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FF:1395-42I2

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Name:cerebellum, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11135
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
tissuecerebellum
dev stage30 days 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  SAMD00005275
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11135 CAGE DRX008942 DRR009816
Accession ID Mm9

Library idBAMCTSS
CNhs11135 DRZ001241 DRZ002624
Accession ID Mm10

Library idBAMCTSS
CNhs11135 DRZ012591 DRZ013974
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

CNhs11135

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.635
10 0
100 0
1000 0.00582
1001 0.0688
1002 --0.104
1003 0.341
1004 0
1005 0.0125
1006 0.767
1007 0.122
1008 0
1009 --0.0572
101 --0.112
1010 0
1011 0.341
1012 0.353
1013 0.167
1014 --0.0874
1015 --0.0754
1016 --0.0483
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.0704
1023 0
1024 0.0341
1025 0
1026 0
1027 0.392
1028 0
1029 0.343
103 --0.0665
1030 0
1031 --0.299
1032 0.286
1033 --0.0526
1034 0
1035 0
1036 --0.183
1037 0
1038 0.221
1039 0.0424
104 0
1040 --0.231
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: CNhs11135

Jaspar motif P-value
MA0002.2 7.78821e-4
MA0003.1 0.208
MA0004.1 0.301
MA0006.1 0.14
MA0007.1 0.434
MA0009.1 0.325
MA0014.1 0.393
MA0017.1 4.14582e-6
MA0018.2 0.0276
MA0019.1 0.471
MA0024.1 0.0825
MA0025.1 0.00829
MA0027.1 0.0273
MA0028.1 0.034
MA0029.1 0.623
MA0030.1 0.511
MA0031.1 0.402
MA0035.2 0.0156
MA0038.1 0.565
MA0039.2 0.00572
MA0040.1 0.34
MA0041.1 0.919
MA0042.1 0.198
MA0043.1 0.278
MA0046.1 3.04348e-12
MA0047.2 6.35817e-4
MA0048.1 0.116
MA0050.1 8.31028e-5
MA0051.1 6.48027e-4
MA0052.1 0.394
MA0055.1 0.0719
MA0057.1 0.263
MA0058.1 0.273
MA0059.1 0.13
MA0060.1 0.329
MA0061.1 0.0109
MA0062.2 6.8731e-5
MA0065.2 1.98177e-6
MA0066.1 0.397
MA0067.1 0.483
MA0068.1 0.625
MA0069.1 0.094
MA0070.1 0.78
MA0071.1 0.943
MA0072.1 0.163
MA0073.1 0.871
MA0074.1 0.152
MA0076.1 0.101
MA0077.1 0.48
MA0078.1 0.948
MA0079.2 0.508
MA0080.2 2.34951e-10
MA0081.1 0.109
MA0083.1 0.00116
MA0084.1 0.988
MA0087.1 0.365
MA0088.1 0.127
MA0090.1 0.042
MA0091.1 0.479
MA0092.1 0.366
MA0093.1 0.329
MA0099.2 7.10762e-5
MA0100.1 0.174
MA0101.1 0.00953
MA0102.2 0.0908
MA0103.1 0.477
MA0104.2 0.72
MA0105.1 0.00252
MA0106.1 0.0517
MA0107.1 0.0151
MA0108.2 2.99667e-9
MA0111.1 0.951
MA0112.2 0.00619
MA0113.1 0.689
MA0114.1 1.10498e-6
MA0115.1 0.00194
MA0116.1 0.0485
MA0117.1 0.86
MA0119.1 0.202
MA0122.1 0.861
MA0124.1 0.8
MA0125.1 0.15
MA0131.1 0.714
MA0135.1 0.943
MA0136.1 8.29967e-16
MA0137.2 0.244
MA0138.2 1.43887e-4
MA0139.1 0.336
MA0140.1 4.05244e-5
MA0141.1 0.0252
MA0142.1 0.971
MA0143.1 0.914
MA0144.1 0.103
MA0145.1 0.119
MA0146.1 0.044
MA0147.1 0.587
MA0148.1 0.00173
MA0149.1 0.131
MA0150.1 0.0672
MA0152.1 0.733
MA0153.1 1.16364e-14
MA0154.1 0.0539
MA0155.1 0.431
MA0156.1 2.40455e-12
MA0157.1 0.192
MA0159.1 0.0164
MA0160.1 0.00926
MA0162.1 0.221
MA0163.1 0.00206
MA0164.1 0.676
MA0258.1 0.118
MA0259.1 0.782



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: CNhs11135

Novel motif P-value
1 0.422
10 0.0725
100 0.582
101 0.633
102 0.776
103 0.0247
104 0.779
105 0.273
106 0.0464
107 0.17
108 0.507
109 0.0065
11 0.212
110 0.0879
111 0.22
112 0.0138
113 0.511
114 0.914
115 0.463
116 0.184
117 0.00738
118 0.409
119 0.223
12 0.81
120 0.822
121 0.368
122 0.855
123 0.0247
124 0.325
125 0.354
126 0.0466
127 0.13
128 0.0397
129 0.197
13 7.14032e-8
130 0.0577
131 0.526
132 0.861
133 0.173
134 0.408
135 0.94
136 0.139
137 0.328
138 0.798
139 0.295
14 0.864
140 0.313
141 0.797
142 0.898
143 0.515
144 0.6
145 9.24022e-5
146 0.429
147 0.121
148 0.836
149 0.8
15 0.211
150 0.0557
151 0.98
152 0.0613
153 0.684
154 0.804
155 0.43
156 0.0669
157 0.302
158 0.285
159 0.491
160 0.297
161 0.681
162 0.839
163 0.992
164 0.0277
165 0.0723
166 0.106
167 0.84
168 0.22
169 0.008
17 0.107
18 0.928
19 0.192
2 0.815
20 0.0433
21 0.163
22 0.193
23 0.597
24 0.0665
25 0.289
26 1.89405e-7
27 0.341
28 0.91
29 0.0153
3 0.0572
30 0.938
31 0.84
32 0.881
33 0.175
34 0.752
35 0.378
36 0.183
37 0.0322
38 0.455
39 0.466
4 0.384
40 0.0489
41 0.266
42 0.216
43 0.162
44 0.257
45 0.668
46 0.0962
47 0.365
48 0.301
49 0.312
5 0.252
50 0.308
51 0.668
52 0.226
53 0.734
54 0.958
55 0.858
56 0.506
57 0.679
58 0.143
59 0.113
6 0.722
60 0.0249
61 0.126
62 0.0869
63 0.237
64 0.966
65 0.361
66 0.598
67 0.732
68 0.677
69 0.554
7 0.00309
70 0.236
71 0.00184
72 0.31
73 0.0355
74 0.862
75 0.0611
76 0.543
77 0.284
78 8.32099e-4
79 0.892
8 0.0642
80 0.917
81 0.862
82 0.469
83 0.3
84 0.424
85 0.428
86 0.225
87 0.178
88 0.788
89 0.431
9 0.49
90 0.231
91 0.346
92 0.212
93 0.063
94 0.827
95 0.0126
96 0.573
97 0.836
98 0.341
99 0.637



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: CNhs11135


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)
0002037 (cerebellum)
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)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011250 (mouse cerebellum- neonate N30 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006215 (rhombic lip)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)