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FF:11644-122D6

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Name:Mouse Neurons - hippocampal, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12110
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 numberRNAMNh3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005482
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12110 CAGE DRX008839 DRR009711
Accession ID Mm9

Library idBAMCTSS
CNhs12110 DRZ001136 DRZ002521
Accession ID Mm10

Library idBAMCTSS
CNhs12110 DRZ012486 DRZ013871
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

CNhs12110

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.277
10 0
100 0.575
1000 --0.0355
1001 --0.0749
1002 0.511
1003 0.191
1004 0
1005 --0.384
1006 0.064
1007 --0.0794
1008 0
1009 --0.2
101 --0.128
1010 0
1011 0.176
1012 0
1013 --0.217
1014 --0.0851
1015 0.396
1016 0.311
1017 0
1018 0
1019 0
102 0
1020 0.922
1021 0.283
1022 --0.124
1023 0
1024 --0.277
1025 --0.0611
1026 0
1027 0.392
1028 0
1029 --0.148
103 --0.0861
1030 0
1031 --0.458
1032 --0.177
1033 0
1034 0
1035 0
1036 --0.0378
1037 0
1038 0.111
1039 --0.338
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: CNhs12110

Jaspar motif P-value
MA0002.2 0.0275
MA0003.1 0.136
MA0004.1 0.87
MA0006.1 0.0675
MA0007.1 0.283
MA0009.1 0.841
MA0014.1 0.387
MA0017.1 5.25118e-5
MA0018.2 0.0328
MA0019.1 0.0977
MA0024.1 0.0834
MA0025.1 0.272
MA0027.1 0.797
MA0028.1 0.67
MA0029.1 0.91
MA0030.1 0.054
MA0031.1 0.0191
MA0035.2 0.221
MA0038.1 0.15
MA0039.2 0.00334
MA0040.1 0.887
MA0041.1 0.206
MA0042.1 0.507
MA0043.1 0.0735
MA0046.1 6.09893e-9
MA0047.2 5.81977e-4
MA0048.1 0.63
MA0050.1 1.65737e-10
MA0051.1 8.18298e-5
MA0052.1 0.0261
MA0055.1 0.768
MA0057.1 0.0774
MA0058.1 0.762
MA0059.1 0.954
MA0060.1 6.24941e-6
MA0061.1 0.0331
MA0062.2 0.23
MA0065.2 1.40217e-4
MA0066.1 0.387
MA0067.1 0.879
MA0068.1 0.375
MA0069.1 0.119
MA0070.1 0.446
MA0071.1 0.539
MA0072.1 0.234
MA0073.1 0.813
MA0074.1 0.768
MA0076.1 0.645
MA0077.1 4.06695e-5
MA0078.1 6.0696e-4
MA0079.2 0.542
MA0080.2 1.72666e-10
MA0081.1 0.347
MA0083.1 3.89726e-5
MA0084.1 0.634
MA0087.1 0.623
MA0088.1 0.303
MA0090.1 0.00575
MA0091.1 0.82
MA0092.1 0.302
MA0093.1 0.823
MA0099.2 8.12468e-5
MA0100.1 0.605
MA0101.1 0.0396
MA0102.2 0.339
MA0103.1 0.163
MA0104.2 0.234
MA0105.1 0.0983
MA0106.1 0.108
MA0107.1 0.0232
MA0108.2 0.00799
MA0111.1 0.981
MA0112.2 7.50073e-4
MA0113.1 0.42
MA0114.1 9.00665e-5
MA0115.1 0.0652
MA0116.1 0.238
MA0117.1 0.623
MA0119.1 0.136
MA0122.1 0.682
MA0124.1 0.879
MA0125.1 0.287
MA0131.1 0.948
MA0135.1 0.34
MA0136.1 1.61246e-8
MA0137.2 0.0216
MA0138.2 0.227
MA0139.1 0.38
MA0140.1 0.0212
MA0141.1 0.0619
MA0142.1 1.7405e-4
MA0143.1 2.0373e-4
MA0144.1 0.0165
MA0145.1 0.0282
MA0146.1 0.0816
MA0147.1 0.258
MA0148.1 6.17297e-6
MA0149.1 0.163
MA0150.1 0.0678
MA0152.1 0.411
MA0153.1 2.66988e-8
MA0154.1 0.0241
MA0155.1 0.596
MA0156.1 7.80708e-7
MA0157.1 0.0298
MA0159.1 0.0132
MA0160.1 0.138
MA0162.1 0.394
MA0163.1 0.018
MA0164.1 0.911
MA0258.1 0.0261
MA0259.1 0.264



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: CNhs12110

Novel motif P-value
1 0.275
10 0.147
100 0.948
101 0.918
102 0.963
103 0.29
104 0.979
105 0.136
106 0.00435
107 0.0208
108 0.509
109 0.00409
11 0.186
110 0.176
111 0.0462
112 0.00166
113 0.795
114 0.541
115 0.153
116 0.635
117 0.114
118 0.467
119 0.269
12 0.48
120 0.848
121 0.188
122 0.39
123 0.343
124 0.158
125 0.185
126 0.0931
127 0.127
128 0.0306
129 0.238
13 2.64717e-6
130 0.972
131 0.517
132 0.813
133 0.227
134 0.316
135 0.277
136 0.0297
137 0.183
138 0.486
139 0.366
14 0.589
140 0.998
141 0.418
142 0.0669
143 0.743
144 0.835
145 0.0699
146 0.313
147 0.799
148 0.478
149 0.143
15 0.217
150 0.172
151 0.456
152 0.0323
153 0.903
154 0.979
155 0.508
156 0.0451
157 0.011
158 0.545
159 0.0801
160 0.251
161 0.357
162 0.975
163 0.162
164 0.0513
165 0.0216
166 0.624
167 0.672
168 0.815
169 0.0102
17 0.0192
18 0.52
19 0.0522
2 0.536
20 0.827
21 0.704
22 0.0553
23 0.285
24 0.0522
25 0.822
26 5.14923e-4
27 0.778
28 0.345
29 0.296
3 0.131
30 0.45
31 0.762
32 0.57
33 0.276
34 0.584
35 0.177
36 0.971
37 0.00809
38 0.666
39 0.125
4 0.742
40 0.425
41 0.707
42 0.521
43 0.185
44 0.907
45 0.37
46 0.205
47 0.313
48 0.231
49 0.272
5 0.217
50 0.158
51 0.62
52 0.0451
53 0.52
54 0.674
55 0.595
56 0.3
57 0.864
58 0.304
59 0.0748
6 0.67
60 0.00556
61 0.532
62 0.171
63 0.161
64 0.573
65 0.712
66 0.56
67 0.743
68 0.588
69 0.624
7 0.0242
70 0.0717
71 0.0227
72 0.383
73 0.0116
74 0.534
75 0.0953
76 0.957
77 0.167
78 0.0304
79 0.71
8 0.461
80 0.79
81 0.339
82 0.0567
83 0.129
84 0.452
85 0.0465
86 0.293
87 0.174
88 0.27
89 0.301
9 0.434
90 0.416
91 0.428
92 0.201
93 0.134
94 0.819
95 0.0847
96 0.796
97 0.965
98 0.967
99 0.227



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: CNhs12110


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)