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FF:11713-123C3

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Name:Mouse Granule cells, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12131
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 numberRNAMG2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005867
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12131 CAGE DRX008820 DRR009692
Accession ID Mm9

Library idBAMCTSS
CNhs12131 DRZ001117 DRZ002502
Accession ID Mm10

Library idBAMCTSS
CNhs12131 DRZ012467 DRZ013852
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

CNhs12131

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.378
10 0
100 0.48
1000 0
1001 --0.0749
1002 0.0437
1003 0.0404
1004 0
1005 --0.191
1006 0.305
1007 0.0237
1008 0
1009 --0.19
101 --0.199
1010 0
1011 0.183
1012 0.08
1013 --0.117
1014 0
1015 0.383
1016 0.299
1017 0
1018 0
1019 0
102 0
1020 0.583
1021 0.0313
1022 --0.0704
1023 0
1024 --0.14
1025 0
1026 0
1027 0.294
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.547
1032 0.0302
1033 0
1034 0
1035 0
1036 --0.217
1037 0
1038 0.0857
1039 --0.196
104 0
1040 --0.171
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: CNhs12131

Jaspar motif P-value
MA0002.2 0.00191
MA0003.1 0.185
MA0004.1 0.618
MA0006.1 0.095
MA0007.1 0.19
MA0009.1 0.888
MA0014.1 0.484
MA0017.1 6.46573e-5
MA0018.2 0.00735
MA0019.1 0.412
MA0024.1 0.59
MA0025.1 0.824
MA0027.1 0.423
MA0028.1 0.504
MA0029.1 0.86
MA0030.1 0.66
MA0031.1 0.0945
MA0035.2 0.177
MA0038.1 0.227
MA0039.2 0.0267
MA0040.1 0.807
MA0041.1 0.189
MA0042.1 0.53
MA0043.1 0.0677
MA0046.1 6.16299e-7
MA0047.2 0.00219
MA0048.1 0.379
MA0050.1 2.79392e-9
MA0051.1 2.05134e-4
MA0052.1 0.0442
MA0055.1 0.469
MA0057.1 0.118
MA0058.1 0.584
MA0059.1 0.365
MA0060.1 9.34294e-5
MA0061.1 0.0529
MA0062.2 0.14
MA0065.2 3.57478e-5
MA0066.1 0.139
MA0067.1 0.75
MA0068.1 0.895
MA0069.1 0.108
MA0070.1 0.139
MA0071.1 0.223
MA0072.1 0.203
MA0073.1 0.939
MA0074.1 0.419
MA0076.1 0.807
MA0077.1 0.00377
MA0078.1 0.0509
MA0079.2 0.558
MA0080.2 2.6858e-10
MA0081.1 0.341
MA0083.1 0.00384
MA0084.1 0.409
MA0087.1 0.332
MA0088.1 0.158
MA0090.1 0.0285
MA0091.1 0.23
MA0092.1 0.183
MA0093.1 0.628
MA0099.2 2.81048e-4
MA0100.1 0.805
MA0101.1 0.098
MA0102.2 0.942
MA0103.1 0.149
MA0104.2 0.687
MA0105.1 0.0304
MA0106.1 0.0942
MA0107.1 0.0701
MA0108.2 0.241
MA0111.1 0.981
MA0112.2 1.18615e-4
MA0113.1 0.221
MA0114.1 1.48614e-4
MA0115.1 0.00957
MA0116.1 0.055
MA0117.1 0.766
MA0119.1 0.0643
MA0122.1 0.465
MA0124.1 0.825
MA0125.1 0.207
MA0131.1 0.815
MA0135.1 0.0852
MA0136.1 6.99451e-8
MA0137.2 0.0182
MA0138.2 0.237
MA0139.1 0.258
MA0140.1 0.00344
MA0141.1 0.0151
MA0142.1 0.02
MA0143.1 0.00992
MA0144.1 0.0224
MA0145.1 0.0509
MA0146.1 0.0576
MA0147.1 0.758
MA0148.1 2.24275e-5
MA0149.1 0.069
MA0150.1 0.0381
MA0152.1 0.0516
MA0153.1 1.91811e-6
MA0154.1 0.0109
MA0155.1 0.665
MA0156.1 2.42299e-5
MA0157.1 0.0336
MA0159.1 0.00276
MA0160.1 0.111
MA0162.1 0.306
MA0163.1 0.00254
MA0164.1 0.759
MA0258.1 0.0127
MA0259.1 0.634



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: CNhs12131

Novel motif P-value
1 0.129
10 0.0842
100 0.74
101 0.8
102 0.915
103 0.0804
104 0.942
105 0.168
106 0.0118
107 0.0427
108 0.391
109 0.00513
11 0.0954
110 0.0876
111 0.0654
112 0.00305
113 0.979
114 0.189
115 0.57
116 0.6
117 0.0433
118 0.405
119 0.0953
12 0.602
120 0.895
121 0.422
122 0.681
123 0.192
124 0.787
125 0.389
126 0.22
127 0.139
128 0.0256
129 0.214
13 1.93392e-5
130 0.379
131 0.499
132 0.916
133 0.374
134 0.36
135 0.704
136 0.276
137 0.212
138 0.612
139 0.109
14 0.622
140 0.0952
141 0.135
142 0.0315
143 0.528
144 0.992
145 0.00844
146 0.434
147 0.892
148 0.492
149 0.124
15 0.138
150 0.165
151 0.405
152 0.047
153 0.576
154 0.613
155 0.8
156 0.00677
157 0.188
158 0.154
159 0.059
160 0.272
161 0.336
162 0.744
163 0.445
164 0.0188
165 0.0377
166 0.655
167 0.956
168 0.603
169 0.00365
17 0.0197
18 0.751
19 0.0548
2 0.86
20 0.44
21 0.488
22 0.111
23 0.25
24 0.0351
25 0.721
26 4.49515e-4
27 0.87
28 0.398
29 0.105
3 0.0646
30 0.757
31 0.906
32 0.459
33 0.16
34 0.578
35 0.607
36 0.316
37 0.0115
38 0.323
39 0.213
4 0.546
40 0.287
41 0.929
42 0.201
43 0.12
44 0.759
45 0.59
46 0.11
47 0.229
48 0.114
49 0.136
5 0.142
50 0.258
51 0.62
52 0.128
53 0.63
54 0.681
55 0.962
56 0.353
57 0.582
58 0.213
59 0.079
6 0.612
60 0.0145
61 0.158
62 0.111
63 0.0981
64 0.88
65 0.261
66 0.712
67 0.688
68 0.209
69 0.527
7 0.0201
70 0.014
71 0.0136
72 0.354
73 0.0227
74 0.235
75 0.107
76 0.637
77 0.211
78 0.0313
79 0.424
8 0.119
80 0.995
81 0.502
82 0.0967
83 0.271
84 0.766
85 0.0568
86 0.262
87 0.314
88 0.326
89 0.277
9 0.287
90 0.134
91 0.289
92 0.2
93 0.0409
94 0.8
95 0.0439
96 0.256
97 0.884
98 0.659
99 0.235



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: CNhs12131


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)