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FF:11645-122D7

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Name:Mouse Neurons - raphe, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12619
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
tissueraphe nuclei
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 numberRNARAP1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005951
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12619 CAGE DRX008842 DRR009714
Accession ID Mm9

Library idBAMCTSS
CNhs12619 DRZ001139 DRZ002524
Accession ID Mm10

Library idBAMCTSS
CNhs12619 DRZ012489 DRZ013874
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

CNhs12619

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.772
10 0
100 0
1000 0
1001 0.161
1002 -0.0851
1003 0.0905
1004 0
1005 0
1006 0.728
1007 -0.116
1008 0
1009 -0.0737
101 -0.129
1010 0
1011 0.346
1012 0.15
1013 0.181
1014 -0.0309
1015 -0.135
1016 0.0128
1017 0
1018 0
1019 0
102 0
1020 0.558
1021 0
1022 0.00628
1023 0
1024 -0.0232
1025 -0.0611
1026 0
1027 0.337
1028 0
1029 -0.0596
103 -0.0861
1030 0
1031 -0.505
1032 0.504
1033 0.0498
1034 0
1035 0.0621
1036 -0.172
1037 0
1038 -0.0146
1039 0.0952
104 0
1040 -0.121
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: CNhs12619
Jaspar motif P-value
MA0002.2 0.00175
MA0003.1 0.301
MA0004.1 0.511
MA0006.1 0.182
MA0007.1 0.293
MA0009.1 0.747
MA0014.1 0.804
MA0017.1 3.35748e-6
MA0018.2 0.00896
MA0019.1 0.626
MA0024.1 0.0754
MA0025.1 0.0017
MA0027.1 0.109
MA0028.1 0.0878
MA0029.1 0.949
MA0030.1 0.863
MA0031.1 0.232
MA0035.2 0.0374
MA0038.1 0.929
MA0039.2 0.0215
MA0040.1 0.656
MA0041.1 0.167
MA0042.1 0.292
MA0043.1 0.0692
MA0046.1 4.86825e-8
MA0047.2 0.00102
MA0048.1 0.0421
MA0050.1 1.82302e-6
MA0051.1 1.27452e-4
MA0052.1 0.77
MA0055.1 0.009
MA0057.1 0.341
MA0058.1 0.529
MA0059.1 0.211
MA0060.1 0.876
MA0061.1 0.0257
MA0062.2 0.00153
MA0065.2 6.99742e-6
MA0066.1 0.107
MA0067.1 0.315
MA0068.1 0.145
MA0069.1 0.0982
MA0070.1 0.457
MA0071.1 0.194
MA0072.1 0.719
MA0073.1 0.873
MA0074.1 0.123
MA0076.1 0.219
MA0077.1 0.272
MA0078.1 0.951
MA0079.2 0.39
MA0080.2 2.82048e-10
MA0081.1 0.236
MA0083.1 0.00264
MA0084.1 0.578
MA0087.1 0.131
MA0088.1 0.339
MA0090.1 0.071
MA0091.1 0.202
MA0092.1 0.198
MA0093.1 0.572
MA0099.2 0.00379
MA0100.1 0.207
MA0101.1 0.0115
MA0102.2 0.664
MA0103.1 0.244
MA0104.2 0.901
MA0105.1 0.00727
MA0106.1 0.0839
MA0107.1 0.0257
MA0108.2 3.76214e-4
MA0111.1 0.999
MA0112.2 0.00101
MA0113.1 0.426
MA0114.1 1.55402e-5
MA0115.1 2.58548e-4
MA0116.1 0.0869
MA0117.1 0.973
MA0119.1 0.125
MA0122.1 0.998
MA0124.1 0.59
MA0125.1 0.1
MA0131.1 0.633
MA0135.1 0.511
MA0136.1 1.77123e-11
MA0137.2 0.164
MA0138.2 1.62955e-4
MA0139.1 0.572
MA0140.1 4.51848e-4
MA0141.1 0.0331
MA0142.1 0.299
MA0143.1 0.796
MA0144.1 0.0778
MA0145.1 0.115
MA0146.1 0.0344
MA0147.1 0.773
MA0148.1 0.00106
MA0149.1 0.184
MA0150.1 0.254
MA0152.1 0.0407
MA0153.1 5.16326e-9
MA0154.1 0.0577
MA0155.1 0.446
MA0156.1 5.86633e-9
MA0157.1 0.134
MA0159.1 0.011
MA0160.1 0.0534
MA0162.1 0.225
MA0163.1 0.00112
MA0164.1 0.894
MA0258.1 0.0176
MA0259.1 0.892



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: CNhs12619
Novel motif P-value
1 0.24
10 0.0464
100 0.287
101 0.89
102 0.877
103 0.0902
104 0.91
105 0.446
106 0.034
107 0.115
108 0.496
109 0.00809
11 0.108
110 0.0536
111 0.311
112 0.0139
113 0.607
114 0.608
115 0.904
116 0.396
117 0.00546
118 0.587
119 0.159
12 0.863
120 0.63
121 0.415
122 0.988
123 1.22443e-4
124 0.0994
125 0.168
126 0.0484
127 0.438
128 0.04
129 0.28
13 1.15308e-7
130 0.122
131 0.314
132 0.729
133 0.756
134 0.0832
135 0.199
136 0.168
137 0.706
138 0.59
139 0.297
14 0.873
140 0.269
141 0.828
142 0.695
143 0.349
144 0.635
145 1.64637e-4
146 0.248
147 0.282
148 0.933
149 0.909
15 0.199
150 0.0661
151 0.836
152 0.118
153 0.463
154 0.633
155 0.458
156 0.00432
157 0.0917
158 0.173
159 0.702
160 0.281
161 0.225
162 0.762
163 0.806
164 0.0402
165 0.255
166 0.514
167 0.528
168 0.553
169 0.00265
17 0.0697
18 0.752
19 0.0988
2 0.62
20 0.0295
21 0.184
22 0.13
23 0.646
24 0.057
25 0.817
26 2.06561e-8
27 0.377
28 0.83
29 0.0439
3 0.0792
30 0.805
31 0.7
32 0.655
33 0.094
34 0.743
35 0.659
36 0.131
37 0.04
38 0.425
39 0.381
4 0.304
40 0.0717
41 0.585
42 0.165
43 0.119
44 0.812
45 0.648
46 0.0493
47 0.401
48 0.315
49 0.135
5 0.169
50 0.234
51 0.782
52 0.272
53 0.562
54 0.97
55 0.996
56 0.459
57 0.54
58 0.299
59 0.183
6 0.928
60 0.0385
61 0.0501
62 0.206
63 0.142
64 0.721
65 0.374
66 0.726
67 0.716
68 0.973
69 0.506
7 0.0143
70 0.0896
71 0.00281
72 0.582
73 0.0506
74 0.912
75 0.0593
76 0.31
77 0.573
78 0.00267
79 0.0712
8 0.0674
80 0.738
81 0.739
82 0.283
83 0.163
84 0.593
85 0.196
86 0.147
87 0.398
88 0.862
89 0.584
9 0.376
90 0.145
91 0.089
92 0.387
93 0.0598
94 0.713
95 0.0612
96 0.275
97 0.764
98 0.743
99 0.409



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: CNhs12619


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)
0002610 (raphe nuclei neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0004684 (raphe nuclei)
0001016 (nervous system)
0002275 (reticular formation)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000205 (mouse raphe nuclei neuron 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)