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FF:11636-122C7

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Name:Mouse Granule cells, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12108
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 numberRNAMG1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004673
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12108 CAGE DRX008822 DRR009694
Accession ID Mm9

Library idBAMCTSS
CNhs12108 DRZ001119 DRZ002504
Accession ID Mm10

Library idBAMCTSS
CNhs12108 DRZ012469 DRZ013854
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

CNhs12108

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.356
10 0
100 0.441
1000 0
1001 --0.0749
1002 0.00879
1003 --0.102
1004 0
1005 --0.0389
1006 0.243
1007 --0.09
1008 0
1009 --0.19
101 --0.233
1010 0
1011 0.355
1012 0
1013 0.0793
1014 0
1015 0.367
1016 0.315
1017 0
1018 0
1019 0
102 0
1020 0.826
1021 0
1022 --0.0704
1023 0
1024 --0.205
1025 --0.0611
1026 0
1027 0.213
1028 0
1029 --0.176
103 --0.0754
1030 0
1031 --0.333
1032 --0.0798
1033 0.032
1034 0
1035 0
1036 --0.183
1037 0
1038 0.0249
1039 --0.138
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: CNhs12108

Jaspar motif P-value
MA0002.2 0.00637
MA0003.1 0.204
MA0004.1 0.678
MA0006.1 0.0807
MA0007.1 0.106
MA0009.1 0.769
MA0014.1 0.472
MA0017.1 3.68511e-5
MA0018.2 0.013
MA0019.1 0.345
MA0024.1 0.987
MA0025.1 0.833
MA0027.1 0.833
MA0028.1 0.227
MA0029.1 0.857
MA0030.1 0.476
MA0031.1 0.0963
MA0035.2 0.228
MA0038.1 0.511
MA0039.2 0.0184
MA0040.1 0.777
MA0041.1 0.216
MA0042.1 0.454
MA0043.1 0.117
MA0046.1 1.39928e-6
MA0047.2 0.00242
MA0048.1 0.22
MA0050.1 1.53129e-11
MA0051.1 1.01478e-5
MA0052.1 0.0981
MA0055.1 0.322
MA0057.1 0.117
MA0058.1 0.65
MA0059.1 0.463
MA0060.1 0.00366
MA0061.1 0.0478
MA0062.2 0.0175
MA0065.2 9.21863e-5
MA0066.1 0.22
MA0067.1 0.935
MA0068.1 0.991
MA0069.1 0.113
MA0070.1 0.182
MA0071.1 0.309
MA0072.1 0.297
MA0073.1 0.821
MA0074.1 0.37
MA0076.1 0.704
MA0077.1 0.00163
MA0078.1 0.0256
MA0079.2 0.689
MA0080.2 6.44829e-10
MA0081.1 0.302
MA0083.1 0.0199
MA0084.1 0.549
MA0087.1 0.592
MA0088.1 0.113
MA0090.1 0.0226
MA0091.1 0.286
MA0092.1 0.197
MA0093.1 0.683
MA0099.2 2.34104e-4
MA0100.1 0.668
MA0101.1 0.0272
MA0102.2 0.411
MA0103.1 0.255
MA0104.2 0.583
MA0105.1 0.0386
MA0106.1 0.0529
MA0107.1 0.0262
MA0108.2 0.647
MA0111.1 0.861
MA0112.2 1.52346e-4
MA0113.1 0.214
MA0114.1 1.18299e-4
MA0115.1 0.0289
MA0116.1 0.0922
MA0117.1 0.7
MA0119.1 0.0951
MA0122.1 0.754
MA0124.1 0.892
MA0125.1 0.159
MA0131.1 0.943
MA0135.1 0.143
MA0136.1 1.63631e-9
MA0137.2 0.00255
MA0138.2 0.124
MA0139.1 0.402
MA0140.1 0.00655
MA0141.1 0.0153
MA0142.1 0.00324
MA0143.1 0.00259
MA0144.1 0.0086
MA0145.1 0.0702
MA0146.1 0.047
MA0147.1 0.654
MA0148.1 5.61224e-6
MA0149.1 0.109
MA0150.1 0.027
MA0152.1 0.0665
MA0153.1 7.41492e-6
MA0154.1 0.0163
MA0155.1 0.784
MA0156.1 2.16272e-7
MA0157.1 0.0504
MA0159.1 0.00641
MA0160.1 0.0769
MA0162.1 0.328
MA0163.1 0.00721
MA0164.1 0.832
MA0258.1 0.01
MA0259.1 0.515



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: CNhs12108

Novel motif P-value
1 0.147
10 0.0984
100 0.656
101 0.91
102 0.997
103 0.0516
104 0.953
105 0.277
106 0.0104
107 0.0598
108 0.425
109 0.00571
11 0.106
110 0.061
111 0.0548
112 0.00285
113 0.924
114 0.368
115 0.583
116 0.638
117 0.017
118 0.6
119 0.134
12 0.634
120 0.749
121 0.322
122 0.541
123 0.0899
124 0.554
125 0.361
126 0.322
127 0.0888
128 0.0518
129 0.186
13 4.49477e-6
130 0.233
131 0.435
132 0.763
133 0.602
134 0.464
135 0.738
136 0.321
137 0.197
138 0.565
139 0.141
14 0.671
140 0.0135
141 0.239
142 0.00826
143 0.962
144 0.911
145 0.0114
146 0.461
147 0.769
148 0.801
149 0.344
15 0.127
150 0.138
151 0.49
152 0.0507
153 0.555
154 0.581
155 0.645
156 0.0127
157 0.0555
158 0.124
159 0.0361
160 0.29
161 0.328
162 0.681
163 0.437
164 0.00561
165 0.0622
166 0.507
167 0.912
168 0.77
169 0.00368
17 0.0114
18 0.511
19 0.0692
2 0.859
20 0.341
21 0.595
22 0.116
23 0.314
24 0.0342
25 0.663
26 9.6553e-5
27 0.918
28 0.318
29 0.0846
3 0.0602
30 0.849
31 0.896
32 0.56
33 0.143
34 0.675
35 0.479
36 0.35
37 0.0102
38 0.345
39 0.2
4 0.618
40 0.357
41 0.967
42 0.196
43 0.142
44 0.874
45 0.622
46 0.102
47 0.295
48 0.154
49 0.171
5 0.163
50 0.228
51 0.55
52 0.117
53 0.655
54 0.778
55 0.73
56 0.382
57 0.835
58 0.203
59 0.0964
6 0.705
60 0.00878
61 0.168
62 0.116
63 0.109
64 0.787
65 0.331
66 0.691
67 0.908
68 0.108
69 0.757
7 0.0195
70 0.035
71 0.00972
72 0.376
73 0.0219
74 0.618
75 0.0749
76 0.683
77 0.242
78 0.0144
79 0.548
8 0.138
80 0.975
81 0.577
82 0.155
83 0.358
84 0.738
85 0.0928
86 0.225
87 0.309
88 0.193
89 0.321
9 0.409
90 0.077
91 0.538
92 0.295
93 0.0153
94 0.833
95 0.0446
96 0.318
97 0.96
98 0.987
99 0.348



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: CNhs12108


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)