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FF:11738-123F1

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Name:Mouse Neurons - dorsal spinal cord, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12635
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
tissuespinal cord
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNADOR2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004921
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12635 CAGE DRX008835 DRR009707
Accession ID Mm9

Library idBAMCTSS
CNhs12635 DRZ001132 DRZ002517
Accession ID Mm10

Library idBAMCTSS
CNhs12635 DRZ012482 DRZ013867
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs12635

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.554
10 0
100 0.0887
1000 0
1001 -0.0749
1002 0.0151
1003 0.0575
1004 0
1005 0
1006 0.667
1007 -0.223
1008 0
1009 -0.151
101 -0.281
1010 0
1011 0.319
1012 0
1013 0.136
1014 -0.0851
1015 0.214
1016 0.216
1017 0
1018 0
1019 0
102 0
1020 0.452
1021 0.109
1022 -0.0554
1023 0
1024 0
1025 0.048
1026 0
1027 0.269
1028 0
1029 -0.176
103 0
1030 0
1031 -0.222
1032 0.508
1033 -0.0665
1034 0
1035 0
1036 -0.173
1037 0
1038 0.0327
1039 0.112
104 0
1040 -0.293
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs12635
Jaspar motif P-value
MA0002.2 0.00516
MA0003.1 0.548
MA0004.1 0.484
MA0006.1 0.223
MA0007.1 0.218
MA0009.1 0.829
MA0014.1 0.548
MA0017.1 5.10269e-6
MA0018.2 0.0543
MA0019.1 0.841
MA0024.1 0.511
MA0025.1 0.818
MA0027.1 0.262
MA0028.1 0.0371
MA0029.1 0.767
MA0030.1 0.575
MA0031.1 0.0823
MA0035.2 0.0795
MA0038.1 0.429
MA0039.2 0.148
MA0040.1 0.804
MA0041.1 0.172
MA0042.1 0.44
MA0043.1 0.589
MA0046.1 1.16136e-5
MA0047.2 8.60336e-4
MA0048.1 0.0797
MA0050.1 3.63345e-7
MA0051.1 3.17976e-5
MA0052.1 0.543
MA0055.1 0.0539
MA0057.1 0.431
MA0058.1 0.519
MA0059.1 0.21
MA0060.1 0.0715
MA0061.1 0.0526
MA0062.2 1.60251e-4
MA0065.2 6.16213e-5
MA0066.1 0.0465
MA0067.1 0.898
MA0068.1 0.882
MA0069.1 0.0609
MA0070.1 0.111
MA0071.1 0.196
MA0072.1 0.201
MA0073.1 0.878
MA0074.1 0.221
MA0076.1 0.0888
MA0077.1 0.0815
MA0078.1 0.866
MA0079.2 0.138
MA0080.2 2.23842e-9
MA0081.1 0.276
MA0083.1 0.0673
MA0084.1 0.396
MA0087.1 0.385
MA0088.1 0.122
MA0090.1 0.085
MA0091.1 0.259
MA0092.1 0.203
MA0093.1 0.531
MA0099.2 0.00684
MA0100.1 0.14
MA0101.1 0.0246
MA0102.2 0.427
MA0103.1 0.198
MA0104.2 0.926
MA0105.1 0.0138
MA0106.1 0.0615
MA0107.1 0.0488
MA0108.2 0.697
MA0111.1 0.996
MA0112.2 4.27394e-4
MA0113.1 0.235
MA0114.1 1.98411e-5
MA0115.1 2.03282e-4
MA0116.1 0.0788
MA0117.1 0.586
MA0119.1 0.192
MA0122.1 0.688
MA0124.1 0.7
MA0125.1 0.285
MA0131.1 0.534
MA0135.1 0.0794
MA0136.1 1.40206e-11
MA0137.2 0.00956
MA0138.2 0.00888
MA0139.1 0.519
MA0140.1 2.44548e-4
MA0141.1 0.0859
MA0142.1 0.593
MA0143.1 0.789
MA0144.1 0.0155
MA0145.1 0.101
MA0146.1 0.0402
MA0147.1 0.808
MA0148.1 8.97309e-5
MA0149.1 0.169
MA0150.1 0.0288
MA0152.1 0.024
MA0153.1 2.87169e-6
MA0154.1 0.0359
MA0155.1 0.943
MA0156.1 4.68132e-9
MA0157.1 0.065
MA0159.1 0.00489
MA0160.1 0.0572
MA0162.1 0.328
MA0163.1 0.00177
MA0164.1 0.904
MA0258.1 0.0244
MA0259.1 0.889



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs12635
Novel motif P-value
1 0.145
10 0.0292
100 0.451
101 0.832
102 0.967
103 0.0756
104 0.649
105 0.552
106 0.0849
107 0.153
108 0.366
109 0.0162
11 0.111
110 0.0338
111 0.0495
112 0.00179
113 0.771
114 0.187
115 0.51
116 0.886
117 0.00257
118 0.262
119 0.093
12 0.947
120 0.842
121 0.339
122 0.849
123 0.00842
124 0.121
125 0.514
126 0.0732
127 0.166
128 0.0781
129 0.221
13 1.89587e-6
130 0.266
131 0.544
132 0.485
133 0.763
134 0.172
135 0.268
136 0.459
137 0.384
138 0.857
139 0.252
14 0.977
140 0.058
141 0.357
142 0.0835
143 0.555
144 0.974
145 0.00142
146 0.504
147 0.517
148 0.734
149 0.709
15 0.0826
150 0.123
151 0.705
152 0.148
153 0.351
154 0.527
155 0.999
156 0.00829
157 0.255
158 0.0326
159 0.0814
160 0.229
161 0.172
162 0.825
163 0.293
164 0.0115
165 0.122
166 0.691
167 0.521
168 0.5
169 0.00177
17 0.0687
18 0.914
19 0.15
2 0.522
20 0.0426
21 0.446
22 0.184
23 0.576
24 0.104
25 0.661
26 2.42206e-8
27 0.43
28 0.527
29 0.0238
3 0.0571
30 0.688
31 0.756
32 0.972
33 0.0753
34 0.74
35 0.987
36 0.25
37 0.0286
38 0.466
39 0.402
4 0.671
40 0.501
41 0.57
42 0.138
43 0.106
44 0.93
45 0.876
46 0.02
47 0.241
48 0.198
49 0.107
5 0.0879
50 0.375
51 0.644
52 0.552
53 0.706
54 0.797
55 0.969
56 0.559
57 0.481
58 0.21
59 0.259
6 0.813
60 0.0481
61 0.0649
62 0.104
63 0.204
64 0.845
65 0.381
66 0.981
67 0.777
68 0.935
69 0.9
7 0.0105
70 0.0797
71 0.00439
72 0.535
73 0.0412
74 0.542
75 0.0439
76 0.374
77 0.58
78 0.00967
79 0.353
8 0.108
80 0.599
81 0.795
82 0.212
83 0.454
84 0.793
85 0.198
86 0.114
87 0.929
88 0.202
89 0.457
9 0.518
90 0.0405
91 0.337
92 0.422
93 0.0314
94 0.429
95 0.0922
96 0.179
97 0.918
98 0.722
99 0.684



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs12635


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)
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)
0002611 (neuron of the dorsal spinal cord)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002240 (spinal cord)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0001948 (regional part of spinal cord)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002256 (dorsal horn of spinal cord)
0001016 (nervous system)
0001137 (dorsum)
0002315 (gray matter of spinal cord)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000206 (mouse neuron of the dorsal spinal cord 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)