 0.174
142 0.206
143 0.528
144 0.846
145 0.0182
146 0.286
147 0.903
148 0.356
149 0.101
15 0.154
150 0.124
151 0.419
152 0.0465
153 0.803
154 0.994
155 0.421
156 0.0402
157 0.26
158 0.356
159 0.96
160 0.155
161 0.126
162 0.961
163 0.382
164 0.0803
165 0.00516
166 0.513
167 0.365
168 0.355
169 0.00566
17 0.0184
18 1
19 0.0339
2 0.616
20 0.559
21 0.412
22 0.0795
23 0.226
24 0.0247
25 0.681
26 3.97978e-5
27 0.699
28 0.559
29 0.112
3 0.11
30 0.733
31 0.727
32 0.342
33 0.279
34 0.541
35 0.675
36 0.584
37 0.0166
38 0.414
39 0.184
4 0.538
40 0.199
41 0.659
42 0.342
43 0.131
44 0.446
45 0.47
46 0.173
47 0.213
48 0.181
49 0.202
5 0.164
50 0.231
51 0.621
52 0.101
53 0.76
54 0.602
55 0.8
56 0.338
57 0.726
58 0.285
59 0.0364
6 0.851
60 0.0157
61 0.181
62 0.141
63 0.101
64 0.725
65 0.227
66 0.991
67 0.471
68 0.909
69 0.519
7 0.0358
70 0.0312
71 0.0165
72 0.359
73 0.0223
74 0.388
75 0.12
76 0.933
77 0.163
78 0.00897
79 0.746
8 0.149
80 0.975
81 0.517
82 0.0787
83 0.0172
84 0.776
85 0.0402
86 0.26
87 0.0493
88 0.257
89 0.391
9 0.364
90 0.341
91 0.114
92 0.239
93 0.0361
94 0.855
95 0.0615
96 0.336
97 0.998
98 0.612
99 0.15



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: CNhs11226


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011392 (mouse corpus striatum- neonate N00 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)
FF:0000294 (mouse embryonic day 11 sample)