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FF:11739-123F2

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Name:Mouse Neurons - hippocampal, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12359
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
tissuehippocampus
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 numberRNAMNh2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004948
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12359 CAGE DRX008838 DRR009710
Accession ID Mm9

Library idBAMCTSS
CNhs12359 DRZ001135 DRZ002520
Accession ID Mm10

Library idBAMCTSS
CNhs12359 DRZ012485 DRZ013870
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

CNhs12359

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.197
10 0
100 0.644
1000 --0.0172
1001 --0.0749
1002 0.331
1003 0.0693
1004 0.0397
1005 --0.193
1006 0.158
1007 0.0694
1008 0
1009 --0.2
101 --0.12
1010 0
1011 0.133
1012 0
1013 --0.177
1014 0
1015 0.401
1016 0.105
1017 0
1018 0
1019 0
102 0
1020 0.519
1021 0.197
1022 --0.124
1023 0
1024 --0.166
1025 --0.0611
1026 0
1027 0.506
1028 0
1029 --0.143
103 --0.0829
1030 0
1031 --0.511
1032 --0.184
1033 0.00967
1034 0
1035 0
1036 --0.0917
1037 0
1038 0.1
1039 --0.272
104 0
1040 --0.176
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: CNhs12359

Jaspar motif P-value
MA0002.2 0.00184
MA0003.1 0.123
MA0004.1 0.791
MA0006.1 0.0762
MA0007.1 0.209
MA0009.1 0.85
MA0014.1 0.291
MA0017.1 1.12608e-5
MA0018.2 0.0176
MA0019.1 0.316
MA0024.1 0.00552
MA0025.1 0.228
MA0027.1 0.713
MA0028.1 0.667
MA0029.1 0.695
MA0030.1 0.263
MA0031.1 0.0578
MA0035.2 0.111
MA0038.1 0.0685
MA0039.2 0.00464
MA0040.1 0.976
MA0041.1 0.303
MA0042.1 0.66
MA0043.1 0.0121
MA0046.1 3.13136e-10
MA0047.2 5.05943e-4
MA0048.1 0.948
MA0050.1 5.6446e-9
MA0051.1 9.60025e-4
MA0052.1 8.95073e-4
MA0055.1 0.847
MA0057.1 0.0569
MA0058.1 0.739
MA0059.1 0.828
MA0060.1 1.07697e-9
MA0061.1 0.0561
MA0062.2 0.991
MA0065.2 4.10713e-5
MA0066.1 0.332
MA0067.1 0.837
MA0068.1 0.505
MA0069.1 0.15
MA0070.1 0.523
MA0071.1 0.321
MA0072.1 0.222
MA0073.1 0.891
MA0074.1 0.518
MA0076.1 0.169
MA0077.1 0.00177
MA0078.1 0.00513
MA0079.2 0.707
MA0080.2 8.40341e-11
MA0081.1 0.486
MA0083.1 2.65846e-5
MA0084.1 0.704
MA0087.1 0.513
MA0088.1 0.372
MA0090.1 0.00817
MA0091.1 0.501
MA0092.1 0.207
MA0093.1 0.785
MA0099.2 6.63132e-5
MA0100.1 0.688
MA0101.1 0.171
MA0102.2 0.678
MA0103.1 0.0755
MA0104.2 0.315
MA0105.1 0.114
MA0106.1 0.153
MA0107.1 0.0914
MA0108.2 0.0057
MA0111.1 0.953
MA0112.2 2.43408e-4
MA0113.1 0.715
MA0114.1 1.33087e-4
MA0115.1 0.0591
MA0116.1 0.186
MA0117.1 0.795
MA0119.1 0.153
MA0122.1 0.845
MA0124.1 0.83
MA0125.1 0.203
MA0131.1 0.594
MA0135.1 0.386
MA0136.1 3.70079e-7
MA0137.2 0.0853
MA0138.2 0.776
MA0139.1 0.228
MA0140.1 0.00348
MA0141.1 0.0142
MA0142.1 0.00435
MA0143.1 9.71555e-4
MA0144.1 0.0473
MA0145.1 0.0154
MA0146.1 0.0717
MA0147.1 0.386
MA0148.1 1.47577e-5
MA0149.1 0.0648
MA0150.1 0.0296
MA0152.1 0.416
MA0153.1 1.54527e-8
MA0154.1 0.0284
MA0155.1 0.723
MA0156.1 3.50178e-4
MA0157.1 0.0303
MA0159.1 0.0046
MA0160.1 0.0967
MA0162.1 0.363
MA0163.1 0.0165
MA0164.1 0.968
MA0258.1 0.0119
MA0259.1 0.368



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: CNhs12359

Novel motif P-value
1 0.21
10 0.233
100 0.889
101 0.912
102 0.943
103 0.0815
104 0.945
105 0.306
106 0.00294
107 0.018
108 0.617
109 0.00372
11 0.112
110 0.222
111 0.0389
112 0.00647
113 0.831
114 0.16
115 0.314
116 0.584
117 0.312
118 0.523
119 0.175
12 0.498
120 0.825
121 0.361
122 0.704
123 0.726
124 0.69
125 0.371
126 0.245
127 0.14
128 0.0219
129 0.149
13 2.8111e-5
130 0.866
131 0.392
132 0.961
133 0.307
134 0.439
135 0.126
136 0.0654
137 0.318
138 0.5
139 0.131
14 0.569
140 0.425
141 0.126
142 0.128
143 0.761
144 0.909
145 0.0918
146 0.448
147 0.885
148 0.415
149 0.0941
15 0.201
150 0.213
151 0.373
152 0.0202
153 0.837
154 0.886
155 0.652
156 0.00462
157 0.183
158 0.298
159 0.036
160 0.3
161 0.418
162 0.761
163 0.144
164 0.0314
165 0.0109
166 0.677
167 0.667
168 0.589
169 0.00734
17 0.0228
18 0.697
19 0.0332
2 0.47
20 0.875
21 0.619
22 0.0633
23 0.211
24 0.0516
25 0.674
26 0.00343
27 0.638
28 0.386
29 0.352
3 0.13
30 0.449
31 0.792
32 0.271
33 0.353
34 0.526
35 0.377
36 0.848
37 0.0097
38 0.422
39 0.204
4 0.553
40 0.294
41 0.904
42 0.393
43 0.177
44 0.693
45 0.364
46 0.194
47 0.212
48 0.185
49 0.218
5 0.185
50 0.282
51 0.552
52 0.0465
53 0.484
54 0.534
55 0.943
56 0.319
57 0.794
58 0.268
59 0.0671
6 0.671
60 0.0088
61 0.308
62 0.162
63 0.129
64 0.933
65 0.372
66 0.57
67 0.72
68 0.662
69 0.525
7 0.0418
70 0.0246
71 0.0475
72 0.326
73 0.0102
74 0.276
75 0.151
76 0.976
77 0.17
78 0.0523
79 0.506
8 0.271
80 0.936
81 0.296
82 0.0374
83 0.0456
84 0.922
85 0.0364
86 0.326
87 0.33
88 0.449
89 0.175
9 0.335
90 0.392
91 0.247
92 0.113
93 0.0215
94 0.892
95 0.0654
96 0.277
97 0.838
98 0.718
99 0.178



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: CNhs12359


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)
0002609 (neuron of cerebral cortex)
0002608 (hippocampal neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0001954 (Ammon's horn)
0000956 (cerebral cortex)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000201 (hippocampal neuron sample)
0000203 (mouse neuron samples)
0000202 (mouse hippocampal 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)