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FF:11743-123F6

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Name:Mouse Neurons - ventral spinal cord, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12638
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 numberRNASPI2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005914
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12638 CAGE DRX008850 DRR009722
Accession ID Mm9

Library idBAMCTSS
CNhs12638 DRZ001147 DRZ002532
Accession ID Mm10

Library idBAMCTSS
CNhs12638 DRZ012497 DRZ013882
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

CNhs12638

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.601
10 0
100 0.154
1000 0.0189
1001 --0.0668
1002 0.099
1003 0.157
1004 0
1005 0
1006 0.497
1007 --0.148
1008 0
1009 --0.0912
101 --0.0689
1010 0
1011 0.233
1012 0.0578
1013 0.116
1014 0.111
1015 0.213
1016 0.23
1017 0
1018 0
1019 0
102 0
1020 0.569
1021 0.106
1022 0.0305
1023 0
1024 0.0247
1025 0.0933
1026 0
1027 0.384
1028 0
1029 --0.0672
103 0.0578
1030 0
1031 --0.115
1032 0.281
1033 0
1034 0
1035 0.109
1036 --0.135
1037 0
1038 0.0523
1039 --0.0181
104 0
1040 --0.242
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: CNhs12638

Jaspar motif P-value
MA0002.2 1.03738e-4
MA0003.1 0.272
MA0004.1 0.398
MA0006.1 0.169
MA0007.1 0.178
MA0009.1 0.635
MA0014.1 0.515
MA0017.1 6.6315e-7
MA0018.2 0.153
MA0019.1 0.529
MA0024.1 0.772
MA0025.1 0.584
MA0027.1 0.255
MA0028.1 0.0752
MA0029.1 0.898
MA0030.1 0.212
MA0031.1 0.00795
MA0035.2 0.00554
MA0038.1 0.281
MA0039.2 0.0344
MA0040.1 0.244
MA0041.1 0.23
MA0042.1 0.614
MA0043.1 0.654
MA0046.1 1.43442e-13
MA0047.2 8.2378e-7
MA0048.1 0.13
MA0050.1 8.60437e-6
MA0051.1 2.07095e-4
MA0052.1 0.105
MA0055.1 0.0684
MA0057.1 0.269
MA0058.1 0.38
MA0059.1 0.189
MA0060.1 0.126
MA0061.1 0.0829
MA0062.2 5.57477e-4
MA0065.2 2.75961e-6
MA0066.1 0.0505
MA0067.1 0.715
MA0068.1 0.561
MA0069.1 0.121
MA0070.1 0.399
MA0071.1 0.0621
MA0072.1 0.047
MA0073.1 0.991
MA0074.1 0.126
MA0076.1 0.164
MA0077.1 0.315
MA0078.1 0.72
MA0079.2 0.385
MA0080.2 1.2721e-10
MA0081.1 0.272
MA0083.1 0.149
MA0084.1 0.578
MA0087.1 0.299
MA0088.1 0.171
MA0090.1 0.0819
MA0091.1 0.233
MA0092.1 0.202
MA0093.1 0.435
MA0099.2 1.03833e-4
MA0100.1 0.273
MA0101.1 0.0486
MA0102.2 0.64
MA0103.1 0.0842
MA0104.2 0.876
MA0105.1 0.0525
MA0106.1 0.089
MA0107.1 0.0883
MA0108.2 0.0602
MA0111.1 0.94
MA0112.2 1.78424e-4
MA0113.1 0.131
MA0114.1 7.52876e-6
MA0115.1 6.38204e-5
MA0116.1 0.0879
MA0117.1 0.628
MA0119.1 0.125
MA0122.1 0.979
MA0124.1 0.941
MA0125.1 0.205
MA0131.1 0.886
MA0135.1 0.997
MA0136.1 2.39575e-13
MA0137.2 0.15
MA0138.2 0.0277
MA0139.1 0.418
MA0140.1 2.5467e-4
MA0141.1 0.00361
MA0142.1 0.325
MA0143.1 0.667
MA0144.1 0.0619
MA0145.1 0.0443
MA0146.1 0.0165
MA0147.1 0.718
MA0148.1 7.50798e-7
MA0149.1 0.0587
MA0150.1 0.0146
MA0152.1 0.0504
MA0153.1 2.5904e-13
MA0154.1 0.0325
MA0155.1 0.713
MA0156.1 1.28954e-8
MA0157.1 0.0158
MA0159.1 0.00183
MA0160.1 0.0164
MA0162.1 0.277
MA0163.1 9.28277e-4
MA0164.1 0.961
MA0258.1 0.00775
MA0259.1 0.975



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: CNhs12638

Novel motif P-value
1 0.133
10 0.0782
100 0.604
101 0.792
102 0.951
103 0.0727
104 0.609
105 0.22
106 0.0383
107 0.124
108 0.412
109 0.00653
11 0.0645
110 0.0474
111 0.0573
112 0.00279
113 0.838
114 0.105
115 0.754
116 0.694
117 0.00687
118 0.294
119 0.0836
12 0.966
120 0.322
121 0.0805
122 0.555
123 0.0126
124 0.248
125 0.552
126 0.0575
127 0.0792
128 0.0319
129 0.118
13 7.75192e-6
130 0.23
131 0.535
132 0.767
133 0.994
134 0.356
135 0.301
136 0.123
137 0.733
138 0.91
139 0.167
14 0.762
140 0.152
141 0.381
142 0.481
143 0.409
144 0.875
145 0.00283
146 0.249
147 0.511
148 0.534
149 0.35
15 0.0882
150 0.099
151 0.441
152 0.0788
153 0.387
154 0.788
155 0.489
156 8.79606e-5
157 0.278
158 0.025
159 0.0538
160 0.263
161 0.132
162 0.826
163 0.307
164 0.0132
165 0.0606
166 0.921
167 0.59
168 0.786
169 0.00183
17 0.032
18 0.965
19 0.122
2 0.906
20 0.105
21 0.378
22 0.114
23 0.448
24 0.0318
25 0.66
26 1.0795e-6
27 0.715
28 0.537
29 0.0527
3 0.0673
30 0.959
31 0.933
32 0.794
33 0.102
34 0.739
35 0.984
36 0.339
37 0.0244
38 0.358
39 0.381
4 0.441
40 0.252
41 0.313
42 0.17
43 0.115
44 0.774
45 0.594
46 0.053
47 0.197
48 0.123
49 0.12
5 0.111
50 0.31
51 0.651
52 0.331
53 0.898
54 0.762
55 0.952
56 0.449
57 0.633
58 0.226
59 0.112
6 0.921
60 0.0343
61 0.0935
62 0.101
63 0.113
64 0.591
65 0.225
66 0.739
67 0.695
68 0.507
69 0.375
7 0.0215
70 0.0141
71 0.00954
72 0.532
73 0.0234
74 0.772
75 0.0488
76 0.518
77 0.355
78 0.0111
79 0.29
8 0.0802
80 0.606
81 0.937
82 0.234
83 0.057
84 0.512
85 0.0856
86 0.156
87 0.26
88 0.213
89 0.245
9 0.373
90 0.0848
91 0.275
92 0.359
93 0.0222
94 0.689
95 0.0384
96 0.155
97 0.922
98 0.404
99 0.609



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: CNhs12638


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)