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FF:11725-123D6

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Name:Mouse Neurons - ventral spinal cord, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12632
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 numberRNASPI1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004838
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12632 CAGE DRX008849 DRR009721
Accession ID Mm9

Library idBAMCTSS
CNhs12632 DRZ001146 DRZ002531
Accession ID Mm10

Library idBAMCTSS
CNhs12632 DRZ012496 DRZ013881
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

CNhs12632

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.599
10 0
100 0.112
1000 0
1001 --0.0275
1002 0.175
1003 0.14
1004 0
1005 0
1006 0.503
1007 --0.215
1008 0
1009 --0.148
101 --0.145
1010 0
1011 0.259
1012 0.112
1013 0
1014 0.112
1015 0.133
1016 0.288
1017 0
1018 0
1019 0
102 0
1020 0.563
1021 0
1022 0
1023 0
1024 0
1025 0.112
1026 0.0763
1027 0.507
1028 0
1029 --0.018
103 0.0545
1030 0
1031 --0.139
1032 0.299
1033 --0.0418
1034 0
1035 0.112
1036 --0.189
1037 0
1038 0.063
1039 --0.0102
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: CNhs12632

Jaspar motif P-value
MA0002.2 8.35172e-4
MA0003.1 0.294
MA0004.1 0.426
MA0006.1 0.184
MA0007.1 0.227
MA0009.1 0.698
MA0014.1 0.49
MA0017.1 7.47927e-7
MA0018.2 0.149
MA0019.1 0.447
MA0024.1 0.968
MA0025.1 0.787
MA0027.1 0.263
MA0028.1 0.0232
MA0029.1 0.896
MA0030.1 0.212
MA0031.1 0.0083
MA0035.2 0.00405
MA0038.1 0.479
MA0039.2 0.0226
MA0040.1 0.357
MA0041.1 0.272
MA0042.1 0.481
MA0043.1 0.766
MA0046.1 2.50377e-11
MA0047.2 2.00594e-6
MA0048.1 0.128
MA0050.1 1.89313e-6
MA0051.1 8.13548e-5
MA0052.1 0.0292
MA0055.1 0.0318
MA0057.1 0.277
MA0058.1 0.355
MA0059.1 0.228
MA0060.1 0.384
MA0061.1 0.0814
MA0062.2 4.01976e-5
MA0065.2 4.0135e-6
MA0066.1 0.0686
MA0067.1 0.954
MA0068.1 0.708
MA0069.1 0.0584
MA0070.1 0.633
MA0071.1 0.104
MA0072.1 0.0849
MA0073.1 0.966
MA0074.1 0.129
MA0076.1 0.0456
MA0077.1 0.169
MA0078.1 0.857
MA0079.2 0.384
MA0080.2 4.19789e-10
MA0081.1 0.18
MA0083.1 0.0654
MA0084.1 0.722
MA0087.1 0.345
MA0088.1 0.13
MA0090.1 0.0749
MA0091.1 0.235
MA0092.1 0.197
MA0093.1 0.44
MA0099.2 1.99782e-4
MA0100.1 0.263
MA0101.1 0.0354
MA0102.2 0.735
MA0103.1 0.101
MA0104.2 0.84
MA0105.1 0.0629
MA0106.1 0.109
MA0107.1 0.0771
MA0108.2 0.0255
MA0111.1 0.938
MA0112.2 1.85186e-4
MA0113.1 0.106
MA0114.1 1.39515e-5
MA0115.1 1.8405e-4
MA0116.1 0.0676
MA0117.1 0.685
MA0119.1 0.158
MA0122.1 0.709
MA0124.1 0.959
MA0125.1 0.213
MA0131.1 0.796
MA0135.1 0.922
MA0136.1 2.063e-13
MA0137.2 0.143
MA0138.2 0.0235
MA0139.1 0.4
MA0140.1 2.45483e-4
MA0141.1 0.00765
MA0142.1 0.156
MA0143.1 0.621
MA0144.1 0.0975
MA0145.1 0.0589
MA0146.1 0.0143
MA0147.1 0.693
MA0148.1 1.21883e-6
MA0149.1 0.109
MA0150.1 0.0178
MA0152.1 0.0459
MA0153.1 1.32653e-11
MA0154.1 0.0369
MA0155.1 0.615
MA0156.1 4.40462e-10
MA0157.1 0.0197
MA0159.1 0.00388
MA0160.1 0.027
MA0162.1 0.281
MA0163.1 0.00147
MA0164.1 0.938
MA0258.1 0.0074
MA0259.1 0.942



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: CNhs12632

Novel motif P-value
1 0.14
10 0.0828
100 0.544
101 0.684
102 0.784
103 0.116
104 0.75
105 0.258
106 0.0547
107 0.17
108 0.391
109 0.00537
11 0.0644
110 0.0383
111 0.0487
112 0.00338
113 0.768
114 0.158
115 0.815
116 0.69
117 0.00484
118 0.283
119 0.1
12 0.856
120 0.674
121 0.0531
122 0.524
123 0.00692
124 0.19
125 0.553
126 0.054
127 0.131
128 0.051
129 0.0969
13 2.17071e-6
130 0.147
131 0.374
132 0.702
133 0.762
134 0.217
135 0.287
136 0.125
137 0.935
138 0.986
139 0.218
14 0.755
140 0.211
141 0.358
142 0.278
143 0.544
144 0.759
145 0.00296
146 0.261
147 0.439
148 0.795
149 0.474
15 0.103
150 0.115
151 0.478
152 0.0871
153 0.713
154 0.681
155 0.518
156 4.09073e-4
157 0.245
158 0.044
159 0.422
160 0.288
161 0.146
162 0.684
163 0.376
164 0.0159
165 0.0656
166 0.966
167 0.81
168 0.444
169 0.00171
17 0.0307
18 0.992
19 0.112
2 0.805
20 0.0805
21 0.271
22 0.111
23 0.6
24 0.0239
25 0.653
26 2.52317e-6
27 0.617
28 0.499
29 0.058
3 0.0551
30 0.981
31 0.806
32 0.988
33 0.124
34 0.795
35 0.984
36 0.305
37 0.0177
38 0.42
39 0.417
4 0.534
40 0.205
41 0.276
42 0.158
43 0.129
44 0.874
45 0.619
46 0.0596
47 0.199
48 0.13
49 0.145
5 0.112
50 0.31
51 0.617
52 0.365
53 0.928
54 0.732
55 0.819
56 0.468
57 0.678
58 0.251
59 0.107
6 0.896
60 0.038
61 0.0731
62 0.11
63 0.115
64 0.63
65 0.278
66 0.772
67 0.703
68 0.543
69 0.461
7 0.0204
70 0.0157
71 0.0105
72 0.383
73 0.0233
74 0.667
75 0.0433
76 0.513
77 0.354
78 0.00911
79 0.231
8 0.0856
80 0.595
81 0.8
82 0.194
83 0.103
84 0.947
85 0.12
86 0.162
87 0.102
88 0.247
89 0.236
9 0.414
90 0.135
91 0.448
92 0.423
93 0.0314
94 0.858
95 0.0244
96 0.174
97 0.819
98 0.441
99 0.663



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: CNhs12632


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)
0002612 (neuron of the ventral 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)
0002257 (ventral 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)
0000207 (mouse neuron of the ventral 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)