Personal tools

FF:15-8B2

From FANTOM5_SSTAR

Jump to: navigation, search


Name:cerebellum, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10494
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 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  SAMD00004796
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10494 CAGE DRX008941 DRR009815
Accession ID Mm9

Library idBAMCTSS
CNhs10494 DRZ001240 DRZ002623
Accession ID Mm10

Library idBAMCTSS
CNhs10494 DRZ012590 DRZ013973
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

CNhs10494

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.625
10 0
100 0
1000 0
1001 0.0841
1002 --0.116
1003 0.421
1004 0
1005 0.0956
1006 0.633
1007 0.0358
1008 0
1009 --0.0786
101 --0.0672
1010 0
1011 0.538
1012 0.274
1013 0.146
1014 --0.0851
1015 --0.116
1016 --0.195
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0411
1023 0
1024 0
1025 0
1026 0
1027 0.331
1028 0
1029 0.443
103 --0.0848
1030 0
1031 --0.455
1032 0.179
1033 0
1034 0
1035 0.112
1036 --0.165
1037 0
1038 0.128
1039 0.078
104 0
1040 --0.121
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: CNhs10494

Jaspar motif P-value
MA0002.2 0.0056
MA0003.1 0.168
MA0004.1 0.453
MA0006.1 0.112
MA0007.1 0.282
MA0009.1 0.365
MA0014.1 0.593
MA0017.1 4.62134e-6
MA0018.2 0.00425
MA0019.1 0.396
MA0024.1 0.0762
MA0025.1 0.00281
MA0027.1 0.026
MA0028.1 0.0841
MA0029.1 0.419
MA0030.1 0.451
MA0031.1 0.364
MA0035.2 0.00814
MA0038.1 0.916
MA0039.2 0.0166
MA0040.1 0.204
MA0041.1 0.885
MA0042.1 0.126
MA0043.1 0.0512
MA0046.1 1.22011e-11
MA0047.2 6.49894e-4
MA0048.1 0.128
MA0050.1 2.29806e-4
MA0051.1 5.39509e-4
MA0052.1 0.915
MA0055.1 0.106
MA0057.1 0.388
MA0058.1 0.366
MA0059.1 0.151
MA0060.1 0.6
MA0061.1 0.013
MA0062.2 7.91389e-4
MA0065.2 8.69887e-7
MA0066.1 0.278
MA0067.1 0.41
MA0068.1 0.26
MA0069.1 0.0921
MA0070.1 0.469
MA0071.1 0.86
MA0072.1 0.138
MA0073.1 0.8
MA0074.1 0.133
MA0076.1 0.185
MA0077.1 0.581
MA0078.1 0.832
MA0079.2 0.572
MA0080.2 3.58083e-10
MA0081.1 0.157
MA0083.1 7.36482e-4
MA0084.1 0.761
MA0087.1 0.322
MA0088.1 0.238
MA0090.1 0.0911
MA0091.1 0.291
MA0092.1 0.369
MA0093.1 0.499
MA0099.2 3.19839e-4
MA0100.1 0.267
MA0101.1 0.0189
MA0102.2 0.218
MA0103.1 0.336
MA0104.2 0.958
MA0105.1 0.00236
MA0106.1 0.0878
MA0107.1 0.0248
MA0108.2 4.92601e-8
MA0111.1 0.967
MA0112.2 0.00313
MA0113.1 0.735
MA0114.1 2.59382e-6
MA0115.1 0.00137
MA0116.1 0.0467
MA0117.1 0.946
MA0119.1 0.24
MA0122.1 0.941
MA0124.1 0.912
MA0125.1 0.0976
MA0131.1 0.859
MA0135.1 0.678
MA0136.1 1.28944e-14
MA0137.2 0.816
MA0138.2 1.74636e-4
MA0139.1 0.449
MA0140.1 1.69506e-4
MA0141.1 0.0204
MA0142.1 0.763
MA0143.1 0.911
MA0144.1 0.172
MA0145.1 0.118
MA0146.1 0.027
MA0147.1 0.777
MA0148.1 0.00125
MA0149.1 0.253
MA0150.1 0.208
MA0152.1 0.976
MA0153.1 5.11991e-14
MA0154.1 0.0591
MA0155.1 0.336
MA0156.1 1.30176e-10
MA0157.1 0.148
MA0159.1 0.0114
MA0160.1 0.0268
MA0162.1 0.196
MA0163.1 4.69073e-4
MA0164.1 0.849
MA0258.1 0.0969
MA0259.1 0.963



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: CNhs10494

Novel motif P-value
1 0.388
10 0.0799
100 0.604
101 0.918
102 0.77
103 0.0225
104 0.723
105 0.432
106 0.0161
107 0.155
108 0.753
109 0.00497
11 0.143
110 0.101
111 0.185
112 0.00927
113 0.348
114 0.84
115 0.996
116 0.131
117 0.00841
118 0.296
119 0.266
12 0.518
120 0.737
121 0.624
122 0.836
123 0.00752
124 0.36
125 0.341
126 0.0296
127 0.264
128 0.0406
129 0.419
13 1.98187e-7
130 0.0444
131 0.46
132 0.856
133 0.339
134 0.348
135 0.896
136 0.0489
137 0.374
138 0.889
139 0.274
14 0.924
140 0.419
141 0.851
142 0.928
143 0.387
144 0.526
145 1.35507e-4
146 0.388
147 0.206
148 0.98
149 0.719
15 0.243
150 0.0637
151 0.937
152 0.0445
153 0.589
154 0.921
155 0.392
156 0.94
157 0.478
158 0.708
159 0.169
160 0.252
161 0.814
162 0.636
163 0.684
164 0.0387
165 0.0497
166 0.15
167 0.733
168 0.338
169 0.00703
17 0.0654
18 0.929
19 0.195
2 0.968
20 0.055
21 0.144
22 0.176
23 0.542
24 0.0314
25 0.42
26 1.85435e-7
27 0.433
28 0.936
29 0.031
3 0.0711
30 0.888
31 0.848
32 0.644
33 0.193
34 0.677
35 0.479
36 0.141
37 0.0272
38 0.464
39 0.336
4 0.237
40 0.0361
41 0.333
42 0.251
43 0.151
44 0.113
45 0.643
46 0.0842
47 0.32
48 0.276
49 0.276
5 0.322
50 0.267
51 0.645
52 0.19
53 0.679
54 0.951
55 0.702
56 0.434
57 0.688
58 0.228
59 0.0813
6 0.677
60 0.0221
61 0.136
62 0.14
63 0.223
64 0.91
65 0.359
66 0.704
67 0.681
68 0.426
69 0.262
7 0.00675
70 0.169
71 0.0022
72 0.337
73 0.0333
74 0.728
75 0.0582
76 0.645
77 0.228
78 6.73397e-4
79 0.611
8 0.0537
80 0.832
81 0.916
82 0.417
83 0.354
84 0.583
85 0.35
86 0.156
87 0.0461
88 0.849
89 0.539
9 0.436
90 0.113
91 0.317
92 0.152
93 0.459
94 0.601
95 0.02
96 0.613
97 0.93
98 0.673
99 0.478



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: CNhs10494


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)
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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011276 (mouse cerebellum - 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006215 (rhombic lip)
UBERON:0010316 (germ layer / neural crest)