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FF:11731-123E3

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Name:Mouse Granule cells, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12357
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
tissuebrain
dev stageNA
sexNA
ageNA
cell typeneuron, granule cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMG3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004825
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12357 CAGE DRX008821 DRR009693
Accession ID Mm9

Library idBAMCTSS
CNhs12357 DRZ001118 DRZ002503
Accession ID Mm10

Library idBAMCTSS
CNhs12357 DRZ012468 DRZ013853
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

CNhs12357

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.413
10 0
100 0.494
1000 --0.0355
1001 --0.0749
1002 0.151
1003 0.0974
1004 0
1005 --0.115
1006 0.336
1007 --0.107
1008 0
1009 --0.2
101 --0.197
1010 0
1011 0.227
1012 0
1013 --0.154
1014 0
1015 0.362
1016 0.197
1017 0
1018 0
1019 0
102 0
1020 0.562
1021 0
1022 --0.134
1023 0
1024 --0.247
1025 --0.0611
1026 0
1027 0.184
1028 0
1029 --0.176
103 --0.0848
1030 0
1031 --0.627
1032 0.211
1033 0.0032
1034 0
1035 0
1036 --0.252
1037 0
1038 0.0152
1039 --0.183
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: CNhs12357

Jaspar motif P-value
MA0002.2 0.00349
MA0003.1 0.211
MA0004.1 0.569
MA0006.1 0.0629
MA0007.1 0.162
MA0009.1 0.899
MA0014.1 0.467
MA0017.1 1.45937e-5
MA0018.2 0.0319
MA0019.1 0.387
MA0024.1 0.938
MA0025.1 0.568
MA0027.1 0.729
MA0028.1 0.279
MA0029.1 0.467
MA0030.1 0.378
MA0031.1 0.0463
MA0035.2 0.155
MA0038.1 0.458
MA0039.2 0.00738
MA0040.1 0.548
MA0041.1 0.258
MA0042.1 0.472
MA0043.1 0.161
MA0046.1 2.42967e-7
MA0047.2 4.22493e-4
MA0048.1 0.252
MA0050.1 3.20303e-10
MA0051.1 1.9644e-5
MA0052.1 0.0494
MA0055.1 0.322
MA0057.1 0.147
MA0058.1 0.549
MA0059.1 0.486
MA0060.1 0.0118
MA0061.1 0.0545
MA0062.2 0.0184
MA0065.2 3.13063e-5
MA0066.1 0.207
MA0067.1 0.859
MA0068.1 0.589
MA0069.1 0.107
MA0070.1 0.495
MA0071.1 0.228
MA0072.1 0.205
MA0073.1 0.971
MA0074.1 0.425
MA0076.1 0.713
MA0077.1 0.007
MA0078.1 0.0886
MA0079.2 0.955
MA0080.2 1.29088e-10
MA0081.1 0.214
MA0083.1 0.00362
MA0084.1 0.343
MA0087.1 0.609
MA0088.1 0.182
MA0090.1 0.00756
MA0091.1 0.232
MA0092.1 0.163
MA0093.1 0.583
MA0099.2 6.08273e-5
MA0100.1 0.7
MA0101.1 0.0263
MA0102.2 0.84
MA0103.1 0.229
MA0104.2 0.521
MA0105.1 0.0989
MA0106.1 0.0629
MA0107.1 0.0226
MA0108.2 0.231
MA0111.1 0.87
MA0112.2 1.17131e-4
MA0113.1 0.323
MA0114.1 6.30025e-5
MA0115.1 0.0107
MA0116.1 0.131
MA0117.1 0.671
MA0119.1 0.0712
MA0122.1 0.49
MA0124.1 0.97
MA0125.1 0.185
MA0131.1 0.91
MA0135.1 0.37
MA0136.1 3.7893e-9
MA0137.2 0.0162
MA0138.2 0.0845
MA0139.1 0.426
MA0140.1 0.00273
MA0141.1 0.03
MA0142.1 0.0135
MA0143.1 0.0113
MA0144.1 0.0124
MA0145.1 0.0494
MA0146.1 0.039
MA0147.1 0.54
MA0148.1 3.02231e-6
MA0149.1 0.0817
MA0150.1 0.0282
MA0152.1 0.0866
MA0153.1 1.26413e-6
MA0154.1 0.0225
MA0155.1 0.795
MA0156.1 1.12519e-7
MA0157.1 0.0292
MA0159.1 0.00311
MA0160.1 0.0832
MA0162.1 0.345
MA0163.1 0.00525
MA0164.1 0.833
MA0258.1 0.0143
MA0259.1 0.504



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: CNhs12357

Novel motif P-value
1 0.156
10 0.102
100 0.779
101 0.932
102 0.992
103 0.0767
104 0.987
105 0.135
106 0.00469
107 0.0344
108 0.448
109 0.00272
11 0.0782
110 0.0938
111 0.101
112 0.00373
113 0.908
114 0.481
115 0.639
116 0.482
117 0.0299
118 0.516
119 0.137
12 0.498
120 0.659
121 0.28
122 0.783
123 0.0943
124 0.416
125 0.518
126 0.245
127 0.0462
128 0.0304
129 0.239
13 1.92126e-6
130 0.178
131 0.793
132 0.98
133 0.39
134 0.43
135 0.962
136 0.144
137 0.317
138 0.548
139 0.106
14 0.676
140 0.0639
141 0.319
142 0.0441
143 0.488
144 0.877
145 0.00936
146 0.369
147 0.711
148 0.406
149 0.212
15 0.157
150 0.11
151 0.451
152 0.0262
153 0.702
154 0.64
155 0.843
156 0.0106
157 0.0663
158 0.164
159 0.0356
160 0.331
161 0.481
162 0.708
163 0.421
164 0.0163
165 0.0198
166 0.825
167 0.954
168 0.609
169 0.00482
17 0.0198
18 0.449
19 0.0557
2 0.95
20 0.32
21 0.395
22 0.0918
23 0.362
24 0.0256
25 0.82
26 4.14059e-4
27 0.958
28 0.345
29 0.151
3 0.0777
30 0.663
31 0.849
32 0.523
33 0.165
34 0.557
35 0.381
36 0.487
37 0.0086
38 0.341
39 0.237
4 0.605
40 0.347
41 0.873
42 0.233
43 0.126
44 0.977
45 0.536
46 0.143
47 0.263
48 0.11
49 0.138
5 0.178
50 0.212
51 0.518
52 0.0966
53 0.74
54 0.752
55 0.975
56 0.431
57 0.73
58 0.231
59 0.105
6 0.829
60 0.0117
61 0.155
62 0.118
63 0.109
64 0.952
65 0.317
66 0.851
67 0.882
68 0.184
69 0.651
7 0.0151
70 0.0348
71 0.0132
72 0.418
73 0.0111
74 0.456
75 0.119
76 0.519
77 0.246
78 0.0256
79 0.688
8 0.125
80 0.977
81 0.787
82 0.202
83 0.158
84 0.685
85 0.191
86 0.228
87 0.192
88 0.337
89 0.382
9 0.261
90 0.217
91 0.284
92 0.284
93 0.0727
94 0.867
95 0.0363
96 0.397
97 0.91
98 0.955
99 0.365



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: CNhs12357


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), 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)
0000120 (granule cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000108 (mouse granule cell 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)